diff options
Diffstat (limited to 'gnu')
99 files changed, 10637 insertions, 2657 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 5fad380bbf..7278c50e4f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1044,9 +1044,6 @@ dist_patch_DATA = \ %D%/packages/patches/dstat-skip-devices-without-io.patch \ %D%/packages/patches/dvd+rw-tools-add-include.patch \ %D%/packages/patches/dynaconf-unvendor-deps.patch \ - %D%/packages/patches/ecl-16-format-directive-limit.patch \ - %D%/packages/patches/ecl-16-ignore-stderr-write-error.patch \ - %D%/packages/patches/ecl-16-libffi.patch \ %D%/packages/patches/efibootmgr-remove-extra-decl.patch \ %D%/packages/patches/efivar-211.patch \ %D%/packages/patches/eigen-fix-strict-aliasing-bug.patch \ @@ -1387,6 +1384,8 @@ dist_patch_DATA = \ %D%/packages/patches/lightdm-vncserver-check.patch \ %D%/packages/patches/lightdm-vnc-color-depth.patch \ %D%/packages/patches/localed-xorg-keyboard.patch \ + %D%/packages/patches/kcontacts-incorrect-country-name.patch \ + %D%/packages/patches/kde-cli-tools-delay-mime-db.patch \ %D%/packages/patches/kdiagram-Fix-missing-link-libraries.patch \ %D%/packages/patches/kiki-level-selection-crash.patch \ %D%/packages/patches/kiki-makefile.patch \ @@ -1440,6 +1439,7 @@ dist_patch_DATA = \ %D%/packages/patches/libofa-ftbfs-2.diff \ %D%/packages/patches/libotr-test-auth-fix.patch \ %D%/packages/patches/libksieve-Fix-missing-link-libraries.patch \ + %D%/packages/patches/libksysguard-qdiriterator-follow-symlinks.patch \ %D%/packages/patches/libmad-armv7-thumb-pt1.patch \ %D%/packages/patches/libmad-armv7-thumb-pt2.patch \ %D%/packages/patches/libmad-length-check.patch \ @@ -1482,7 +1482,8 @@ dist_patch_DATA = \ %D%/packages/patches/lierolibre-remove-arch-warning.patch \ %D%/packages/patches/lierolibre-try-building-other-arch.patch \ %D%/packages/patches/linbox-fix-pkgconfig.patch \ - %D%/packages/patches/linphone-desktop-without-sdk.patch \ + %D%/packages/patches/linphone-desktop-without-sdk.patch \ + %D%/packages/patches/linux-libre-infodocs-target.patch \ %D%/packages/patches/linux-libre-support-for-Pinebook-Pro.patch \ %D%/packages/patches/linux-pam-no-setfsuid.patch \ %D%/packages/patches/linuxdcpp-openssl-1.1.patch \ @@ -1989,6 +1990,8 @@ dist_patch_DATA = \ %D%/packages/patches/vtk-7-gcc-10-compat.patch \ %D%/packages/patches/vtk-7-hdf5-compat.patch \ %D%/packages/patches/vtk-7-python-compat.patch \ + %D%/packages/patches/wacomtablet-add-missing-includes.patch \ + %D%/packages/patches/wacomtablet-qt5.15.patch \ %D%/packages/patches/warsow-qfusion-fix-bool-return-type.patch \ %D%/packages/patches/webkitgtk-adjust-bubblewrap-paths.patch \ %D%/packages/patches/webrtc-audio-processing-big-endian.patch \ diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index bc31a12594..439fdf72a8 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -36,6 +36,7 @@ #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages curl) + #:use-module (gnu packages databases) #:use-module (gnu packages flex) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) @@ -58,6 +59,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) + #:use-module (gnu packages python-compression) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) @@ -78,6 +80,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system meson) #:use-module (guix build-system python) + #:use-module (guix build-system pyproject) #:use-module (guix download) #:use-module (guix gexp) #:use-module (guix git-download) @@ -1099,7 +1102,7 @@ to access online Astronomical data. Each web service has its own sub-package.") (define-public python-cdflib (package (name "python-cdflib") - (version "0.4.4") + (version "0.4.9") (source (origin (method git-fetch) ; no tests in pypi archive @@ -1108,16 +1111,14 @@ to access online Astronomical data. Each web service has its own sub-package.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1h7750xvr6qbhnl2w3bhccs3pwp3hci3624pvvxym0yjinmskjlz")))) - (build-system python-build-system) + (base32 "1k557najk7ln293zwyghnhw48ays3nqf9s94kibsc7r70c2q7p08")))) + (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" (getcwd)) - (invoke "pytest" "-vv" "tests"))))))) + (add-before 'check 'set-home-env + (lambda _ + (setenv "HOME" (getcwd))))))) (propagated-inputs (list python-attrs python-numpy)) (native-inputs @@ -1129,7 +1130,8 @@ to access online Astronomical data. Each web service has its own sub-package.") python-xarray)) (home-page "https://github.com/MAVENSDC/cdflib") (synopsis "Python library to deal with NASA's CDF astronmical data format") - (description "This package provides a Python CDF reader toolkit + (description "This package provides a Python @acronym{CDF, Computable +Document Format} reader toolkit. It provides the following functionality: @itemize @item Ability to read variables and attributes from CDF files @@ -1138,9 +1140,46 @@ It provides the following functionality: time formats @item Can convert CDF files into XArray Dataset objects and vice versa, attempting to maintain ISTP compliance -@end itemize\n") +@end itemize") (license license:expat))) +(define-public python-drms + (package + (name "python-drms") + (version "0.6.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "drms" version)) + (sha256 + (base32 "1b0w350y4wbgyy19zcf28xbb85mqq6gnhb6ppibbc4hbn2ixbcvj")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs tests? + #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (setenv "JSOC_EMAIL" "jsoc@sunpy.org") + (invoke "python" "-m" "pytest" "-vv"))))))) + (native-inputs + (list python-astropy + python-pytest-astropy + python-pytest + python-setuptools-scm)) + (propagated-inputs (list python-numpy python-pandas)) + (home-page "https://sunpy.org") + (synopsis "Access astronomical HMI, AIA and MDI data with Python") + (description + "DRMS module provides an easy-to-use interface for accessing HMI, AIA and +MDI data with Python. It uses the publicly accessible +JSOC (@url{http://jsoc.stanford.edu/}) DRMS server by default, but can also be +used with local NetDRMS sites.") + (license license:bsd-2))) + (define-public python-ephem (package (name "python-ephem") @@ -1164,6 +1203,53 @@ for a table giving the position of a planet, asteroid, or comet for a series of dates.") (license license:expat))) +(define-public python-hvpy + (package + (name "python-hvpy") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "hvpy" version)) + (sha256 + (base32 "0r0asyflz2sw9zn5vgs138nh81m0rbwbakmrncbc1ghdr3g6jahv")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f)) ; Requires HTTP(S) access to api.beta.helioviewer.org + (propagated-inputs (list python-pydantic python-requests)) + (native-inputs (list python-pytest python-pytest-astropy)) + (home-page "https://helioviewer.org/") + (synopsis "Helioviewer Python API Wrapper") + (description "@code{hvpy} is a Python API wrapper around the formal +@url{Helioviewer API, https://api.helioviewer.org/docs/v2/}.") + (license license:bsd-2))) + +(define-public python-mpl-animators + (package + (name "python-mpl-animators") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "mpl_animators" version)) + (sha256 + (base32 "12kjmj7rn3pk9ly82h5s5hn0kl3kxkr7bgkz9zr9k59pir8z1r8b")))) + (build-system pyproject-build-system) + (native-inputs + (list python-pytest + python-pytest-mpl + python-setuptools-scm)) + (propagated-inputs + (list python-astropy + python-matplotlib + python-numpy)) + (home-page "https://sunpy.org") + (synopsis "Interactive animations with matplotlib") + (description + "The @code{mpl_animators} package provides a set of classes which allow +the easy construction of interactive matplotlib widget based animations.") + (license license:bsd-3))) + (define-public python-photutils (package (name "python-photutils") @@ -1270,6 +1356,146 @@ Virtual observatory (VO) using Python.") (description "Regions is an Astropy package for region handling.") (license license:bsd-3))) +(define-public python-reproject + (package + (name "python-reproject") + (version "0.9.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "reproject" version)) + (sha256 + (base32 "1msysqbhkfi3bmw29wipk250a008bnng7din56md9ipbwiar8x55")))) + (build-system pyproject-build-system) + (arguments + (list + ;; FIXME: Failing tests + ;; + ;; reproject/adaptive/core.py:7: in <module> + ;; from .deforest import map_coordinates + ;; E ModuleNotFoundError: No module named 'reproject.adaptive.deforest' + ;; + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'writable-compiler + (lambda _ + (make-file-writable "reproject/_compiler.c"))) + (add-before 'check 'writable-compiler + (lambda _ + (make-file-writable "reproject/_compiler.c"))) + (add-before 'check 'writable-home + (lambda _ + (setenv "HOME" (getcwd))))))) + (propagated-inputs + (list python-astropy + python-astropy-healpix + python-numpy + python-scipy)) + (native-inputs + (list python-asdf + python-cython + python-extension-helpers + python-gwcs + python-pytest-astropy + python-pyvo + python-semantic-version + python-pytest + python-setuptools-scm + python-shapely)) + (home-page "https://reproject.readthedocs.io") + (synopsis "Astronomical image reprojection in Python") + (description + "This package provides a functionality to reproject astronomical images using +various techniques via a uniform interface, where reprojection is the +re-gridding of images from one world coordinate system to another e.g. +changing the pixel resolution, orientation, coordinate system.") + (license license:bsd-3))) + +(define-public python-sunpy + (package + (name "python-sunpy") + (version "4.0.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sunpy" version)) + (sha256 + (base32 "0aiirb6l8zshdrpsvh6d5ki759ah9zfm9gbl0in985hprwwxyrq1")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'writable-compiler + (lambda _ + (make-file-writable "sunpy/_compiler.c"))) + (add-before 'check 'prepare-test-environment + (lambda _ + (setenv "HOME" "/tmp") + (make-file-writable "sunpy/_compiler.c") + ;; TODO: (Sharlatan-20221106T115800+0000): Review failing tests + (substitute* "sunpy/image/tests/test_transform.py" + (("def test_clipping") "def __off_test_clipping") + (("def test_nans") "def __off_test_nans") + (("def test_endian") "def __off_test_endian")) + (substitute* "sunpy/map/tests/test_mapbase.py" + (("def test_derotating_nonpurerotation_pcij") + "def __off_test_derotating_nonpurerotation_pcij")) + (substitute* "sunpy/map/sources/tests/test_mdi_source.py" + (("def test_synoptic_source") + "def __off_test_synoptic_source")) + (substitute* "sunpy/tests/tests/test_self_test.py" + (("def test_main_nonexisting_module") + "def __off_test_main_nonexisting_module") + (("def test_main_stdlib_module") + "def __off_test_main_stdlib_module"))))))) + (native-inputs + (list python-aiohttp + python-extension-helpers + python-hvpy + python-packaging + python-pytest + python-pytest-astropy + python-pytest-doctestplus + python-pytest-mock + python-pytest-mpl + python-pytest-xdist + python-setuptools-scm)) + (propagated-inputs + (list parfive + python-asdf + python-asdf-astropy + python-astropy + python-beautifulsoup4 + python-cdflib + python-dask + python-dateutil + python-drms + python-glymur + python-h5netcdf + python-h5py + python-hypothesis + python-jplephem + python-matplotlib + python-mpl-animators + python-numpy + ;; python-opencv-python ; not packed yet + python-pandas + python-reproject + python-scikit-image + python-scipy + python-semantic-version + python-sqlalchemy + python-tqdm + python-zeep)) + (home-page "https://sunpy.org") + (synopsis "Python library for Solar Physics") + (description + "SunPy is package for solar physics and is meant to be a free alternative to the +SolarSoft data analysis environment.") + (license license:bsd-2))) + (define-public python-astral (package (name "python-astral") @@ -1619,7 +1845,7 @@ It can be used to calculate the trajectory of satellites.") (define-public imppg (package (name "imppg") - (version "0.6.4") + (version "0.6.5") (source (origin (method git-fetch) @@ -1628,7 +1854,7 @@ It can be used to calculate the trajectory of satellites.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "04synbmyz0hkipl1cdc26nr42r57v494yjw8pi4jx0jrxrawgj9h")))) + (base32 "0a6wb1a9adwd01dmy0r03xxp8iz9y7mvh30088ajilhj4lf90vxa")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no test provided @@ -1957,26 +2183,40 @@ datetime object.") (define-public python-asdf (package (name "python-asdf") - (version "2.8.3") + (version "2.13.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf" version)) (sha256 - (base32 "0i4vq1hsympjgb1yvn4ql0gm8j1mki9ggmj03533kmg0nbzp03yy")))) - (build-system python-build-system) + (base32 "1zixzv4n2fryaszsfchqh2nvp0gzvarhz03fc721yw6iafdadqij")))) + (build-system pyproject-build-system) (arguments - ;; NOTE: (Sharlatan-20211229T201059+0000): Tests depend on astropy and - ;; gwcs, astropy gwcs depend on asdf. Disable circular dependence. + ;; FIXME: Tests fail a lot with + ;; + ;; ERROR - _pytest.pathlib.ImportPathMismatchError: + ;; ('asdf.conftest', '/gnu/sto... + ;; `(#:tests? #f)) (native-inputs - (list python-setuptools-scm + (list python-astropy + python-packaging + python-psutil + python-pytest + python-pytest-doctestplus + python-pytest-openfiles + python-pytest-remotedata python-semantic-version - python-packaging)) + python-setuptools-scm)) (propagated-inputs - (list python-importlib-resources - python-jsonschema + (list python-asdf-standard + python-asdf-transform-schemas + python-asdf-unit-schemas + python-importlib-metadata + python-importlib-resources python-jmespath + python-jsonschema-next + python-lz4 python-numpy python-pyyaml)) (home-page "https://github.com/asdf-format/asdf") @@ -1987,31 +2227,63 @@ interchange format for scientific data. This package contains the Python implementation of the ASDF Standard.") (license license:bsd-3))) +(define-public python-asdf-standard + (package + (name "python-asdf-standard") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asdf_standard" version)) + (sha256 + (base32 + "0i7xdjwn5prg2hcnf1zhw57mszc68jjr5sv4rimpzcg7f2dgzn5g")))) + (build-system pyproject-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-before 'check 'remove-blocking-tests + (lambda _ + ;; Remove tests require python-asdf where + ;; python-asdf require python-asdf-standard, + ;; break circular dependencies. + (for-each delete-file + (list "tests/test_manifests.py" + "tests/test_integration.py"))))))) + (native-inputs (list python-astropy + python-jsonschema-next + python-pypa-build + python-pytest-7.1 + python-packaging + python-setuptools-scm)) + (propagated-inputs (list python-importlib-resources)) + (home-page "https://asdf-standard.readthedocs.io/") + (synopsis "ASDF standard schemas") + (description + "This package provides Python implementation of @acronym{ASDF, Advanced +Scientific Data Format} - a proposed next generation interchange format for +scientific data. ASDF aims to exist in the same middle ground that made FITS +so successful, by being a hybrid text and binary format: containing human +editable metadata for interchange, and raw binary data that is fast to load +and use. Unlike FITS, the metadata is highly structured and is designed +up-front for extensibility.") + (license license:bsd-3))) + (define python-asdf-transform-schemas (package (name "python-asdf-transform-schemas") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf_transform_schemas" version)) (sha256 - (base32 "1gmzd81hw4ppsvzrc91wcbjpcw9hhv9gavllv7nyi7qjb54c837g")))) - (build-system python-build-system) + (base32 "1midgn575970p5cnsh9y6bz77fjr392b5nfxb3z0id6c49xzzwhc")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "python" "-m" "pytest"))))))) - (native-inputs - (list python-pytest - python-semantic-version - python-setuptools-scm)) - (propagated-inputs - (list python-asdf)) + ;; Dependency cycle with python-asdf + (list #:tests? #f)) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-asdf-standard python-importlib-resources)) (home-page "https://github.com/asdf-format/asdf-transform-schemas") (synopsis "ASDF schemas for transforms") (description @@ -2052,25 +2324,111 @@ coordinates tags. Users should not need to install this directly; instead, install an implementation package such as asdf-astropy.") (license license:bsd-3))) +(define python-asdf-fits-schemas + ;; TODO: No release, change to tag when it's ready. + (let ((commit "572bb370d777f3a325b25c1af9d76e1b7d27dcea") + (revision "0")) + (package + (name "python-asdf-fits-schemas") + (version (git-version "0.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/asdf-format/asdf-fits-schemas") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1yqnzd0gcrdfl0jqm8m8kz5fd36i8lgh7xkglmp1chsi1cc6mkz2")))) + (build-system pyproject-build-system) + (arguments + (list + ;; Dependency cycle with python-asdf + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" "0.0.1")))))) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-asdf-standard python-importlib-resources)) + (home-page "https://github.com/asdf-format/asdf-fits-schemas") + (synopsis "ASDF schemas to support the FITS format") + (description + "This package provides ASDF schemas for validating FITS tags.") + (license license:bsd-3)))) + +(define python-asdf-time-schemas + ;; TODO: No release, change to tag when it's ready. + (let ((commit "e9174083d9cfd3c6f7ded9eeb360d99ccb8d9d18") + (revision "2")) + (package + (name "python-asdf-time-schemas") + (version (git-version "0.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/asdf-format/asdf-time-schemas") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1i40hcxp8sds2zq939fwczjlshfqb9r9pnzy3a44c3wqdbwhcbdb")))) + (build-system pyproject-build-system) + (arguments + (list + ;; Dependency cycle with python-asdf + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" "0.0.1")))))) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-asdf-standard + python-asdf-unit-schemas + python-importlib-resources)) + (home-page "https://github.com/asdf-format/asdf-fits-schemas") + (synopsis "Schemas for storing time in ASDF") + (description + "This package provides ASDF schemas for validating time tags.") + (license license:bsd-3)))) + +(define python-asdf-unit-schemas + (package + (name "python-asdf-unit-schemas") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asdf_unit_schemas" version)) + (sha256 + (base32 + "16grpx3a9h0v1wirp0zqrfsxm867v5c0xyr98pylzziy45kqvds2")))) + (build-system pyproject-build-system) + (arguments + ;; Dependency cycle with python-asdf + (list #:tests? #f)) + (native-inputs (list python-setuptools-scm)) + (propagated-inputs (list python-asdf-standard python-importlib-resources)) + (home-page "https://asdf-unit-schemas.readthedocs.io/") + (synopsis "ASDF serialization schemas for the units defined by @code{astropy.units}") + (description "This package provides ASDF schemas for validating unit tags.") + (license license:bsd-3))) + (define-public python-asdf-astropy (package (name "python-asdf-astropy") - (version "0.1.2") + (version "0.2.2") (source (origin (method url-fetch) (uri (pypi-uri "asdf_astropy" version)) (sha256 - (base32 "0bzgah7gskvnz6jcrzipvzixv8k2jzjkskqwxngzwp4nxgjbcvi4")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "python" "-m" "pytest"))))))) + (base32 "1b0v4cl7xvly3x1k5k2rvc2l32jqgqp0iyf1j20fkvj450sx74f2")))) + (build-system pyproject-build-system) (native-inputs (list python-coverage python-h5py @@ -2130,24 +2488,16 @@ install an implementation package such as gwcs.") (define-public python-gwcs (package (name "python-gwcs") - (version "0.18.0") + (version "0.18.2") (source (origin (method url-fetch) (uri (pypi-uri "gwcs" version)) (sha256 - (base32 "194j49m8xjjzv9pp8cnj06igz8sdxb0nphyybcc7mhigw0f0kr30")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "python" "-m" "pytest"))))))) + (base32 "0v9qcq6zl74d6s882s6xmas144jfalvll6va8rvrxmvpx4vqjzhg")))) + (build-system pyproject-build-system) (native-inputs - (list python-jsonschema + (list python-jsonschema-next python-jmespath python-pytest python-pytest-doctestplus diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 70d9d4421d..ead5ce5963 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -14,7 +14,7 @@ ;;; Copyright © 2018, 2020, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org> ;;; Copyright © 2018 Brett Gilio <brettg@gnu.org> -;;; Copyright © 2018, 2019 Marius Bakke <mbakke@fastmail.com> +;;; Copyright © 2018, 2019, 2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2018, 2021 Thorsten Wilms <t_w_@freenet.de> ;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2018 Brendan Tildesley <mail@brendan.scot> @@ -727,7 +727,7 @@ purposes developed at Queen Mary, University of London.") (define-public ardour (package (name "ardour") - (version "7.0") + (version "7.1") (source (origin (method git-fetch) (uri (git-reference @@ -744,7 +744,7 @@ purposes developed at Queen Mary, University of London.") namespace ARDOUR { const char* revision = \"" version "\" ; const char* date = \"\"; }"))))) (sha256 (base32 - "1xzgcd2d8zzgx3s9sr3kcxl3vz3vfr5l1xs9qpjplmk22dfj8b08")) + "11ca9xpzmzafl8xl0r0w32lxjqwy532hfd2bzb0d73bdpngpvcbq")) (file-name (string-append name "-" version)))) (build-system waf-build-system) (arguments @@ -849,19 +849,26 @@ engineers, musicians, soundtrack editors and composers.") (define-public audacity (package (name "audacity") - (version "3.1.3") + (version "3.2.1") (source (origin ;; If built from the release tag, Audacity will describe itself ;; as an "Alpha test version" and suggest to users that they use ;; the "latest stable released version". - (method url-fetch) - (uri (string-append "https://github.com/audacity/audacity/releases/download/" - "Audacity-" version "/audacity-" version - "-source.tar.gz")) + ;; XXX: For 3.2.1 we rebelliously use a git tag anyway because the only + ;; "processed" download is a .zip containing a .tar.gz which does not + ;; fare well with the patch and snippet machinery: + ;; https://github.com/audacity/audacity/issues/3811 + ;; TODO: Find a way to control the "alpha" status even when using git + ;; so we're not reliant on preprocessed source code. + (method git-fetch) + (uri (git-reference + (url "https://github.com/audacity/audacity") + (commit (string-append "Audacity-" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "189agx11361k9j958s6q5bngnnfx0rwaf0dwbjxy6fwvsb1wv3px")) + "00mal30jxbcacs1ka4yb5s8xq81zm7mv3y8l5hvg77abkyvfvdzf")) (patches (search-patches "audacity-ffmpeg-fallback.patch")) (modules '((guix build utils))) (snippet @@ -891,14 +898,13 @@ engineers, musicians, soundtrack editors and composers.") jack-1 expat lame - linux-libre-headers flac ffmpeg libid3tag libjpeg-turbo - libmad ;;("libsbsms" ,libsbsms) ;bundled version is modified libsndfile + mpg123 soundtouch soxr ;replaces libsamplerate sqlite @@ -909,20 +915,24 @@ engineers, musicians, soundtrack editors and composers.") lilv ;for lv2 suil ;for lv2 portaudio - portmidi)) + portmidi + wavpack)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gettext-minimal) ;for msgfmt - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("python" ,python) - ("which" ,which))) + (list autoconf + automake + gettext-minimal ;for msgfmt + libtool + pkg-config + python + which)) (arguments `(#:configure-flags (list "-Daudacity_conan_enabled=off" "-Daudacity_lib_preference=system" + ;; Disable support for VST 3 SDK, which is not yet in Guix (and has + ;; a dubious licensing agreement despite GPL code). + "-Daudacity_has_vst3=off" ;; TODO: enable this flag once we've packaged all dependencies ;; "-Daudacity_obey_system_dependencies=on" ;; disable crash reports, updates, ..., anything that phones home @@ -944,24 +954,20 @@ engineers, musicians, soundtrack editors and composers.") "CMAKE_BUILD_WITH_INSTALL_RPATH TRUE") (("CMAKE_INSTALL_RPATH_USE_LINK_PATH [A-Z]*") "CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE")) + (substitute* "libraries/image-compiler/CMakeLists.txt" + (("PROPERTIES") + ;; This scripts needs to run during build, make sure it finds + ;; the required libraries. + "PROPERTIES BUILD_WITH_INSTALL_RPATH FALSE")) (substitute* "src/CMakeLists.txt" + ;; Despite the name, this script breaks rpath. Don't run it. + (("install.*linux/fix_rpath\\.cmake.*") + "") (("-Wl,--disable-new-dtags") "-Wl,--enable-new-dtags")))) - (add-after 'unpack 'comment-out-revision-ident - (lambda _ - (substitute* "src/CMakeLists.txt" - (("file\\( TOUCH \".*RevisionIdent\\.h\" \\)" directive) - (string-append "# " directive))) - (substitute* "src/AboutDialog.cpp" - (("(.*RevisionIdent\\.h.*)" include-line) - (string-append "// " include-line))))) (add-after 'unpack 'use-upstream-headers (lambda* (#:key inputs #:allow-other-keys) (substitute* '("libraries/lib-files/FileNames.cpp") (("\"/usr/include/linux/magic.h\"") "<linux/magic.h>")))) - (add-after 'install 'delete-gratuitous-script - (lambda* (#:key outputs #:allow-other-keys) - (delete-file (string-append (assoc-ref outputs "out") - "/audacity")))) (add-after 'wrap-program 'glib-or-gtk-wrap (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))) ;; The test suite is not "well exercised" according to the developers, @@ -3707,7 +3713,8 @@ analysis plugins or audio feature extraction plugins.") (symlink (search-input-file inputs (string-append "/share/automake-" - ,(package-version automake) + ,(version-major+minor + (package-version automake)) "/ar-lib")) "ar-lib") #t))))) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index fd17992ab3..67708138a6 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -1036,7 +1036,7 @@ precious backup space. (arguments `(#:tests? #f)) ;no test (inputs - (list lzo libressl protobuf xz zlib)) + (list lzo libressl protobuf-3.6 xz zlib)) (home-page "http://zbackup.org") (synopsis "Versatile deduplicating backup tool") (description diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index bf6435585e..36b27a4e25 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -130,7 +130,19 @@ command-line arguments, multiple languages, and so on.") (substitute* (list (string-append bin "/egrep") (string-append bin "/fgrep")) (("^exec grep") - (string-append "exec " bin "/grep"))))))) + (string-append "exec " bin "/grep")))))) + ,@(if (hurd-target?) + '((add-before 'check 'skip-triple-backref-test + (lambda _ + ;; This test is marked as malfunctioning on glibc systems + ;; due to + ;; <https://sourceware.org/bugzilla/show_bug.cgi?id=11053> + ;; and it triggers a segfault with glibc 2.33 on GNU/Hurd. + ;; Skip it. + (substitute* "tests/triple-backref" + (("^warn_" all) + (string-append "exit 77\n" all)))))) + '())) #:make-flags ,(if (hurd-target?) ''("XFAIL_TESTS=test-perror2 equiv-classes") ;XXX ''()))) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f3b67fd2bf..bb319a13e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -506,6 +506,31 @@ ID and species. It is used by functions in the GenomeInfoDb package.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) +(define-public r-hdo-db + (package + (name "r-hdo-db") + (version "0.99.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "HDO.db" version 'annotation)) + (sha256 + (base32 + "14ngyxailmxrbxqqi9m7mchqcvchmbg7zm34i8a927b20s6z4z61")))) + (properties `((upstream-name . "HDO.db"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi)) + (native-inputs + (list r-knitr)) + (home-page "https://bioconductor.org/packages/HDO.db") + (synopsis "Annotation maps describing the entire Human Disease Ontology") + (description + "This package provides a set of annotation maps describing the entire +Human Disease Ontology. The annotation data comes from +@url{Humam Disease Ontology repository, +https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}.") + (license license:artistic2.0))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") @@ -1659,13 +1684,13 @@ and @code{Sailfish}. Alevin example output is also included.") (define-public r-abarray (package (name "r-abarray") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABarray" version)) (sha256 (base32 - "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r")))) + "02rjxzbrzphl28z8zpgw3gavzlzlx71n5ld8sb3im6xpn81ykvfh")))) (properties `((upstream-name . "ABarray"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest)) @@ -1685,13 +1710,13 @@ into folders according to the analysis settings used.") (define-public r-absseq (package (name "r-absseq") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABSSeq" version)) (sha256 (base32 - "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv")))) + "1ypd0wg3k2zzl0zf15c16dc38hfpsm5vv4x0x0yf90x0f8b6jpaz")))) (properties `((upstream-name . "ABSSeq"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit)) @@ -1714,13 +1739,13 @@ ranking by fold-change and visualization.") (define-public r-adam (package (name "r-adam") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 - "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn")))) + "1s1mzjxqld8gllfh6z9kg30klb4y1jrkrif7vwr18c0mhamf47a6")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -1749,13 +1774,13 @@ functionally associated genes} (GFAG).") (define-public r-adamgui (package (name "r-adamgui") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAMgui" version)) (sha256 (base32 - "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs")))) + "1ks799kgdmlxn5iyj6rzj04cm28klivclz3bg6bc4wad2q7h4ra9")))) (properties `((upstream-name . "ADAMgui"))) (build-system r-build-system) (propagated-inputs @@ -1797,13 +1822,13 @@ the @code{GFAGpathUi} function.") (define-public r-adimpute (package (name "r-adimpute") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADImpute" version)) (sha256 (base32 - "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w")))) + "0wrprxd91vi4wwh9wixhx1ppbjsb56r4kcxgqz8w6ahr3z2387im")))) (properties `((upstream-name . "ADImpute"))) (build-system r-build-system) (propagated-inputs @@ -1846,13 +1871,13 @@ results from different methods into an ensemble.") (define-public r-adsplit (package (name "r-adsplit") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 - "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm")))) + "0a05j1g42wnw5lcn6g6vp2z3mnjz185b2hvdg362ln270r19gch6")))) (properties `((upstream-name . "adSplit"))) (build-system r-build-system) (propagated-inputs @@ -1874,13 +1899,13 @@ the supporting gene set is determined.") (define-public r-affixcan (package (name "r-affixcan") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffiXcan" version)) (sha256 (base32 - "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq")))) + "1jsdl477qhsq3rpqvgdm7navr4izpppfkiw0fvlhxwspgp3fjs6c")))) (properties `((upstream-name . "AffiXcan"))) (build-system r-build-system) (propagated-inputs @@ -1902,13 +1927,13 @@ expression values are known.") (define-public r-affyrnadegradation (package (name "r-affyrnadegradation") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyRNADegradation" version)) (sha256 (base32 - "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf")))) + "1n6x2c0h6xmcll7mxq4n1y8ahqfmba8ppdcrjk9hf3nh5wngprkz")))) (properties `((upstream-name . "AffyRNADegradation"))) (build-system r-build-system) (propagated-inputs (list r-affy)) @@ -1927,13 +1952,13 @@ of samples that are affected by RNA degradation.") (define-public r-agdex (package (name "r-agdex") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AGDEX" version)) (sha256 (base32 - "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9")))) + "0yvdx32yr4mv7dl5ycpbxhrkm6csrr7k3398ggjavdcfhz54dgr8")))) (properties `((upstream-name . "AGDEX"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-gseabase)) @@ -1954,13 +1979,13 @@ experiment.") (define-public r-aggregatebiovar (package (name "r-aggregatebiovar") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aggregateBioVar" version)) (sha256 (base32 - "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1")))) + "1snsc2430cc7cd0k01n1rwa6vympd79g1mcch0paxxkq7msvfn42")))) (properties `((upstream-name . "aggregateBioVar"))) (build-system r-build-system) (propagated-inputs @@ -1988,13 +2013,13 @@ bulk RNA-seq tools.") (define-public r-agilp (package (name "r-agilp") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "agilp" version)) (sha256 (base32 - "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf")))) + "15cw004g1vxfwvf939018vmlv9gym4r473jissamkygqdv78hcr0")))) (properties `((upstream-name . "agilp"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/agilp") @@ -2010,13 +2035,13 @@ but which also provides utilities which may be useful for other platforms.") (define-public r-adductomicsr (package (name "r-adductomicsr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductomicsR" version)) (sha256 (base32 - "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys")))) + "0h180k4r1lrij1smpibbqgiki1hb2q87n5ay6habig4bxzbx773x")))) (properties `((upstream-name . "adductomicsR"))) (build-system r-build-system) (propagated-inputs @@ -2055,13 +2080,13 @@ mass spectrometry} (MS1) data.") (define-public r-agimicrorna (package (name "r-agimicrorna") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AgiMicroRna" version)) (sha256 (base32 - "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa")))) + "0q3hynyd4dhhh1a2b27y3rrshgvxfwv17k7yabh6g4pc12c33mf7")))) (properties `((upstream-name . "AgiMicroRna"))) (build-system r-build-system) (propagated-inputs @@ -2082,16 +2107,40 @@ using the linear model features implemented in limma. Standard Bioconductor objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-aims + (package + (name "r-aims") + (version "1.30.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AIMS" version)) + (sha256 + (base32 + "1civ4a14ynccv6xs27fm95fw6254l1z0q37546ivyv2mhbz0d2i1")))) + (properties `((upstream-name . "AIMS"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-e1071)) + (home-page "https://git.bioconductor.org/packages/AIMS") + (synopsis + "Absolute assignment of breast cancer intrinsic molecular subtype") + (description + "This package contains an implementation of @code{AIMS} -- Absolute +Intrinsic Molecular Subtyping. It contains necessary functions to assign the +five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, +Basal-like, Normal-like). Assignments could be done on individual samples as +well as on dataset of gene expression data.") + (license license:artistic2.0))) + (define-public r-airpart (package (name "r-airpart") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "airpart" version)) (sha256 (base32 - "0ljankgvgf8rby4z340wxx8v7acs9yz955p3a40jl6y8rz1svc06")))) + "07zxv0sjhlajaw4gxpjni14qyyqn70ar8ph5cpibzcky1lx6pmkl")))) (properties `((upstream-name . "airpart"))) (build-system r-build-system) (propagated-inputs @@ -2132,13 +2181,13 @@ datasets.") (define-public r-amountain (package (name "r-amountain") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMOUNTAIN" version)) (sha256 (base32 - "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54")))) + "0zzl5dv64yhdivsm2pgsfjikygib9pkfiv34h1lnmqrj6yivvvw8")))) (properties `((upstream-name . "AMOUNTAIN"))) (build-system r-build-system) (inputs (list gsl)) @@ -2156,13 +2205,13 @@ in multi-layer WGCN using a continuous optimization approach.") (define-public r-amaretto (package (name "r-amaretto") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMARETTO" version)) (sha256 (base32 - "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx")))) + "18w65sf3h4yzw9v5xgkalxnkmgzgsx100v7qc7z4ifx10lgpji5n")))) (properties `((upstream-name . "AMARETTO"))) (build-system r-build-system) (propagated-inputs @@ -2208,13 +2257,13 @@ canonical cancer pathways.") (define-public r-anaquin (package (name "r-anaquin") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Anaquin" version)) (sha256 (base32 - "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd")))) + "08y2syaacy15rxcf3x2r3906kfm58fkx7ainaqvy5inlc9f670j5")))) (properties `((upstream-name . "Anaquin"))) (build-system r-build-system) (propagated-inputs @@ -2235,16 +2284,69 @@ of Medical Research. The goal is to provide a standard library for quantitative analysis, modelling, and visualization of spike-in controls.") (license license:bsd-3))) +(define-public r-ancombc + (package + (name "r-ancombc") + (version "2.0.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ANCOMBC" version)) + (sha256 + (base32 + "1bwzvi6j3s66dcll1lb4xy25j4nfn1ln6mc3flh0wgy13l26x8m6")))) + (properties `((upstream-name . "ANCOMBC"))) + (build-system r-build-system) + (propagated-inputs + (list r-cvxr + r-desctools + r-doparallel + r-dorng + r-dplyr + r-emmeans + r-energy + r-foreach + r-hmisc + r-lme4 + r-lmertest + r-magrittr + r-mass + r-mia + r-nloptr + r-rdpack + r-rlang + r-rngtools + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-tibble + r-tidyr + r-treesummarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/FrederickHuangLin/ANCOMBC") + (synopsis "Analysis of compositions of microbiomes with bias correction") + (description + "@code{ANCOMBC} is a package containing @dfn{differential abundance} (DA) +and correlation analyses for microbiome data. Specifically, the package +includes @dfn{Analysis of Compositions of Microbiomes with Bias +Correction}(ANCOM-BC) and @dfn{Analysis of Composition of Microbiomes} (ANCOM) +for DA analysis, and @dfn{Sparse Estimation of Correlations among +Microbiomes} (SECOM) for correlation analysis. Microbiome data are typically +subject to two sources of biases: unequal sampling fractions (sample-specific +biases) and differential sequencing efficiencies (taxon-specific biases). +Methodologies included in the @code{ANCOMBC} package were designed to correct +these biases and construct statistically consistent estimators.") + (license license:artistic2.0))) + (define-public r-aldex2 (package (name "r-aldex2") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALDEx2" version)) (sha256 (base32 - "0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9")))) + "0585s5pb8zr9il1vhxw9vjzzajmdcjmf9zz3zlc5vpczd3fnzfkf")))) (properties `((upstream-name . "ALDEx2"))) (build-system r-build-system) (propagated-inputs @@ -2276,16 +2378,130 @@ paired or unpaired study designs.") ;; package's LICENSE is specified as GPL-3. (license (list license:agpl3+ license:gpl2+ license:gpl3)))) +(define-public r-alevinqc + (package + (name "r-alevinqc") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "alevinQC" version)) + (sha256 + (base32 + "0rd64j4hkdk2d6mlld6qkv2m96lqc93807xjdf05xm8qkyx8g8y2")))) + (properties `((upstream-name . "alevinQC"))) + (build-system r-build-system) + (propagated-inputs + (list r-cowplot + r-dplyr + r-dt + r-ggally + r-ggplot2 + r-rcpp + r-rjson + r-rlang + r-rmarkdown + r-shiny + r-shinydashboard + r-tximport)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/csoneson/alevinQC") + (synopsis "Quality control reports for @code{Alevin} output") + (description + "The package @code{r-alevinqc} generates quality control reports +summarizing the output from an @code{alevin} run. The reports can be +generated as HTML or PDF files, or as Shiny applications.") + (license license:expat))) + +(define-public r-alphabeta + (package + (name "r-alphabeta") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AlphaBeta" version)) + (sha256 + (base32 + "000apg879li9wkbyrl8cm73z6h0xasqp41h9ir9hywy2v38rmc5b")))) + (properties `((upstream-name . "AlphaBeta"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-data-table + r-dplyr + r-expm + r-ggplot2 + r-gtools + r-igraph + r-optimx + r-plotly + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AlphaBeta") + (synopsis "Estimate epimutation rates and spectra from DNA methylations in plants") + (description + "The package @code{AlphaBeta} is a computational method for estimating +epimutation rates and spectra from high-throughput DNA methylation data in +plants. The method has been specifically designed to: + +@itemize +@item analyze @emph{germline} epimutations in the context of + multi-generational mutation accumulation lines; +@item analyze @emph{somatic} epimutations in the context of plant development + and aging. +@end itemize") + (license license:gpl3))) + +(define-public r-alpine + (package + (name "r-alpine") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "alpine" version)) + (sha256 + (base32 + "1nl1hxwakh5m9rqm3ksn2jzknsj9xnwl51bmc30knknm4q35wdv9")))) + (properties `((upstream-name . "alpine"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-speedglm + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alpine") + (synopsis "Modeling and correcting fragment sequence bias") + (description + "The package @code{alpine} helps to model bias parameters and then using +those parameters to estimate RNA-seq transcript abundance. @code{Alpine} is a +package for estimating and visualizing many forms of sample-specific biases that +can arise in RNA-seq, including fragment length distribution, positional bias on +the transcript, read start bias (random hexamer priming), and fragment GC-content +(amplification). It also offers bias-corrected estimates of transcript +abundance in @dfn{FPKM}(Fragments Per Kilobase of transcript per Million +mapped reads). It is currently designed for un-stranded paired-end RNA-seq +data.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl")))) + "154cg63n7h9h5jkj00aqf0hzbmmjg16bzvvk50fyixwq0a4q1j00")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2321,13 +2537,13 @@ sequencing data.") (define-public r-anf (package (name "r-anf") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ANF" version)) (sha256 (base32 - "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj")))) + "0yfwvgx7144r894fr13sx4gyyq6ljh7y734wx74sb7q80cl2gs1j")))) (properties `((upstream-name . "ANF"))) (build-system r-build-system) (propagated-inputs @@ -2349,13 +2565,13 @@ network fusion.") (define-public r-annmap (package (name "r-annmap") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annmap" version)) (sha256 (base32 - "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv")))) + "18ia189qgsbcivpfsfss05dnd3kdc6gmswq8i1whwf9n227b2cv3")))) (properties `((upstream-name . "annmap"))) (build-system r-build-system) (propagated-inputs @@ -2383,13 +2599,13 @@ Functions to plot gene architecture and BAM file data are also provided.") (define-public r-antiprofiles (package (name "r-antiprofiles") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "antiProfiles" version)) (sha256 (base32 - "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40")))) + "0f32373ncfjbvy05yngmfhhdgyc99a4idz3ry2xlabdmrbs5yac3")))) (properties `((upstream-name . "antiProfiles"))) (build-system r-build-system) (propagated-inputs @@ -2406,16 +2622,64 @@ reproducible gene expression signatures capable of accurately distinguishing tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-arrayexpress + (package + (name "r-arrayexpress") + (version "1.57.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ArrayExpress" version)) + (sha256 + (base32 + "1fzi951mjc4kbkkvlfvwlfrpfnjckkmw4xz4m5dapy1z2jkgp8w6")))) + (properties `((upstream-name . "ArrayExpress"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-limma + r-oligo + r-xml)) + (home-page "https://bioconductor.org/packages/ArrayExpress") + (synopsis "Building R objects from ArrayExpress datasets") + (description + "This package offers the possibility to access the ArrayExpress repository +at @dfn{EBI} (European Bioinformatics Institute) and build Bioconductor data +structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") + (license license:artistic2.0))) + +(define-public r-asafe + (package + (name "r-asafe") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASAFE" version)) + (sha256 + (base32 + "1q4i33rw1qb8bnvkl06izl4nyl9lzgwy8rwrmvbrz1c384pmy8yj")))) + (properties `((upstream-name . "ASAFE"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASAFE") + (synopsis "Ancestry Specific Allele Frequency Estimation") + (description + "The @code{ASAFE} package contains a collection of functions that can be +used to carry out an @dfn{EM} (Expectation–maximization) algorithm to estimate +ancestry-specific allele frequencies for a bi-allelic genetic marker, e.g. an +@dfn{SNP} (single nucleotide polymorphism) from genotypes and ancestry +pairs.") + (license license:artistic2.0))) + (define-public r-aseb (package (name "r-aseb") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASEB" version)) (sha256 (base32 - "1i0r4vimk6is4j4rr14ajp8papznpmmr0bhwd96s8w53cqdqph7p")))) + "1kr6l2ma7wzy8i9dn86zx927yvx1l4bnkxhv97ra3sh5vr6m8ywa")))) (properties `((upstream-name . "ASEB"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/ASEB") @@ -2436,13 +2700,13 @@ RNAs.") (define-public r-asgsca (package (name "r-asgsca") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASGSCA" version)) (sha256 (base32 - "0mxrrkm2lg7gxjh8ynn6qmryn8wqda7b83sr51dpgblay83jcbaq")))) + "12wap8xbq6xl7p430yd9yy5kdhs15n7nmv2h3k9bsi0f4m6md02i")))) (properties `((upstream-name . "ASGSCA"))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix)) @@ -2459,13 +2723,13 @@ model as latent variables.") (define-public r-aspli (package (name "r-aspli") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASpli" version)) (sha256 (base32 - "1frlcwa8m4imfx6ncav8r8yskyaf4ibha177mfnp9y84w6mphynz")))) + "0gwp5ijpxjy6hd1090cmwbfrfac1qqrzxc06n1j89c0va7wm9l4k")))) (properties `((upstream-name . "ASpli"))) (build-system r-build-system) (propagated-inputs @@ -2507,13 +2771,13 @@ that might arise in splicing patterns.") (define-public r-assessorf (package (name "r-assessorf") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AssessORF" version)) (sha256 (base32 - "1l87bpny9k3jbzbzmb9h2ijvblrj471gqv26fyzbvb3vr6y406z7")))) + "125qkjsjyxp6zk3nzfamakyfgm7wd7w9vv1vn7xyyylpqpa8rpml")))) (properties `((upstream-name . "AssessORF"))) (build-system r-build-system) (propagated-inputs @@ -2536,13 +2800,13 @@ start codons as the forms of evidence.") (define-public r-asset (package (name "r-asset") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASSET" version)) (sha256 (base32 - "029acl5k9d4hnvy3jia9cr4rk6w31zn8b5s79i6lazq1cp236hbg")))) + "13zwnjap4y0s3qqv10mv2i4mqan9nmkm2l29i448h1j3wwfq18j2")))) (properties `((upstream-name . "ASSET"))) (build-system r-build-system) (propagated-inputs (list r-mass r-msm r-rmeta)) @@ -2563,13 +2827,13 @@ variant.") (define-public r-atena (package (name "r-atena") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atena" version)) (sha256 (base32 - "0b89wb7cc44c8jd6868dn8pwgid768bprkncsi87qkdz0abbhzhp")))) + "1a3qv66caz2pg67ff9c5424pygsgqnfx67ybzc3zkzaw4fj8cp54")))) (properties `((upstream-name . "atena"))) (build-system r-build-system) (propagated-inputs @@ -2604,13 +2868,13 @@ transcripts in an integrated manner.") (define-public r-atsnp (package (name "r-atsnp") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atSNP" version)) (sha256 (base32 - "0dmv34xqwr3l2rznapxmyrkyf1w78qzxdv88s5nn8s1m8qdkgwkz")))) + "12za1agpbjjg4i94mikbkdbwqnkzzwz07v0gwdc7lpa9899q2ycb")))) (properties `((upstream-name . "atSNP"))) (build-system r-build-system) (propagated-inputs @@ -2637,13 +2901,13 @@ SNP-led changes in motif matches.") (define-public r-attract (package (name "r-attract") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "attract" version)) (sha256 (base32 - "0f1fsv278kpnxvqg9qa5rw2k3zr8zws0ab73ldl60h6pv9cy8x82")))) + "0r5vykjqq33gchqv0wp2i6wpnk95cv26w5j4yqxcnw0bnqfhrgkm")))) (properties `((upstream-name . "attract"))) (build-system r-build-system) (propagated-inputs @@ -2668,13 +2932,13 @@ transcriptionally-coordinated changes in gene expression.") (define-public r-awfisher (package (name "r-awfisher") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AWFisher" version)) (sha256 (base32 - "050k7w0azsl7rqx2pxgccihzc2q8pmh6fyy4gib2d42sdyijr2n1")))) + "1psbxxrwb6mk2jwjw963vwdczb3i5590rcm7hk43kpiw45i1q1j9")))) (properties `((upstream-name . "AWFisher"))) (build-system r-build-system) (propagated-inputs @@ -2692,13 +2956,13 @@ meta-pattern.") (define-public r-awst (package (name "r-awst") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "awst" version)) (sha256 (base32 - "0iw3zycmj95rmdx7f2w0j4yxkzd90y87lrzgdn9cyvvzi5avflav")))) + "0dvzkqpjv7whns9q8zj6n2nyvnaw2ib7i53vf049n94x52vh9x15")))) (properties `((upstream-name . "awst"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -2719,13 +2983,13 @@ artifacts.") (define-public r-baalchip (package (name "r-baalchip") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaalChIP" version)) (sha256 (base32 - "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q")))) + "16s67v6mkv14dkk1r7c50brm7198b84h87h1wrahmrrcnzq8pi0n")))) (properties `((upstream-name . "BaalChIP"))) (build-system r-build-system) (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl @@ -2759,13 +3023,13 @@ alleles, a known phenotypical feature of cancer samples.") (define-public r-basespacer (package (name "r-basespacer") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaseSpaceR" version)) (sha256 (base32 - "0jyw4pnybsd6ywpaamk5ywkrcib2z48farsnszmwq97zlbmra7fj")))) + "07pqs0jkwcbxavc65sanvhvzc9spkk46bqnwz162f3pvrz15b5h7")))) (properties `((upstream-name . "BaseSpaceR"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjsonio)) @@ -2782,13 +3046,13 @@ rich environment of statistical and data analysis tools.") (define-public r-bac (package (name "r-bac") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BAC" version)) (sha256 (base32 - "0dkw7438d2sf6nb577dnzija54qs0nhlr47lb73li60fhlnvqmh2")))) + "00dkhns9n1x4wmlxjcw75h7iwwk37zlv1c2fi0g1mmsw1xvdjzp6")))) (properties `((upstream-name . "BAC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BAC") @@ -2806,13 +3070,13 @@ you will have to normalize your data beforehand.") (define-public r-bader (package (name "r-bader") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BADER" version)) (sha256 (base32 - "0i5x1r2ns1hxhqk5jyfqird81hck1hllvvgx5bn0rb5vl99g8spm")))) + "1hkvmfik4m2yw5xg4k2g551l27i64blbsdvp1kmvvyix66p53hsr")))) (properties `((upstream-name . "BADER"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BADER") @@ -2830,13 +3094,13 @@ can be used for further down-stream analyses such as gene set enrichment.") (define-public r-badregionfinder (package (name "r-badregionfinder") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BadRegionFinder" version)) (sha256 (base32 - "1a1pqmh5ak9s3k1lxw6flanchk24zyznwm34ixi2b78wdc3hqgm9")))) + "0bsgdjchwsfc8aiwiacr454kw97dbymq6v450m1fx7hxmmpqz1sm")))) (properties `((upstream-name . "BadRegionFinder"))) (build-system r-build-system) (propagated-inputs @@ -2857,13 +3121,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "2.2.0") + (version "3.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "0dc2hpnykr575jbrq9whmdabknl70s2hcs6gkmkl4kpv7xfqdq6w")))) + "0246cn5l1kxysjrzy4prfdxn71vc47a8kciqw384nm2mi3vsy4vx")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs @@ -2900,13 +3164,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "1423djb7cij68y0q2dcp8q7lrcn2fxjn6d25v4qy3w00b2w8ppg9")))) + "18xq8gg1j07gbbxy7r0cc34zwn40mh4fr39zzi8l3z0cymw73qs8")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs @@ -2938,13 +3202,13 @@ the posterior densities for the average relative abundance of transcripts.") (define-public r-banocc (package (name "r-banocc") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "banocc" version)) (sha256 (base32 - "10vaggq1w5jkxd8r2k1mhymzvb7x3h8afwn2pvmcpj022ka7xhbx")))) + "0d7ss3df6zcfsh8kgy35ghxa6f27ynjhdbi6mdypgk9q24f64r78")))) (properties `((upstream-name . "banocc"))) (build-system r-build-system) (propagated-inputs @@ -2966,13 +3230,13 @@ estimates for each correlation element.") (define-public r-barcodetrackr (package (name "r-barcodetrackr") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "barcodetrackR" version)) (sha256 (base32 - "0yxa15xkgqazw31vq4wm8v747bw4qb18m6i602pvynk0n5bgg3d3")))) + "1b3z83nkl8csxs88rcbmkkfjps71mwnylvpy3kjzyi02xw0kh0c1")))) (properties `((upstream-name . "barcodetrackR"))) (build-system r-build-system) (propagated-inputs @@ -3008,14 +3272,14 @@ retrieval analyses, or similar technologies.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.15.2") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn")))) + "1djp23y131dyx4g22f9r7an177bq0mky94bvpqvc8b14166g0ynw")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -3028,13 +3292,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.42.0") + (version "0.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc")))) + "17dhr7vaph8dnvyklszyas7y8i64mxqxhnfhb6q3l47gq5if8645")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -3048,13 +3312,13 @@ packages.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp")))) + "0cqvwp0ybxgnk9kif3ly780v23pwv4cyh46kk47gxcxqqkjv36ld")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors @@ -3075,13 +3339,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q")))) + "1fzkhnlgv4zd0slr12d5aichyxsca86p82fyjymiz7f5fqdvqmd9")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -3105,13 +3369,13 @@ used visualizations.") (define-public r-dama (package (name "r-dama") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "daMA" version)) (sha256 (base32 - "1mpjvl24wsdmpgra3iasgfvy29m71318gj6j1gg6081w0n4cq72m")))) + "062nxfry9w674ja3q9zs4df2hvf4wws9jdqpy84g6nb0309vbhqf")))) (properties `((upstream-name . "daMA"))) (build-system r-build-system) (propagated-inputs (list r-mass)) @@ -3127,13 +3391,13 @@ factorial microarray data.") (define-public r-damefinder (package (name "r-damefinder") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DAMEfinder" version)) (sha256 (base32 - "123ra94bij0m45j2fzqr7fjipj4ld9kgk0kir1zfdbbd5h8h4mdf")))) + "0ygsgg51473sycsh367rf8plca6zb1jg2l39zcprwvgpiln8mjdg")))) (properties `((upstream-name . "DAMEfinder"))) (build-system r-build-system) (propagated-inputs @@ -3168,14 +3432,14 @@ offers nice visualization of methyl-circle plots.") (define-public r-dearseq (package (name "r-dearseq") - (version "1.8.4") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl")))) + "1f9hz4jp862jm1grf4qzdvnzp17ri0n1rhfafgkc1j73z6whw1b0")))) (build-system r-build-system) (propagated-inputs (list r-compquadform @@ -3188,6 +3452,7 @@ offers nice visualization of methyl-circle plots.") r-pbapply r-reshape2 r-rlang + r-scattermore r-statmod r-survey r-tibble @@ -3206,13 +3471,13 @@ set analyses, and can deal with repeated or longitudinal data.") (define-public r-debcam (package (name "r-debcam") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "debCAM" version)) (sha256 (base32 - "1ynz57kkxl8nx80zhh1vhhydqb5n6r9d7p69f0k9nj8rp4hdgng7")))) + "09dm861adbxdy3ncfdxq46wjr4hpn56c66n64xm9gwzkzsrxyc2a")))) (properties `((upstream-name . "debCAM"))) (build-system r-build-system) (inputs (list openjdk)) @@ -3245,13 +3510,13 @@ knowledge can achieve semi-supervised deconvolution of mixtures.") (define-public r-decipher (package (name "r-decipher") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5")))) + "01hzxd5f5v2kspx5jd7l21bn87cfgm9aah3zd4d6kyxv98h5a3n1")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -3269,13 +3534,13 @@ biological sequences.") (define-public r-deco (package (name "r-deco") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deco" version)) (sha256 (base32 - "18n5zgln33c79jbjzjlivs8ihyg8zci6minfqlvagxgzcpa67k0m")))) + "0d4abif3v62cbas6hl7pfw8q8jihh7nsra76k9cm6kz54qw4fbnw")))) (properties `((upstream-name . "deco"))) (build-system r-build-system) (propagated-inputs @@ -3311,13 +3576,13 @@ higher deregulation levels.") (define-public r-decomplexdisease (package (name "r-decomplexdisease") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEComplexDisease" version)) (sha256 (base32 - "09a967x1rnv7byjwh29ngjhs67rgg27zblmlzx6pyqlwy5jsp89d")))) + "12gw9b0gdwyih51j2gzay6vxhycgc52n8svd0slv6wsbw5rc19lh")))) (properties `((upstream-name . "DEComplexDisease"))) (build-system r-build-system) (propagated-inputs @@ -3344,13 +3609,13 @@ mechanism based on the shared signatures.") (define-public r-decomptumor2sig (package (name "r-decomptumor2sig") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decompTumor2Sig" version)) (sha256 (base32 - "04hg9bbga2s8scjxfd8wjlmr45nzzvh8d6gr0w929sybx4nj2qz6")))) + "0agvmgwyk458lhhhspd8243n4897f0q7jf9yqhwsl5wi8011vmqd")))) (properties `((upstream-name . "decompTumor2Sig"))) (build-system r-build-system) (inputs (list perl)) ;script/extractSpecColumns.pl @@ -3387,13 +3652,13 @@ of the signatures to the mutation load of the tumor.") (define-public r-deconrnaseq (package (name "r-deconrnaseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DeconRNASeq" version)) (sha256 (base32 - "10smk88srxm58hli0fhkdfd6l5z02q58xc9mww39gkn71y0127k6")))) + "05rwqchfspy8i9fcj9526rl5vvk0rrgr95nvxzdj0sa2136my8y4")))) (properties `((upstream-name . "DeconRNASeq"))) (build-system r-build-system) (propagated-inputs @@ -3414,13 +3679,13 @@ single expression profiles.") (define-public r-decontam (package (name "r-decontam") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decontam" version)) (sha256 (base32 - "1g9hcfcfnpq6z21069yw0pyzncwznmvxb2xalg4y6y1604dy98q9")))) + "0bk7ia2flnxwa99b8mf3xdvap3xqa4pvpsrgbnyapxbaqxr5zf82")))) (properties `((upstream-name . "decontam"))) (build-system r-build-system) (propagated-inputs @@ -3440,13 +3705,13 @@ negative control samples.") (define-public r-deconvr (package (name "r-deconvr") - (version "1.2.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3")))) + "1wa8l9zxdwx32122slnzqyk32klyznxnbziwn98jbp5fxmjka92l")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs @@ -3484,13 +3749,13 @@ make mapping WGBS data to their probe IDs easier.") (define-public r-decoupler (package (name "r-decoupler") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decoupleR" version)) (sha256 - (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m")))) + (base32 "1872pi2v9gymdpqdhab10ash4b2w8sbk1p635lf0p6s4679syhdi")))) (properties `((upstream-name . "decoupleR"))) (build-system r-build-system) (propagated-inputs @@ -3525,13 +3790,13 @@ targeted by a kinase.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn")))) + "051xcg9lx8plbfhiacrv1wsxfac0qqspysq960ppibkf4m8crk81")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs @@ -3561,13 +3826,13 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.22.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy")))) + "0nl1v0mxb759wiia2rsxay0cv0q631gqyzgaa10s175lhzsb8r6p")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -3591,13 +3856,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-derfinderhelper (package (name "r-derfinderhelper") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinderHelper" version)) (sha256 - (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5")))) + (base32 "118rjmqy53viczdwj70kaszkpg2r2zbq60k49jg7fqb81prdwy04")))) (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs @@ -3616,13 +3881,13 @@ calculation in parallel.") (define-public r-drimseq (package (name "r-drimseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 - (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l")))) + (base32 "0cj3fyb99fh30f35ra1gpvzwplszbwvwk33ppgyh1zx2axsx164w")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs @@ -3651,13 +3916,13 @@ results.") (define-public r-bluster (package (name "r-bluster") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8")))) + "1xi9vl09nm95l35kb9n3pn3j9qxw8976lss3cx0ppwnxd2mjr6vy")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs @@ -3681,13 +3946,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3")))) + "0jpj8bkfm3jcb5fj0xhh13vqh2dcgdgi4i1qk3wx1301irkk7fgf")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -3705,14 +3970,14 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-infercnv (package (name "r-infercnv") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "infercnv" version)) (sha256 (base32 - "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl")))) + "11hgw6c67gd3ih5q14a520sjmnlv56qw19z0i6s5pz2slmgflpry")))) (properties `((upstream-name . "infercnv"))) (build-system r-build-system) (inputs (list python)) @@ -3736,15 +4001,16 @@ arbitrary genomic intervals along chromosomal ideogram.") r-gplots r-gridextra r-hiddenmarkov - r-leiden + r-igraph r-matrix r-paralleldist r-phyclust r-rann r-rcolorbrewer - r-reshape + r-reshape2 r-rjags r-singlecellexperiment + r-seurat r-summarizedexperiment r-tidyr)) (native-inputs (list r-knitr)) @@ -3764,13 +4030,13 @@ over-abundant or less-abundant as compared to that of normal cells.") (define-public r-iranges (package (name "r-iranges") - (version "2.30.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3")))) + "0jvavhl6p2di0n5176gg7shfmpg79rngl2gaw423icswdf8kay89")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -3792,13 +4058,13 @@ possible.") (define-public r-isoformswitchanalyzer (package (name "r-isoformswitchanalyzer") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) (sha256 - (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd")))) + (base32 "06kcx0a7xxzqhf4y8l69my5chh06sfahsaz6anhana7shym3yif5")))) (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs @@ -3994,14 +4260,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7")))) + "1iix9mq4aph6avs2qr64a7hip461cif56k6npvs5g69nj3rn50gj")))) (build-system r-build-system) (propagated-inputs (list r-affyio @@ -4022,14 +4288,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0")))) + "18bxnjcl7cbgwm3yf58608ghwnpci94xgil11zmbpgzgrpv9pkrs")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -4043,14 +4309,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda")))) + "1bg7iqasvfsgd9x3ykgpblqnz1q06g3ifmzj4jf2kn8kxj63wfbl")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) @@ -4088,14 +4354,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p")))) + "0phf9rvxr45zq9m5rcjsiixmj9ilz518l628l8cd1hzfdk240ffy")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -4111,14 +4377,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.68.1") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww")))) + "17slls8dihjnpm6bynic8cm2fbnfl5iqwimz0wz7c9x44d1bxi4l")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -4153,14 +4419,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp")))) + "1bdcz9sz4khs7p4ddryc4ir0fwcjrkwqka8y0c9n36ykiv4myfib")))) (build-system r-build-system) (propagated-inputs (list r-zlibbioc)) @@ -4177,14 +4443,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.68.1") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils")))) + "0p42rpyh96aph9jr8kiyjvv860jn7m7ji2nrib2vr2nl0jyaxqjs")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -4205,14 +4471,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g")))) + "06jmnv36y3n6pl1vs6mp14sgyzl4l37g13diaa49k7qwp1kdpl3a")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -4232,13 +4498,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn")))) + "1srv0jizmwgmsmgb9cfgy5nbgd3jsgxgzzax6wfsahckb5zihrqp")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -4262,13 +4528,13 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald")))) + "0m16kfssxbblf03ykawkmqa038cl90prhb23k6y88g2hwm00wynk")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -4287,14 +4553,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.38.1") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v")))) + "15shh8rmcx69g3zd256720vh0c3qbly5zrvwm463dws41cjla48x")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -4319,14 +4585,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.4.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs")))) + "1hk02q6mwx49khbhydndfa1qry8ylhmwz2dff8845a510hm0di7n")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -4360,14 +4626,14 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.26.0") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys")))) + "01g9vfkmpfkn9nv71jyybq93lid6x93jbadjahngy98w67n3sin4")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -4384,14 +4650,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky")))) + "059pkm5pg9ssd0l8xrm13d0hscqnmlqcb4qb5p4fbzgx6088zg05")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -4414,13 +4680,13 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv")))) + "0rp541nphbcya6kbk1nzrrb05g5m6pxb3yqz5cj873di9vsqlyfv")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -4436,13 +4702,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg")))) + "0c6agi652kbffqwd1r3c22ncisqaiy3gqbc9fz13767rr71im6lq")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -4521,13 +4787,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.30.3") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92")))) + "1fkfbs0n0sdssli7ibrswkfag080kgv8n1zf6ssxx729g1fz3m3h")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -4539,18 +4805,16 @@ only one command.") ;; Remove generated documentation. (for-each delete-file '("inst/doc/BiocParallel_BatchtoolsParam.pdf" - "inst/doc/Introduction_To_BiocParallel.pdf" "inst/doc/Errors_Logs_And_Debugging.pdf" "inst/doc/BiocParallel_BatchtoolsParam.R" "inst/doc/Introduction_To_BiocParallel.R" - "inst/doc/Errors_Logs_And_Debugging.R")) + "inst/doc/Errors_Logs_And_Debugging.R" + "inst/doc/Random_Numbers.R")) ;; Remove time-dependent macro (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw" - "inst/doc/Introduction_To_BiocParallel.Rnw" "inst/doc/Errors_Logs_And_Debugging.Rnw" "vignettes/BiocParallel_BatchtoolsParam.Rnw" - "vignettes/Introduction_To_BiocParallel.Rnw" "vignettes/Errors_Logs_And_Debugging.Rnw") (("\\today") "later")) @@ -4560,7 +4824,7 @@ only one command.") (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) (propagated-inputs - (list r-bh r-codetools r-futile-logger r-snow)) + (list r-bh r-cpp11 r-codetools r-futile-logger r-snow)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocParallel") @@ -4574,13 +4838,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.64.1") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33")))) + "1z86s8ncl91pxcjnv8fwvgwjjnd384dn5paylwyymrigph4ca4kk")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -4602,14 +4866,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd")))) + "0k56bq3g5vwnd0vkqg7x7v7i9bakwb8s1yl7k5nwj26k4aw96lw6")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -4644,13 +4908,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.64.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc")))) + "1gzpvajw5n3qmym3312qaks450sq3w456kj4gqwaabgpjxbq7frm")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -4675,14 +4939,14 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd")))) + "1j62b3ycvb27p80k1a1qj4pdf8cjynf5fkj65v74c3l1hgl9qxnh")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -4706,13 +4970,13 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.32.1") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf")))) + "0jr9mc79di0r3xrc7m27vwk85qa4fpcwp4nb77pr9s6jbv23773r")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -4753,14 +5017,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i")))) + "1gmspbf5bmlqgbq280lnh4m9bmhzv6d0aj15dmggizsgb9d34vp5")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -4779,14 +5043,14 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.12.1") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8")))) + "1mf0h2j31m57jd3s1sj8ijn9wdgbg452d79drdkxypxqvpm7b927")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -4819,14 +5083,14 @@ self-defined annotation graphics.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.28.0") + (version "2.29.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb")))) + "1h4cyrjwdazgk49yzi9lvya8bfz9r4cpq19hyzikvc81ia8zdxs6")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -4890,14 +5154,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.36.0") + (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7")))) + "0xp3rfhwn8k1bqzqnjzjqlaq8lqyad7kqjhb29vkbxgzjvafvxmk")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -4928,14 +5192,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am")))) + "01728hag1c5fh4n0v57k1p9ss5rqgckab4cnj5flp750myi1fbps")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -4973,13 +5237,13 @@ exploration of the results.") (define-public r-diffcyt (package (name "r-diffcyt") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "diffcyt" version)) (sha256 - (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb")))) + (base32 "10xhvksnnn4m1hly16fwmbr28xgym6a9zkqj8y476jph4wpnhc2s")))) (properties `((upstream-name . "diffcyt"))) (build-system r-build-system) (propagated-inputs @@ -5011,14 +5275,14 @@ adapted from transcriptomics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx")))) + "009nnl3zwcsg6mh7wl3j856dpi7awkyxdy660rqmiskn7m2ah4l1")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -5038,13 +5302,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-dittoseq (package (name "r-dittoseq") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dittoSeq" version)) (sha256 (base32 - "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4")))) + "0sxpwg2cjw70pzdxbdw68nic521w65ryn83mj0pb2m1ncpimin4b")))) (properties `((upstream-name . "dittoSeq"))) (build-system r-build-system) (propagated-inputs @@ -5082,14 +5346,14 @@ code{dittoColors()}.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws")))) + "0hx4als33lvdchz5s6cv2axvjyp0k8p3v0lm51jayhjcjpmihqzp")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -5122,13 +5386,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.38.4") + (version "3.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6")))) + "18vap3qp9blncr4sdl9q1szb4qhm46gldhxy3k3abw9fckcvggwg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -5147,14 +5411,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.20.2") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc")))) + "1v1in3imqbwak3v9w99l6hq8kihai5xvpgxvg7imna7jn1w8kmji")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -5192,14 +5456,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy")))) + "1m1x7xmbxwa15vzd45h16pnib944f20pwinx1pyhba5hcngkikfi")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-iranges @@ -5219,14 +5483,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.46.1") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl")))) + "08qvg1cmrln7w5z33r81kz1zjs8fcj3qbxm1crbsazvb6gdpqyyi")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) @@ -5247,14 +5511,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq")))) + "0swdqdyz956gx44crbx3qai0qx7n7yazg3yw7i93djcgahyz3kk7")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -5271,13 +5535,13 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93")))) + "0ii3ymysqkhyvj204zigpgjny0cglggqmvw311gvgkdi16dib1qs")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-gplots)) @@ -5290,13 +5554,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79")))) + "098ldnh45f48145jfsbdw5dqv5yiqkfci1fy6h6gjz7nh3dvnil5")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -5337,13 +5601,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.32.4") + (version "1.34.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v")))) + "1pw8ml6b33z7zh7h592xl23l8dy32nqq4lzq20p57n9f0krqj1iv")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -5364,13 +5628,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz")))) + "0y9yjyzch0cn2j4yrwfp0z8qw3yqvl8h1dlrl7ylzy9mwsqc6wg5")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -5397,13 +5661,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.48.4") + (version "1.50.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v")))) + "10w15j107hy9qb0lh6jmyw7rinfvy3ca34xsskxw3wf25mh6vhzz")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -5441,14 +5705,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz")))) + "0k64m9f5y88p90wd87hy0ixj5ly5yi413al9p2bn10b1fjx2c451")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -5475,13 +5739,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.48.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn")))) + "14m4pvvd9m8kpc7k905km9vib7giq0i9g11bxc1ygw30ifi96966")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -5502,14 +5766,14 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-gostats (package (name "r-gostats") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm")))) + "07chyfkq8nwxjgnlrrwza8jw996dq0ki4bzdfalj9yl1iac1pnys")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -5533,14 +5797,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g")))) + "0i8fliln3v9sw9x34pqafdx1z6jkys8b11fkz4ihmw8lc8lfd0x5")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -5562,14 +5826,14 @@ Enrichment Analysis} (GSEA).") (define-public r-hpar (package (name "r-hpar") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj")))) + "1dls59d2ysk8ngk5c6nx7xqgc2iygbdlzf88gccf2wm8zhy8m3f4")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -5582,14 +5846,14 @@ the Human Protein Atlas project.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.28.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f")))) + "1ri76wwv44hgxji2bmlqi6v8gbvhr72q0d6nlgpfgfwb9sgvz62h")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -5611,13 +5875,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.70.0") + (version "1.72.1") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2")))) + "0862mpbmznizcq5bgnp85dl9q0bip76jkga45gssdrv90wsi2192")))) (native-inputs (list gfortran)) (build-system r-build-system) @@ -5631,14 +5895,14 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg")))) + "1j2cz929q9hwkchnzcs3mnbmhg68mm06r9bgylnbll4j5ibqicrz")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -5656,14 +5920,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.36.3") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni")))) + "0623p6px259v000pp14c2rknjgivx9c90b626q9bln0qw6wy97zc")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -5680,13 +5944,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lfa (package (name "r-lfa") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l")))) + (base32 "1l3ip0bsvbz9nagzv47qjh5hf7qf8ffk4hlnkwagngiwyq84vyp1")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) @@ -5701,13 +5965,13 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.52.4") + (version "3.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h")))) + "1jy75nbkhl0kgv4gw88acx58r9f1kywrd36405x6g05xy05bprma")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -5720,13 +5984,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-made4 (package (name "r-made4") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "made4" version)) (sha256 (base32 - "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5")))) + "0ylcigzbahic99afqk1q29d4wczmsqmp2hasvihcykybb440a6f2")))) (properties `((upstream-name . "made4"))) (build-system r-build-system) (propagated-inputs @@ -5749,13 +6013,13 @@ datasets (coinertia analysis).") (define-public r-methylkit (package (name "r-methylkit") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35")))) + "0w6wv8x1jggbvymb07b2z47myf239mwpwbgz5p5yi60qb0k7p2q9")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -5823,14 +6087,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-muscat (package (name "r-muscat") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 - "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd")))) + "07b1z8rd0zibmv3rm4zggjf49lh37p2bp1h919zcw3n0fy2hax1k")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs @@ -5873,14 +6137,14 @@ platform that mimics both single and multi-sample scRNA-seq data.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.6.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg")))) + "071s1hfxln8zdr303g0ifmajd3kcfxxb6dds0pz67chc2gmgnd9q")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -5919,14 +6183,14 @@ in SNV base substitution data.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3")))) + "16apm4qn7sbv06pk2i8k5z7qgkv0yq0h8ri32vikdplqxxh7h0cz")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -5964,14 +6228,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq")))) + "1ljhxbyq5pa32sh44f06cwcdq79xh5nm51bpx1i8xig3bvwyg7p9")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments @@ -6021,14 +6285,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961")))) + "0h5w5ykbziaif6m61pa5x92f2rblfgldvj9vajfhkmxj1b2ks9za")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -6052,14 +6316,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds")) + "0p7mkvvaf25si95lpwpr65jm3dzxmgs9i0wilyb2mbxkdcz9vm71")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) @@ -6103,14 +6367,14 @@ previously been used in XCMS.") (define-public r-organism-dplyr (package (name "r-organism-dplyr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 - "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as")))) + "1hawn8pp63kal5ml0sm3h1j1wnkq02z64sliyaf6apv7vl60ja9g")))) (properties `((upstream-name . "Organism.dplyr"))) (build-system r-build-system) (propagated-inputs @@ -6142,14 +6406,14 @@ functionality of the @code{TxDb} packages (e.g., (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.38.1") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619")))) + "11l1xqwbqs129vxd6lxdaizpp6j08spyh6799rv5wqmlymap1ykw")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -6174,14 +6438,14 @@ the fact that each of these packages implements a select methods.") (define-public r-pcaexplorer (package (name "r-pcaexplorer") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 - "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl")))) + "0gs4az4h5mwnr3s8fq7im5p3mm4mhc0x5amjr2badqkw1fih3jp7")))) (properties `((upstream-name . "pcaExplorer"))) (build-system r-build-system) (propagated-inputs @@ -6229,14 +6493,14 @@ application encapsulates the whole analysis.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.88.0") + (version "1.90.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b")))) + "1cjmkfpbbfzkx6bi3r9jjx54iwkm4gl8hqa1776hxicq2x2c83s4")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -6298,14 +6562,14 @@ chromosome. Both tumor-normal paired and tumor-only analyses are supported.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05")))) + "1k5pg0zbhz9mjsl5i3j33p7qv2adax2lf7yqv6qz229fxxaxs5li")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -6318,14 +6582,14 @@ proteomics packages.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y")))) + "0dccxsynfnhjzjk22hr5kg068zbg33g6kyhlhlhqh78582181j9m")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -6340,13 +6604,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf")))) + "0wja7m3b3zr0m8nwcq5m5appsr09jdwkvvvxzh2r5mhksn0abs6p")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -6390,14 +6654,14 @@ library implementing most of the pipeline's features.") (define-public r-regioner (package (name "r-regioner") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f")))) + "01anwhz0axdl0g2zsaqz1qdxswxrryarbw6pmn5kmlpz4ipiq049")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -6421,14 +6685,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh")))) + "1nrgnb002qv0yzmrvg59i9b5wzxda0fdkrmdi6vr15g0g7j3yry0")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -6471,13 +6735,13 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff")))) + "1vxs227d1295fz8irr6fsv603cw96a801j8njhblvs0cry38d087")))) (build-system r-build-system) (propagated-inputs (list r-rhdf5filters r-rhdf5lib)) @@ -6498,14 +6762,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs")))) + "17x2a3122mm3z9qnalw25am2x08cfpm17nwhigabid3ha3d2mgz1")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs @@ -6524,13 +6788,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10")))) + "0wd4hsn19msz0fkwfq7gvi97vlfpsbzzw3rjj4b6z7s5a83zir2z")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -6589,13 +6853,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.56.1") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls")))) + "1qxr0ffmmkbfkbijz7pbks3kvms9k4a5rmma4j9p7ar477fxvlmk")))) (build-system r-build-system) (arguments `(#:phases @@ -6668,13 +6932,13 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-scannotatr (package (name "r-scannotatr") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scAnnotatR" version)) (sha256 - (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b")))) + (base32 "0rc035kzbzrxvlcpphzg0yg7q82jvlxpi9xjq8q59hvbpyg1sz93")))) (properties `((upstream-name . "scAnnotatR"))) (build-system r-build-system) (propagated-inputs @@ -6705,13 +6969,13 @@ cell types based on specific research needs.") (define-public r-scdblfinder (package (name "r-scdblfinder") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 - (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0")))) + (base32 "0gslh28rycx0p6a6fmzbsqy1hg2sn3pp5blxgw01qk9f0ank7szi")))) (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs @@ -6750,13 +7014,13 @@ comprehensive scDblFinder method.") (define-public r-scmap (package (name "r-scmap") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l")))) + (base32 "14vyjvfs2n4h0xsy25xg4zdmc8dqbg5vyl3qns6f0rh4bsshqdlm")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs @@ -6792,13 +7056,13 @@ different experiment.") (define-public r-scry (package (name "r-scry") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scry" version)) (sha256 (base32 - "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193")))) + "0vx6fi8hnxms6d3hm3qxkrdx1qpyd7vhwdk7ds98ads070miqr21")))) (properties `((upstream-name . "scry"))) (build-system r-build-system) (propagated-inputs @@ -6824,14 +7088,14 @@ single-cell RNA-seq.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr")))) + "1xlxi1iaqj7iabzbx15j6pk4551dyj6pa6a6qf5ffr3v7k2pmznp")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs @@ -6847,13 +7111,13 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn")))) + "17nvxy8kdc1k0kyf0qny6jp3gzr024q37mmh5x18jjr794hnf9s5")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -6870,14 +7134,14 @@ reference point and sorted by a user defined feature.") (define-public r-shortread (package (name "r-shortread") - (version "1.54.0") + (version "1.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq")))) + "1dvnjjc6cwn9wicki3ff3w3zx7i0szj0lnfw4n6lbmipg4ia5bkb")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -6913,14 +7177,14 @@ ungapped alignment formats.") (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6")))) + "130x5hy6jzglc6clwanh2kmhw567i802w620ffs3977kjfpjsjgy")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) @@ -6954,13 +7218,13 @@ and comparing the clusterings.") (define-public r-transcriptr (package (name "r-transcriptr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "transcriptR" version)) (sha256 - (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03")))) + (base32 "03v8xn777vyma82ma5dzk07i1g7406cvsybdz4bf6hj8bgx5ynw7")))) (properties `((upstream-name . "transcriptR"))) (build-system r-build-system) (propagated-inputs @@ -7004,14 +7268,14 @@ able to deal also with novel and case specific events.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj")))) + "130w4vpsmrkg458n3wbhvlchg171gjqybvs2w14bxa608f3fzw03")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) @@ -7031,13 +7295,13 @@ structures to hold pseudotime inference results.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2")))) + "00h9iid2z9r55l4hlaa1q0nkbcfq0f7k2afkw4ymjwhm1b8yqj33")))) (build-system r-build-system) (propagated-inputs (list r-igraph @@ -7063,13 +7327,13 @@ graph construction.") (define-public r-stager (package (name "r-stager") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "stageR" version)) (sha256 - (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y")))) + (base32 "1layvv9akzijw2br9jzw6cwxn2rimha4m48fm8wn465n1nqcns0m")))) (properties `((upstream-name . "stageR"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -7086,13 +7350,13 @@ Biology at (define-public r-stringdb (package (name "r-stringdb") - (version "2.8.4") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379")))) + (base32 "1md79vx4270wgh07g3m1mypdki1b9d4a558zxplcalwppqh0dsmp")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs @@ -7119,13 +7383,13 @@ that integrates the various evidences.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6")))) + (base32 "11z3acsbaifrxkghd7i8503ki9s1lc6c22880yna6qcfprlzb44g")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -7156,13 +7420,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39")))) + "0897v6x1ki4m7kajnd60yv5qj6xa1293sj572b4dhcnfjvsf9rcn")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -7190,14 +7454,14 @@ samples.") (define-public r-sva (package (name "r-sva") - (version "3.44.0") + (version "3.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4")))) + "0c1b7w4rvyy8i0jygj8g9xgf46rmgx8bpdlp2x4fdjr9xsrsl23g")))) (build-system r-build-system) (propagated-inputs (list r-edger @@ -7221,14 +7485,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im")))) + "0lwc4d4k6qmnwsh8fpp5rmiaxhzwl2f0dhzs23ska5xy04466r49")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -7264,13 +7528,13 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6")))) + "1ripdn7mcabh96bm4p807dbwj7jv05a54kss4snhz84svqq383m4")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -7297,13 +7561,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x")))) + "1w1m6r85a5nvcfxbkq5dmczaar8vf3vbrgrmxqkjqhlpcq58z5ng")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -7355,13 +7619,13 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1")))) + "08rm27jcx6amawqdh59291r0qzkr5cdhbhm0xbjbd5mvdpp1icl8")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs @@ -7393,14 +7657,14 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.64.0") + (version "3.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf")))) + "1k77rg5jf646m1pn59qhlsbb9fzhlpnrj4dzxagknawcbpnnjl0z")))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) @@ -7462,13 +7726,13 @@ inference.") (define-public r-xina (package (name "r-xina") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XINA" version)) (sha256 - (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g")))) + (base32 "1c97lsb5shixh4n4mi9kh4gz4qnia9vq736rnzxbs03n5bvlmwlq")))) (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs @@ -7498,13 +7762,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.") (define-public r-xmapbridge (package (name "r-xmapbridge") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 - (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10")))) + (base32 "0wxr3db2daj4xlr9df6iqwm00m71kln7rhqnq2ckdsricblanhs7")))) (properties `((upstream-name . "xmapbridge"))) (build-system r-build-system) (home-page "https://git.bioconductor.org/packages/xmapbridge") @@ -7525,13 +7789,13 @@ describing each of the graphs.") (define-public r-xvector (package (name "r-xvector") - (version "0.36.0") + (version "0.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk")))) + "0ygdyh3s4qsaay930a5lbnmgh6a4gqp5ck9ww466yk0jyk1hxfp9")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -7559,13 +7823,13 @@ describing each of the graphs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv")))) + "0c75mf0iw6bgwrn3zxpz1dz03aw7p6a1mfhssk6i1mp24avic9lb")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -7578,13 +7842,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.6.5") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6")))) + (base32 "0b14v6lyhfapmfj8j729k5cmgxc4df6wsk2rds0q4y6z4hiwgmxy")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs @@ -7610,14 +7874,14 @@ saving AnnData objects to disk.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc")))) + "094v4skdvsnc7bp3acj801ih022w9k96f2b857326vd19khz0ava")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -7635,14 +7899,14 @@ saving AnnData objects to disk.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk")))) + "1ik9xfx6g4gf54hm5f5prip1iz6694czpbhlgwd3p9qh8ddndgp8")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -7670,14 +7934,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy")))) + "0l6yb58frh4c080k6h8wyipc5kiz4qi7jimnr62jg8d737rrvnk2")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) @@ -7706,14 +7970,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw")))) + "1dsia1c9ir989aqrgl5j5v4bysm3pyw9225yrcajiwgl8fxymph4")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) @@ -7761,13 +8025,13 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby")))) + "1hk2y7r734wdd56f18l03kyq9p35kv653a5f7z2cjkq37gvcqrd1")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs @@ -7788,13 +8052,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg")))) + "02qzvs8fmh79g4cc5j2gxj1wazpmly7vjr527qlsgi3jmc3swxgz")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs @@ -7815,14 +8079,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.6.4") + (version "3.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr")))) + "1wgnrd1xpl49pdxxjzzl0v9535naapwp3ayqzvrx3z4m6iai2awj")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -7893,13 +8157,13 @@ processing to visualization and annotation.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg")))) + "1ghv2j88p3sppqph3wxpm8z84nw7bi4idkn11wf806d8h1krfjm7")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -7925,14 +8189,14 @@ large datasets, including support for on-disk data representation.") (define-public r-multtest (package (name "r-multtest") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82")))) + "0ciz0fl0pzm4hjqw8af32s540lwjbkwvwnzgbfwadax40hgjs0g7")))) (build-system r-build-system) (propagated-inputs (list r-survival r-biocgenerics r-biobase r-mass)) @@ -7960,13 +8224,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4")))) + "1hdbxjvgkxb9m341i9qbskb41g2z8qifkhgkpj2xb20s2dnxn3cc")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) @@ -8053,14 +8317,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.30.1") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y")))) + "13syh3mvqpaqgfndcrwdmn7815f4myxhzjga9a9q3lspci25rvy6")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -8107,13 +8371,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f")))) + "05a83gh5bvgadi2msgql5nmcgr8zp398rhdbmiqna608hqbymyq9")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -8134,12 +8398,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i")))) + (base32 "1bad4cjxv22h6vxxn86mxp7xvxhhzj81pikxq3h3hc2a858qfkgs")))) (build-system r-build-system) (propagated-inputs (list r-limma)) @@ -8153,12 +8417,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr")))) + (base32 "01n1z525h4h6yr3jfalgjg2g6lhd77sc3n33q0485x7l6xqv1dvp")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -8172,12 +8436,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65")))) + (base32 "0860w2vf662qqii09pjdx85yl346jcldxiikhbwv0vg86blwb2g2")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -8191,12 +8455,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm")))) + (base32 "1qv3vmc6i7r35pqhi45hmvg8h7v3bl82lv7yifs59k250zsdls59")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -8223,14 +8487,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.30.0") + (version "2.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j")))) + "0lq2wfm3ibrpha9mqhhp6dgsx4jm2kwxvvrj0b62dzqspvg743wh")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -8247,14 +8511,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0")))) + "1wnc7zrnnxk3nlk2l9y4il75dzirndp4vs5ivxn5rzqr6p7h4bhw")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -8281,14 +8545,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp")))) + "0wmmpcabi1ngwmvfhxkp44kj1wvzyrcckkrzpjlzcq016lr67iwn")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -8322,14 +8586,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26")))) + "0la8kmxxh5jnqsrmmvyhi313bjdbqkiq16hcxar6mgyjhxlsm610")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -8350,14 +8614,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5")))) + "14fb780f2g24ay28dy9xkmfziavbkj75v4vc2cmqbxfdsfp4yn0w")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -8384,14 +8648,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx")))) + "0l14hz5pr0wlin46y8ycpvk5hp2ld9ajx11y85rw5hlwv50byfbb")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -8425,14 +8689,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb")))) + "098a65fk9la639sqihhsghhgb3hyzv35j6akph908zwq5grsv0c5")))) (build-system r-build-system) (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") @@ -8445,14 +8709,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48")))) + "0x89lv84l3qcahca54njcza326553zij2xyagy18mwlprdrq4iy8")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -8471,14 +8735,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz")))) + "1fskabpd3xlrbhqvzam9ibpxmbdys7y1b265np8hz4k704ww1g22")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs @@ -8504,14 +8768,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r")))) + "1wirblji4ckiwrvnh14cfwc9cjypazbaqr00ka5ndyz39cc31shn")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -8527,14 +8791,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77")))) + "0hnhfdrlg4907dc4s17cy4kgmq5nr616f1wi7jn72acxwqfl4bk8")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) @@ -8551,14 +8815,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax")))) + "126cbanan2fr916spacw6lm8hzkys56k7z3gq0r351zd7q13gky3")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -8597,14 +8861,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6")))) + "18sivwzl8gk52dnhwls0i4imw78rkjlwbfrcaas1i53q0bmw15i5")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -8624,14 +8888,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x")))) + "1qb4k7pm8w86d2p9q2r4n63iyi34wdib5x9rsjx4vhcxrnzyyygm")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -8649,14 +8913,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x")))) + "09f00rf5gwwlxxaycsciq4l53gjg5kjayx8xzhns2yf1fv297j9p")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -8677,14 +8941,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.4.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz")))) + "0lxr6z9zdrgvm06inc1d8gl2agqmbjvgs8f5ryn5x68hqlnchnl1")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs @@ -8703,14 +8967,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1")))) + "1xl8497ya79hlp3v3fihnz9grwni29v6860i273lrpcljv8868l9")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs @@ -8732,22 +8996,56 @@ heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.") (license license:artistic2.0))) +(define-public r-treesummarizedexperiment + (package + (name "r-treesummarizedexperiment") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "TreeSummarizedExperiment" version)) + (sha256 + (base32 + "136zgpn1l059i64gj6iappr6nz42z4wbxlg3zpc5npwkqrz3val2")))) + (properties `((upstream-name . "TreeSummarizedExperiment"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocparallel + r-biostrings + r-dplyr + r-iranges + r-rlang + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-treeio)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/TreeSummarizedExperiment") + (synopsis "S4 class for data with tree structures") + (description + "@code{TreeSummarizedExperiment} extends @code{SingleCellExperiment} to +include hierarchical information on the rows or columns of the rectangular +data.") + (license license:gpl2+))) + (define-public r-ggtree (package (name "r-ggtree") - (version "3.4.4") + (version "3.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5")))) + "177nq6arhxp0x6zsf2c6cn3xxwfk65dihbpni6mb9ifgnmfqdjmx")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs (list r-ape r-aplot + r-cli r-dplyr r-ggfun r-ggplot2 @@ -8772,14 +9070,14 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b")))) + "06ala1qz9bfq7nnj92m0c5r85kk7h4zrljjh0hgrap5sjlsm09bb")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs @@ -8801,14 +9099,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x")))) + "041izymcifvi0pa97fh5000bwlyl0mdk9003i5bbvlld6mbbv2kk")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -8836,14 +9134,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.10.0") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy")))) + "0rgd723azjrdxv441k96vircqb18w31q0ljhksbdrvcp9qb85r6i")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -8880,14 +9178,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k")))) + "1b7kjgj2r6lgkdnrq91wcwvwb5an0gfdsbyp7j0pvn2byfm4lply")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs @@ -8902,14 +9200,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz")))) + "0k4vbdwpp7z06fzjgqnmrx2yllayc0z2baj26bh4vji5vb48k9ik")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -8942,13 +9240,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd")))) + "1a664bllaq9pbb5cpd01j919qirylvnm8qd49lwlz89jvqjdri19")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors r-iranges r-genomicranges r-biocgenerics)) @@ -8962,14 +9260,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc")))) + "0z2hl68f5f6d2w6gbhax4531g3zbgiihj99h32sa44hp29al38ld")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -9060,14 +9358,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y")))) + "1gh1cyb76gv2h0knh780648gsbgpn76adfj6x3pjzily5m5bmin0")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -9082,13 +9380,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk")))) + "1dcxq3651903wwzr7bww8c4wd8h5h7rklnqfgklqpss0psx59d2w")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -9120,14 +9418,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g")))) + "0ryl48zxscb35s1gizyspxg48dlqg1j51h9iw2flq16y7y63ppzi")))) (build-system r-build-system) (arguments (list @@ -9159,14 +9457,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf")))) + "04vbf42bzqydf5mi4mqmcyh0xdx4phs4cjhsm6fimhmjhxm8jyry")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -9188,14 +9486,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9")))) + "0mh7arn5rv26picz05ywil5ynras91xv6diwh47s9ip75vp9s3cy")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -9225,14 +9523,14 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd")))) + "0zqifr1zhsfhrkjlp0ajqiqc9f96yz8zr13yhl19lvw30pwg9rj9")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) @@ -9254,14 +9552,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.12.3") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc")))) + "1cdpq8zfn718qmsqjp79siddh3kzag4a90p276v261xbjvrxavjv")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs @@ -9297,14 +9595,14 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi")))) + "133ijkw5sd0gl38dfr7qfqvvp2df7lg6j8vkvy54zlpamkg6l2x1")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs @@ -9332,14 +9630,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.24.1") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn")))) + "1d3xgh9xgqa28bgyd06zkjmg75lq7hdah3d140l1bqq2ii1bv62g")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -9517,14 +9815,14 @@ user-defined and/or data-driven sets of hypotheses.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27")))) + "1j0yafl5r1vsn99zkhvaz2mrwv37l4p8ldgiq09d9hxpjq9ls7i2")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -9543,14 +9841,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0")))) + "0kmnmlzww2xfd04lp9nsh0wkigab9ipgqlsn2jrd77fizpd0kvwg")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -9581,14 +9879,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851")))) + "0pg09r28xqjlvb6nbswglnmwi05q63fag6rp3sw41g6z8gm5wap7")))) (build-system r-build-system) (propagated-inputs (list r-aroma-light @@ -9625,14 +9923,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.64.2") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x")))) + "0ck2aml1kxdahwcszi3j7hcikwi8fdnzphlrsn3h2q4dkk5x00kn")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs @@ -9660,14 +9958,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.38.0") + (version "0.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62")))) + "1cw526mbhh0czkwk99qnr6hfwi4k4xi2bm5p14kw9sr00if59x12")))) (build-system r-build-system) (propagated-inputs (list r-base64)) @@ -9681,14 +9979,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l")))) + "0gis34s56y4xa61a9gywjwgd6525ywasa6r4xxhj3rshh1dz5jkv")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest r-scrime)) @@ -9705,14 +10003,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw")))) + "0jwbhd2fhm1w5slwhz8krnw835a8qb4akm3n3pv867bvi0xnp3g2")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -9736,16 +10034,64 @@ to identify differentially methylated regions in epigenetic epidemiology studies.") (license license:artistic2.0))) +(define-public r-mia + (package + (name "r-mia") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "mia" version)) + (sha256 + (base32 + "0yz88ggv6d5rccdwzixwg9y1bc4xysazlmv1ph88wxs8r6fcmync")))) + (properties `((upstream-name . "mia"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocparallel + r-biostrings + r-decipher + r-decontam + r-delayedarray + r-delayedmatrixstats + r-dirichletmultinomial + r-dplyr + r-iranges + r-mass + r-multiassayexperiment + r-rlang + r-s4vectors + r-scater + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-tibble + r-tidyr + r-treesummarizedexperiment + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/microbiome/mia") + (synopsis "Microbiome analysis") + (description + "The mia package implements tools for microbiome analysis based on the +@code{SummarizedExperiment}, @code{SingleCellExperiment} and +@code{TreeSummarizedExperiment} infrastructure. Data wrangling and analysis +in the context of taxonomic data is the main scope. Additional functions for +common task are implemented such as community indices calculation and +summarization.") + (license license:artistic2.0))) + (define-public r-microbiome (package (name "r-microbiome") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "microbiome" version)) (sha256 (base32 - "1z9arkjp5xszlg07mzb4p163i74jfbd9p4gbwv5syivnpl040k12")))) + "1j3lrrz6yxfzsr037c0bbdhrs0ll7jg0mpcvk3iqdryi5rysnx0x")))) (properties `((upstream-name . "microbiome"))) (build-system r-build-system) (propagated-inputs @@ -9776,13 +10122,13 @@ standardization of the analyses and the development of best practices.") (define-public r-milor (package (name "r-milor") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "miloR" version)) (sha256 (base32 - "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs")))) + "07p9rs1jmgxqaahjbrnvvs94c142n2qfw8ip3qqkr6mhzwr19ly3")))) (properties `((upstream-name . "miloR"))) (build-system r-build-system) (propagated-inputs @@ -9824,14 +10170,14 @@ model.") (define-public r-minfi (package (name "r-minfi") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6")))) + "15989zilgy2j4k4nw046qg8wli7ynjh2b1yzfv7cwgn87mp618lc")))) (build-system r-build-system) (propagated-inputs (list r-beanplot @@ -9875,14 +10221,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww")))) + "07kfyv3kkayzh0akxfl3p9gckw8qiplkxbyxw8npc7cb03ihgmc4")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -9922,14 +10268,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d")))) + "1091458is69dxnjrcd11czqy55c68sdnkrmpvlm6hw2cbghs2bjq")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -9961,14 +10307,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb")))) + "0ndhvdd9gkqyayxqgj5320sgj15di7ji945lpdi3rj5lwldh7na0")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -10022,14 +10368,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi")))) + "1xkxqavhcw22lhij87cpd5ps1ldkzzi0pp93d38pxbbhj15gc3d3")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -10118,13 +10464,13 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0")))) + "0wkbjhwqk094nd5h6sl2nw5jp5vmkh9why635l8qkqmxa2jm3gh0")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -10187,14 +10533,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix")))) + "181igcmlyx3ddmhml9wqcgw6ffdrqpmg4imd6ipf68c90agdgaz0")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -10227,14 +10573,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.4.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1")))) + "0zbjw9f616dz1fpp6q6whbmlrf2gypq8pp9i66c376cs2aifp1si")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -10252,14 +10598,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd")))) + "14wc7qgk1psknld05246cn0nqxpbjprax7j75h5yyd0w7hjyly2s")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -10279,14 +10625,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c")))) + "1a9xgcp48zjql6an3kiv8li4saw10k1dl7qzyyw84xvx856ilv97")))) (build-system r-build-system) (propagated-inputs (list r-multtest r-qvalue)) @@ -10309,14 +10655,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif")))) + "0vb6v61ak8z3hx7d65lr1hrxk89n36j0zi3x0pp828khdyh3zvag")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -10331,13 +10677,13 @@ phenotype of interest.") (define-public r-fcscan (package (name "r-fcscan") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp")))) + (base32 "0z83ncjxw9x8nvc6pncrvpf6lmamvgrv56j96s1f0x9jydk18chy")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs @@ -10364,22 +10710,22 @@ presence of additional sites within the allowed window size.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg")))) + "1frl5mchbrgqyxxdlw76qqq5i8vv2fdmy8xl8h8c8cvvmlz393qk")))) (build-system r-build-system) (propagated-inputs (list r-bh r-biocparallel + r-cowplot r-data-table r-fastmatch r-ggplot2 - r-gridextra r-matrix r-rcpp)) (native-inputs @@ -10396,23 +10742,23 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.22.1") + (version "3.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i")))) + "0scp6sgb1iwwfh7gdak4dxf1hb870745km9nc9hga8pnsnqi5v3g")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biocparallel - r-do-db r-fgsea r-ggplot2 r-gosemsim + r-hdo-db r-qvalue r-reshape2)) (native-inputs @@ -10431,20 +10777,21 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.16.2") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss")))) + "1x84wlkqisq1x2zniy4mp02zlsp4v85kxbflalmq0pixlkagq0vr")))) (build-system r-build-system) (propagated-inputs (list r-aplot r-dose r-ggplot2 r-ggraph + r-ggnewscale r-ggtree r-gosemsim r-igraph @@ -10453,6 +10800,7 @@ data.") r-purrr r-rcolorbrewer r-reshape2 + r-rlang r-scatterpie r-shadowtext r-yulab-utils)) @@ -10469,14 +10817,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.4.4") + (version "4.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5")))) + "0fm2cz2464xh075p4yl6bha9m6didc41ng4a3flkw1f1cvvpi4g0")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -10488,6 +10836,7 @@ All the visualization methods are developed based on ggplot2 graphics.") r-enrichplot r-go-db r-gosemsim + r-gson r-magrittr r-plyr r-qvalue @@ -10506,13 +10855,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f")))) + "04kdiwz8qzr7cr1an1c7a684wqv9pkca0iaym5f069pdjhqvvq0a")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -10552,14 +10901,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5")))) + "0xnaghm65ydk01gzx5g38jyq7vfdw206c2w59k0qg8lhy9fqky9x")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -10582,6 +10931,7 @@ expression data sets.") r-rpart r-sfsmisc r-shiny + r-summarizedexperiment r-threejs)) (home-page "https://bioconductor.org/packages/MLInterfaces/") (synopsis "Interfaces to R machine learning procedures") @@ -10594,14 +10944,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq")))) + "0qxihlhx7ijspvgzdp8zxzrc44y9pwkygvsllh4v47p85ham49fg")))) (build-system r-build-system) (arguments `(#:phases @@ -10626,14 +10976,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390")))) + "0plgfzsvg220v6k6p0g7izsfw2lj78331lqyvz0p9vd91ynwp41k")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -10650,14 +11000,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw")))) + "0lirj0qzzrm996g8yh30x61cg1qkh436qd8xzgv3y3y3n5jj5d3w")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -10680,14 +11030,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9")))) + "00xs1vayl8v6in79iv7lwbn52yyyq4lv6k3k727g7il8x17mi8i0")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -10704,14 +11054,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0")))) + "09q8ng5kp47bqpj7m2y2112fkjxcnhzxk9v80hqksm8h1df46riv")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -10728,14 +11078,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn")))) + "14diri7gswd6h5p3bdhh20fy7i54d270mq985qcdvdyhx4kpw6g6")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -10759,14 +11109,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r")))) + "1sis4hwrxyn2x96yysz82gffl2kkj68ry945y15zwikwk80s31hb")))) (build-system r-build-system) (propagated-inputs (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) @@ -10780,14 +11130,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b")))) + "1z5an4vsm55a0qr46qmp8562vc3xdam5f3840r8hcdnn5dvzw414")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -10828,14 +11178,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8")))) + "1v5kvvbc5fwvs84d2aq6gq6f6z0l68n7626gcnc8mh3sc27lxz53")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-ellipse r-ggplot2)) @@ -10853,14 +11203,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.44.1") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q")))) + "070i3jdq8b5w7k42xw2fc3vcmv312i19fa1am4fbk3g3ssnm61p3")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -10907,12 +11257,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi")))) + (base32 "122ifxmbi0v3192cd9chq265i3dyw3hzwsndq3w97f4d68vll7gl")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs @@ -10934,12 +11284,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg")))) + (base32 "0lq79as9gb48hf3v2xj895s0nsjr37fqah4p405kdybzry56gvrq")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -10984,14 +11334,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z")))) + "18gfx5dq83s2ny39a7cgg4r3b05gg9l0kfg83brwrm1cby08jdhm")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs @@ -11016,14 +11366,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.8.2") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j")))) + "1sz0gmwc5iam83pxnc702pd5h6nsa46kb0wsqs8ysb1ximbkfh5h")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -11054,14 +11404,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp")))) + "12ggi2dzf8qyzjrxprvk099f61yrabg2d84iqnjxzrn77v6z19b2")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -11101,14 +11451,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk")))) + "0d0xis4nns5icsr16w4ik2d95n3p2h93c47jvlp22crv7f4rlaa5")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -11206,14 +11556,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51")))) + "1z5vgblhi1kj2n9d4kbqgvwnm48372q0szgjshch8g39dypijvhd")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -11231,14 +11581,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z")))) + "0zn8pp4pl5wr957mf6agjpn61f9qpnjx0nbxb5wnbr40672x0263")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -11274,14 +11624,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.18.1") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr")))) + "0bq729kavqkam2s4dmfzixgznsys61j0lvj5pk3b70gxv44gmpsh")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -11314,14 +11664,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.38.0") + (version "4.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si")))) + "1k6gbivwlai451whq2vr3c0shzs9p4g188jn5waw7973gdzdi00q")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -11353,14 +11703,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8")))) + "0bh06mncjrkihz2j29hasbipfl50x7393wshdcnlxrs5rrq73r0n")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -11386,14 +11736,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff")))) + "09f20qam59iwr48g854b7ydbsbqy90mdy83i2i0am4gybv5isgqg")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-genomicranges r-getoptlong r-iranges)) @@ -11412,14 +11762,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6")))) + "0xyh4pwwbpa1bmamqdhp84qhjdc2qsxc43xgknjrrja24d06ji2j")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -11451,14 +11801,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid")))) + "17yxzqvyaa423k0rskahlgqxcsi70flgsxniry3f4m8yvmghxxkz")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -11500,14 +11850,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.68.0") + (version "2.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d")))) + "0a3wjwjgjkpmfvgg0b4jc1rkwzsqrjbaziydjfnkll4rw9xcavy1")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -11582,14 +11932,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3")))) + "0f274wh0w6nyipac05y6s2m2p60vkls5j4fwa5bc419j68h4znnz")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -11615,14 +11965,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg")))) + "0sqbll7ja0qr8r28dqmydmkvg4ijfm7z8hbrsrz3xxdan70bmd2r")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -11652,14 +12002,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc")))) + "1bf3ii3zaxkzw5y1wc5c474bq4cgavb67df54czmd3zi1lbhzphd")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -11720,14 +12070,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39")))) + "0l86gwq073nbx973v99b0lr9cz0pb72c4asmgj5w16jykicrnxn9")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -11744,14 +12094,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.18.0") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm")))) + "1gj0nd90c6ykwn1n7xndzrgfv5dzy0y2lh3bf8120nacccgxl2qx")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -11785,13 +12135,13 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wppi (package (name "r-wppi") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wppi" version)) (sha256 (base32 - "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f")))) + "0kc3nkim8fhajhai5bwzwirsg74zbdib3dd7cfr75ddwd8myc913")))) (properties `((upstream-name . "wppi"))) (build-system r-build-system) ;; This is necessary because omnipathr attempts to write a configuration @@ -11826,14 +12176,14 @@ scores and a path search algorithm.") (define-public r-wrench (package (name "r-wrench") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca")))) + "0n7mvj9jdp8w5w64i49kkqzbrvpv2vzx6y6fb7g2sqp24wqrn39x")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs @@ -11850,14 +12200,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i")))) + "1yp9siy4249wkwd0yy5lkwp79xir53f8mihiv4dkir8fscgampl3")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -11884,14 +12234,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d")))) + "1p93dzf7w9z1ria0f8n32aymam9abxyg50ngnh7s6a8n24mvvjy5")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -11905,14 +12255,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah")))) + "1mgag0gjavpld4xxlpfafq6fhzjafxgqyf677xrm6ff26z6z1ja2")))) (build-system r-build-system) (inputs (list netpbm perl)) @@ -11937,14 +12287,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i")))) + "1356ms5y6fg7ndn8hvs6zsyr0jg6ah7a56qxd2x4xgyjj3xcakbv")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -11970,14 +12320,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji")))) + "1wsmv4fld4s7l0qh84ghizq8k388ybdz9hzzis2gn1nn57q1c7wi")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -11995,14 +12345,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg")))) + "05cczwkhv7kfnhlr0qznk6vdjncaj907895923f8mwx4j4cy5gcz")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs @@ -12022,14 +12372,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b")))) + "0f5sfi9r9dr6w3xmspsbzby8dpza8x7djif7p2h6l99kwkf68jsb")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -12054,14 +12404,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1")))) + "14mffjsy7cwpa2xf8zdqwdk6mnfj3lf06y8s59ndh531b45nw5wc")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -12077,14 +12427,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw")))) + "0skrvmkm6ch8gbpdi4wr59zk5vxzxs7cyqvz3jhki9d8w492wylg")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -12110,14 +12460,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm")))) + "01bl1gmc1v1b4lh88sdazjvm8pl7383dgzxnhmzpxwz7lkcxi1h2")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -12140,14 +12490,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q")))) + "1kbpqhidj2bwhp9gxqx2qjaby6fc2dfrnnyjkciswgxckis6h2pc")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (arguments @@ -12176,14 +12526,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp")))) + "03ddz0mpgqqb52r7wa46bcr1ybf40126pg0n0n0pv6fnbq0ifwyc")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -12219,14 +12569,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7")))) + "19dc9fadgl55icqc5xv834kigicxxr6cny83247jjbgf5zp16piv")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -12257,14 +12607,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf")))) + "1pp94368aj5wx0zcnbbm6zrxrfhixmbcdzpj2lka3blvq5j7sncj")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs @@ -12299,14 +12649,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k")))) + "02k64pjd1dlz5sksdbkbii9z4ihf1833ws7wwj81w3757zzabx0x")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -12342,14 +12692,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm")))) + "0nr40nm87qzbni3w0cik887csc899jh7j8z82i94v15fc30vfilh")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs @@ -12395,14 +12745,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf")))) + "1qja5xd42wh8qbcil4hhnmh9zlby2gfglax2qbf5bzg3h6yzpy4g")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -12432,19 +12782,21 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.28.2") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c")))) + "0vjwci0z83b56q1wi1k00926f0vh3220a44m0zzfxg2cm5j3fwxb")))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-ggplot2 r-multiassayexperiment r-multidataset + r-plotly r-summarizedexperiment)) (native-inputs (list r-knitr)) ; for vignettes @@ -12472,14 +12824,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m")))) + "11ncmxy4wqdg30w8a6dgcsywyzda49f9al435fz3pfj5rmlbbrlj")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -12507,14 +12859,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0")))) + "08f3xikgb0z1j7n8i04yn1dlfj8rxc76nmf5b7i5ljcp0jqiv07n")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -12548,14 +12900,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.10.5") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2")))) + "0iha7xln7l3mrmka8rcmmlp74f5km9rc88k9nv6bxw0krr03089n")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -12600,14 +12952,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p")))) + "15cz3bbl21vzf5xn5xb791sy2yvzir7h4fdqm0a5anhbh8jg0iaq")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -12666,14 +13018,14 @@ of the analyses while minimizing technical noise.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg")))) + "1y06x7z3p938kfvjx6zqab9hh1xzlrlhdxczyprx7lsd34ylz46n")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs @@ -12695,24 +13047,24 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr")))) + "0j0ryyz3vcih964is5gdm2jp39ssdli9q6r03q6rj9nwzplq5asj")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs (list r-bh r-biobase r-biocgenerics + r-cpp11 r-cytolib r-matrixstats r-rcpp - r-rcpparmadillo r-rprotobuflib r-s4vectors)) (native-inputs @@ -12727,14 +13079,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y")))) + "1hmr2i5svg1wvdgqhnp25k1c21p2pdd0ia9py5kp9sm5qvc9vngw")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -12750,14 +13102,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.42.1") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "0759xvkp22dnbhq5wpgvpk8p61w0d50r5jrbh9n7sj8sga4lvvv7")))) + "0ak1rrd0r899nz4zdg9v3pkvlp94sbcc3q6xl249krgbx0a3sizm")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs @@ -12781,14 +13133,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "1cw60x78vqzjmgb5xd3sxyz6zwdaffp3byk34z8d4b3wkh530325")))) + "0phhm54wcqihj62a0jk46whmf6wwg7wj3306wvnszy7yik4z857w")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -12818,14 +13170,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.60.2") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "08rwzc26jns0wwjsqqmf60bpxsckr5x8skdn9iwl8grp81npcc95")))) + "0yz2b3l0bv5i7vrr893wrs3jl215i17m2hr92iisdc6mh9i0lpz8")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs @@ -12849,14 +13201,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.34.0") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk")))) + "1l1lfgm6x06gyzda36m6gvqmb91zbrz8m83b1fnfzpxkhqha20yq")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -12883,14 +13235,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp")))) + "07d5skr8cp0hyjbs7whw4h8scrf2w4hyn0wzj3khqdss53zmmr2m")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -12912,14 +13264,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.8.0") + (version "4.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss")))) + "07w2pnnzmivfc621c8pvndqrn1k245cwjrb0nnk2i85i3si4j9c3")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -12966,14 +13318,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.8.2") + (version "4.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc")))) + "10xq0rfnshvam2yh34566ywmsby44aa1fg8wqwmllm202rhcgl2p")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs @@ -13004,14 +13356,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.8.4") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0")))) + "1pkpm98fs17zqdvyymd58sl4cib7gdi7drvdkagilrafjcrpq31m")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs @@ -13048,14 +13400,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.8.1") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw")))) + "105vdmwwglknwk7x7cb6b2jf6bngbxsly0ymjf8175p2lfv98jsa")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs @@ -13100,14 +13452,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645")))) + "1s7xilhhc55igq0zmvpfzhnh5df8bzmm3daknz75xhzhhg5b7z1c")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs @@ -13143,14 +13495,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.20.0") + (version "6.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7")))) + "0w6shihvnvkjycba1hy8drd8wcxxcl2rimkrb4vdl8aygdifrarx")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -13189,14 +13541,14 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp")))) + "1j4gxgw1s3a0nm888k02qi1smxqsplc42827ks666md025h9bxcj")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -13235,14 +13587,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.16.0") + (version "1.17.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im")))) + "1anwin5476q2n0zgywrmp3nj6sgy07i6pw1lczydvn4h1a8n1rvk")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -13277,14 +13629,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm")))) + "1b24iiy6d5kzpixgpdkg4s1cb50jdrmgn9sjgvwr1qinckwz6zdn")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs @@ -13323,14 +13675,14 @@ expression space.") (define-public r-cicero (package (name "r-cicero") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5")))) + "0grzp9k06dz04bw07nf9qka19mara1kplyd24y8mg8208wk949f6")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -13390,14 +13742,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j")))) + "07l8vaqbw36hvs8pyn1gk6dglnmkcmbafvd4rdrhg2wqwnlpsf40")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) @@ -13525,14 +13877,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l")))) + "096crx7n75x60s9sx3l7nld3yvrsqs0clvjsdarxc6bbn2qxk81i")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs @@ -13549,14 +13901,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2")))) + "00pw6xmxjzprbx8wskq6gbyqkfak764vic5yxrzs6wpram352vmv")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs @@ -13571,14 +13923,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") (define-public r-watermelon (package (name "r-watermelon") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv")))) + "0m8mra0jb6sgm13dagqn1pj81dha4dyj65xc6r2sh0yc3pyjb20h")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -13609,14 +13961,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0")) + "1ck3qq4vhjp6vvicpldr7d2rkpspp5albjkbqjbshnbq11fhrk06")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -13665,14 +14017,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k")))) + "094d43yv8af8sijp43ndcaincnsf3ng32vgwh6bfazlq5d601r6y")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -13696,14 +14048,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg")))) + "0mc6lv7vkch138n46gk1q1hfhv37mfxjij39q36wa0jy7s8cagfa")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs @@ -13720,14 +14072,14 @@ genome sequence.") (define-public r-reqon (package (name "r-reqon") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r")))) + "1r4dzwnqv6a4zy5q9l3axqq23sbk9pjfb2y3fmwxjvdwq6c1qnp0")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs @@ -13743,14 +14095,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6")))) + "1z7y3wnrqr2xqrvs2xwmv419aqlizq0az17dpxmj1hg9knyls1bx")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -13831,14 +14183,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8")))) + "110db9gcla796mbll3pin0hv2qp8r6khx0zzqfgzkp4mcyjxi62y")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -13937,14 +14289,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv")))) + "1mn91r0yrhz08m3vs2h3i35rcbxyc7sdfknmk6vcw1z75znjsnpl")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -13985,14 +14337,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc")))) + "1kclvh8f2sf534cjw07ry9nx74n6p7r0vmc3mk2nr37yvpf26b3q")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs @@ -14015,14 +14367,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh")))) + "0zkqr1s8gagwsh33kzp0n2n7ff5jhfn6a60gvab5spk7vr76j442")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) @@ -14039,14 +14391,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr")))) + "1vfg703wxbgxw2cwqqz3kfyqj4za5n3skxxzi8c31azamg4hxs18")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -14087,13 +14439,13 @@ motifs, and others.") (define-public r-ace (package (name "r-ace") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACE" version)) (sha256 (base32 - "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m")))) + "12gmdkzm9wnrq793xqvw3mzwmmsm1vkh36llapr7m7q4dmcfgxr0")))) (properties `((upstream-name . "ACE"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) @@ -14116,13 +14468,13 @@ of @dfn{tumor cells} (cells with divergent segments).") (define-public r-acgh (package (name "r-acgh") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aCGH" version)) (sha256 (base32 - "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d")))) + "05q303bf8acvhbdzqxqk2gf12vg0fdqknlxryn2cs8nijx40zp46")))) (properties `((upstream-name . "aCGH"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-cluster r-multtest r-survival)) @@ -14140,13 +14492,13 @@ printing and plotting @code{aCGH} objects.") (define-public r-acme (package (name "r-acme") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACME" version)) (sha256 (base32 - "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25")))) + "0prcaxqmzm4hhpv228xh0glhm166gs17sa9h4lqrm03pwrjrdqdw")))) (properties `((upstream-name . "ACME"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics)) @@ -14167,13 +14519,13 @@ on whole-genome tiling array experiments quite easily with enough memory.") (define-public r-acde (package (name "r-acde") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "acde" version)) (sha256 (base32 - "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2")))) + "1d47hbna68qm517afk1wb0w9gb8j52p7nqh5axcc6h76zppsc1sp")))) (properties `((upstream-name . "acde"))) (build-system r-build-system) (propagated-inputs (list r-boot)) @@ -14260,14 +14612,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj")))) + "0r4cxrjvf3qr5514lsw1s53h4by3djb9ipkz7bi979w343dn9xfx")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs @@ -14282,14 +14634,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk")))) + "1ylg9bnq8iwax0ap4c19v4mkbq673s8dfv49d94znsryg3fp93dl")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (arguments @@ -14318,14 +14670,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5")))) + "0ryd9lg8pywqlxj802y9jad5nxy40ivnzdq2ldldypwyalgk9ahm")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") @@ -14344,14 +14696,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2")))) + "1z7x30705a4ww9vdam2668pk064na5ispigqnaqy8zqvlfvp3c8d")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs @@ -14366,14 +14718,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq")))) + "0awzq3i7ga6jsh7xgmrpzz8klx69p8cxj73p6h7ya43bgcr0iff0")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs @@ -14395,14 +14747,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v")))) + "1syg49qz6vwzyw2zrxwrfb7kzgk0lim1q674f7mfvjah1fnv8bgc")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs @@ -14421,14 +14773,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp")))) + "1jvnvzjivjwqxh19c3g37kpyl6i6mxw99ma3ypjjgxzx898nsg45")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs @@ -14443,14 +14795,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6")))) + "1fl4ia2jskvmbwk0y1wd0x4dgqph0av7bx2zffrvd1a5ppcjmsra")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs (list graphviz)) @@ -14465,14 +14817,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw")))) + "07b80qpkbas3x2yhndcm6vdkba0cpricyvnjf18dxklj5j612wfy")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs @@ -14529,14 +14881,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj")))) + "1smf3w5a60jc0bpip5131ad9ykmnrcd33qi3pc3m50g6kn023wz2")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs @@ -14572,14 +14924,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.48.0") + (version "3.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma")))) + "0rk4ydanqxjh5yj0m9qlj06a12j7rkx9gxv6x7zpiyvnscahw63i")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -14615,13 +14967,13 @@ structures.") (define-public r-fmcsr (package (name "r-fmcsr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fmcsR" version)) (sha256 - (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30")))) + (base32 "00xi01wz61ip8pnbrpnpp8hncb8gyiw69qkbg0cl425rv6qjb3mr")))) (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs @@ -14644,14 +14996,14 @@ searching and clustering.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz")))) + "0r56r4qxibgblriyfbd46i8jhc2bfr9ndr8i30920v9kc3n83cav")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -14679,14 +15031,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh")))) + "02gdc26bs0yx7hb53b8ncipsaw6ynfvjcx64qxkxxq1c4awjkhzy")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs @@ -14708,18 +15060,18 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g")))) + "0gkjab12ncag1vslc5bwlr0m5ac3ifq9ka5nfq7ckrpns98s7k0w")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs - (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang)) + (list r-annotationdbi r-graph r-httr r-purrr r-rappdirs r-rlang)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description @@ -14731,14 +15083,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5")))) + "06994hk9nrzlgz8sby61656rdbf1r954v71djl1i7141dgw5rif2")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -14748,6 +15100,7 @@ symbols).") r-ggplot2 r-ggraph r-graphite + r-gson r-igraph r-reactome-db)) (native-inputs @@ -14763,14 +15116,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk")))) + "0kg22appd9sd6knm129hchkamzilwr3h8wi4ibrvllbfmx31v9q8")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs @@ -14782,6 +15135,28 @@ enrichment analysis and several functions for visualization.") microarray data.") (license license:gpl2+))) +(define-public r-biocbaseutils + (package + (name "r-biocbaseutils") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocBaseUtils" version)) + (sha256 + (base32 + "0p6siidrx8q6qr36fc67hzi091m2zwik3zngj27yllbfz6sn5k69")))) + (properties `((upstream-name . "BiocBaseUtils"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BiocBaseUtils") + (synopsis "General utility functions for developing Bioconductor packages") + (description + "The package provides utility functions related to package development. +These include functions that replace slots, and selectors for show methods. +It aims to coalesce the various helper functions often re-used throughout the +Bioconductor ecosystem.") + (license license:artistic2.0))) + (define-public r-bioccasestudies (package (name "r-bioccasestudies") @@ -14807,13 +15182,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.32.1") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw")))) + "1zj43kbzvi2ws8c182fp6vn5r6iiqsr6p2iyy3k8n3ifm2acqw2h")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -14836,14 +15211,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn")))) + "0ysdmv2hyl8jnmr42lkyvgfqb0z89f5p649ahx0ygs6fw0z226xa")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs @@ -14858,13 +15233,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5")))) + "092hpmyhra755j32vc8w2l6xqwg09jm8apnk5rvxi1cm5034yvsl")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -14882,13 +15257,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38")))) + "1rgn0agw5m4y8838lxzq1r658h1pblaidmm444yfimjffa8znj23")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -14910,14 +15285,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl")))) + "1j71zmxwiz82gg6kii2bmynzwll1r6fmsq972kmvxvm6crpvi15s")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -14944,14 +15319,14 @@ access.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai")))) + "1as3k6avyc4l7saw02x0ql68c06msvs1s824vc1xg6lkdsi4lsyc")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -14971,20 +15346,22 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1")))) + "00lhnqa4yz3lm5kl79bghad93iijihnassy2caf87czc540why09")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-biocbaseutils r-biocgenerics + r-delayedarray r-genomicranges r-iranges r-s4vectors @@ -15006,14 +15383,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi")))) + "1x4mzzjvjgcxg5xyxjib8r2n55hpf2vzcci0xkb7d8frakfncn9s")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -15051,14 +15428,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3")))) + "0a8xyrmarb2ja5zyvx5sndd67hylmwi29gpr5lwrzinww8w8b8w6")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs @@ -15078,14 +15455,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd")))) + "1av7vnw6z9cw7j4d3vpi8mfs5h4pn4yr2wc8ybg7ad1d686ah845")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -15105,11 +15482,10 @@ gene selection, testing relationships, and so on.") r-rbgl r-readr r-rlang + r-rorcid r-rvest r-stringr r-tibble - r-tidyr - r-tidyselect r-xml2)) (native-inputs (list r-knitr)) @@ -15126,14 +15502,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh")))) + "197cy5gdlvac7jqwb4dm4dbqfms2nvc3paqs75nsg9mpp1h5z8l8")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -15164,14 +15540,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l")))) + "00cy5lqmfap57bm2s00bis9ddci2lv1lrp0mk5ydgx061p4ym29i")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) @@ -15197,14 +15573,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0")))) + "1fnx3q5arsilrvnhndplap8h4ydi9bvmlpfllj1li124hn5n2w3d")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs @@ -15219,14 +15595,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v")))) + "1r32ajjmrhlwl0ylwavlfzph6m01mq3y7r87x8mbkmqw9ld1y2fd")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs @@ -15265,18 +15641,40 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "1.28.0") + (version "2.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky")))) + "1vmm7s5p8wqz1r8g1hy1l3mra3kkf76qgy5jkf84jxz7pi0clbld")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs - (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson)) + (list r-annotationdbi + r-circlize + r-digest + r-doparallel + r-dt + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-getoptlong + r-globaloptions + r-go-db + r-iranges + r-org-hs-eg-db + r-progress + r-rcolorbrewer + r-rcurl + r-rcpp + r-rjson + r-s4vectors + r-shiny + r-txdb-hsapiens-ucsc-hg19-knowngene + r-txdb-hsapiens-ucsc-hg38-knowngene)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/rGREAT") (synopsis "Client for GREAT analysis") @@ -15289,14 +15687,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012")))) + "1djgbnxsdp1w9hhc6346gmvad3x8avy8nc85gpvg9i4x52wcrn4j")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs @@ -15322,14 +15720,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc")))) + "13ygc467nqh0235sf1ags1ihv7pg2yriva6qi7z46c534vxv6b8n")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs @@ -15445,14 +15843,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf")))) + "1l0m591scln024jdpib47fndhx2wfp9jgkj3mdmwd9nkc5y0qjda")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -15466,13 +15864,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.34.0") + (version "0.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k")))) + "05al4diwdbsa9b37i8msxnp79fxk7k24dk2vhh131s3snb89jvfs")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -15533,14 +15931,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l")))) + "0blymdax10zzg2lpj4hgvyh9c01b1qaivrc0gx95swji37zkqnwm")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments @@ -15571,13 +15969,13 @@ objects from the @code{graph} package.") (define-public r-fishpond (package (name "r-fishpond") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fishpond" version)) (sha256 (base32 - "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym")))) + "112jd53wbiv1w0n8dc4qn6257wbbbg5i20s9wlvaw98jma94afa6")))) (properties `((upstream-name . "fishpond"))) (build-system r-build-system) (inputs (list zlib)) @@ -15609,13 +16007,13 @@ working with Salmon and Alevin quantification files.") (define-public r-fithic (package (name "r-fithic") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq")))) + "1c7jscl82knbh5ha1i1hlm46nnhz6aw5h0j5xnl4hlgx8mnn05fl")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -15633,13 +16031,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s")))) + "10m3pq22a8m8bbfkmq5r44ydg2668g6dxmxp7km47jxgf9hlqhcl")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -15662,14 +16060,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1dzx5463ig3ag72a47slc4jbq5id11w77cj0zgzr85h0dbxklrr9")))) + "1y25mlsqf2inij6w2825xxl30bdba971az6rjf7j9bnya3gpvi6h")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -15693,14 +16091,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g")) + "0zxgpc2krfwqzm8c05cdlfs3dyyf5ll43ff9mw8xzj89wcmlcfx7")) (modules '((guix build utils))) (snippet '(begin @@ -15773,14 +16171,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c")))) + "0sa1wh997jfiz2y0dr7v12b7pvlf7icgv6arlyqy57winbnqa96m")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) @@ -15799,13 +16197,13 @@ matrices.") (define-public r-cner (package (name "r-cner") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq")))) + (base32 "15y27ca14fdhn2prqgkyikff7p7490xn0bp2c7cnwhw173mm1syw")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs (list zlib)) @@ -15847,14 +16245,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w")))) + "05kgkwmh5mcrm0xd81rzicysgknb8wrf71y2llikvma1b9c1g789")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs @@ -15893,13 +16291,13 @@ provides a wrapper of de novo motif discovery software.") (define-public r-maftools (package (name "r-maftools") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maftools" version)) (sha256 - (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6")))) + (base32 "1f1r0frikaj6aw137dk523gagkxdygg7gzc3pd303ds5cqynwiqx")))) (properties `((upstream-name . "maftools"))) (build-system r-build-system) (propagated-inputs @@ -15922,14 +16320,14 @@ customizable visualzations with minimal effort.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878")))) + "01k2ngf4nj2cazb3a2c96by86xwdkdngzwhb73n2wadibamnqnfv")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs @@ -15956,13 +16354,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m")))) + (base32 "1rwgbicbmszdkr05ksxfsisyhk0a4pvc3jrxbzjyc13jj5h6m5kp")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -16003,14 +16401,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p")))) + "1y9c9wf3009w4qh03zpsmc0ff0nkzal673a4nql5c11cn55sza2g")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -16031,13 +16429,13 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "1.10.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y")))) + (base32 "05rw6l0d4n9m1dd7dp55zfripx036x1riwy83sx3aj5mw4r1awb6")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs @@ -16063,14 +16461,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.6.3") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671")))) + "10wk46zgi57m9q9ab6wlmljcss3fph2r9yp1bp01s9yv7sd749b2")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -16098,13 +16496,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.24.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw")))) + "1mjnf2y41lvni77g9hyw8qlvlsi5nxv5ha0fnch1kmw9814nycq3")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -16117,8 +16515,10 @@ of other packages.") r-ggbeeswarm r-ggplot2 r-ggrepel + r-ggrastr r-gridextra r-matrix + r-pheatmap r-rcolorbrewer r-rcppml r-rlang @@ -16127,6 +16527,7 @@ of other packages.") r-scuttle r-singlecellexperiment r-summarizedexperiment + r-uwot r-viridis)) (native-inputs (list r-knitr)) @@ -16140,14 +16541,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni")))) + "11iwpw44600pfx01vqil97k728m1wf4dljr27k2ak4s7z75kxfih")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -16183,14 +16584,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2")))) + "1rq23ra4nnz9dx0gsg9bh8zcbz6s0pyvjwq30xl6g4hbqz927xb0")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) @@ -16208,14 +16609,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1kq643fmfzq1qjvpj3kc092ahc3qamqgx53layqsyvz5mil55jjv")))) + "0qcn7rlq0bsj11sc31wzks2xv900fpmbsblxp9cng5lj5cn2djk3")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -16244,14 +16645,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh")))) + "1shrvb2vmvk1m6xk59jqpvrxi8vzcr978aalbx1gjcmaqf6abzcq")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs @@ -16273,13 +16674,13 @@ within the R for Mass Spectrometry packages.") (define-public r-msfeatures (package (name "r-msfeatures") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsFeatures" version)) (sha256 - (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3")))) + (base32 "1q1224w31wdaagfv8ysc1w0d0n34y547c0jzkff1vxri9pb0w1j1")))) (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs @@ -16303,14 +16704,14 @@ the respective packages (such as e.g. @code{xcms}).") (define-public r-biocio (package (name "r-biocio") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp")))) + "15d4xsn3k32q7lzcyxvs70f0jbh9fgwl3vi7xd6sqpggar12hh9f")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs @@ -16336,14 +16737,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42")))) + "17xklsg483zd205q5hyxy6b3cgrb53pplb1wc7pmv5638y7nsq2v")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs @@ -16359,14 +16760,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi")))) + "10frsvqhi3i0v2w4q4q9xz1ykyf6s3nrjlmn94x3kd06p3s839k3")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs @@ -16388,14 +16789,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza")))) + "0n3x5w074x5hhgdf2qa0pkma4vrjwrcgjna7hx0az6ixkgpbkrpv")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -16451,14 +16852,14 @@ preprocessing of cytometry data, including: (define-public r-erma (package (name "r-erma") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b")))) + "06zxqzbzb0jrk357900gv1r2n81i49rbmrxla02f879kq2ik9cyd")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -16491,14 +16892,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.44.1") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg")))) + "1gm3y1nx0ah8wcrg2dh1xd688izm2sijz7bhgsasxckmmkmkp60g")))) (build-system r-build-system) (arguments `(#:phases @@ -16659,14 +17060,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi")))) + "09j94kk3dd3bbfw6a2l14i7vd4rh11g9lxhw4zsm15vg71cm1lv9")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -16708,14 +17109,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.28.1") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl")))) + "0sj51cli1p8k7z1nl5rfswjlzrk9cqnpr1a1pr618gk74kfwqf5a")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -16742,13 +17143,13 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx")))) + (base32 "0hpsb009qmhy9p67d5wd0cl60smhgjlhxsz5f52i1c6qy4jk1niq")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs @@ -16766,14 +17167,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm")))) + "0i8v4wfp207f5dpf3y2n8fqn7mc4khj92gb209vzc3y3kbwp2c6n")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -16890,13 +17291,13 @@ other functional sequencing data.") (define-public r-pathview (package (name "r-pathview") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71")))) + (base32 "0p7cdq03863zpw009prs1yh3gps1kw135anjfq6wpdkwza7xy4py")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs @@ -16924,14 +17325,14 @@ large-scale and fully automated analysis.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2")))) + "14rkrav4iydc85194skdy33sk365pjmmvxxvzaxxh0k9ds009qwx")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs (list zlib)) @@ -16948,14 +17349,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7")))) + "17p22vsmb9h8ap0f2rzyg2r71srj3sxiapzyaz1csad2vfjxfi2r")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs @@ -16986,14 +17387,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh")))) + "0lrw1v82amr54bkfh98953b16fhlgd1i6kz1g7zy8gj0hd417ms1")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs @@ -17039,14 +17440,14 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708")))) + "0iy24vj4lg1k4fzdxf9blc47xsp4dmplajgabsb2s925l7jpxfvw")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs @@ -17073,14 +17474,14 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8")))) + "1krk5iqqzkkkxfgsvi9j6mj14i2rzisrrq0xmxjsrkgfh19awhr8")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) (inputs (list megadepth)) @@ -17106,14 +17507,14 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15")))) + "05znaj2fialxi937mhj2dlrm3v4j2wgqafcy78qrkz7xxn13pr01")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs @@ -17122,6 +17523,7 @@ regions or annotations of your choice from BigWig files.") r-data-table r-dixontest r-futile-logger + r-ids r-matrix r-rcpp r-rdpack)) @@ -17139,14 +17541,14 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.12.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil")))) + "05w6b10vc4mmwdqnkcj7vnfigk03f03n776vqhlb38k0lx8k4hk3")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs @@ -17175,14 +17577,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.22.3") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k")))) + "14fja1dikzq60zjx1arcv1q16qd0hmibqjy0nbaivmk3zh16spkc")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs @@ -17209,14 +17611,14 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa")))) + "1j6w19k124x46gj2p8f1z0i2c03yhiiy1w0fqf504b2r7wy90jxc")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs @@ -17233,14 +17635,14 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.54.0") + (version "3.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam")))) + "1xknyc2m03dyqrnx6np2y2lr41w06arl114f6cncl6wsnanqxzrz")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs @@ -17255,14 +17657,14 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70")))) + "1ahlml1ssjmg126ki1phdprq4v0nawzbbfq8jray5ypaj32qx3r2")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) @@ -17280,14 +17682,14 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq")))) + "1ix31jcfi3dg12pa0sz4k4izwc9rsydy6krl7f949lkam2g7s5f8")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs (list r-filelock)) @@ -17304,14 +17706,14 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk")))) + "0gh29w8arg0glawprwshaixv07y756c4lx21h8jjbqlsrbspp8fw")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) @@ -17328,14 +17730,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.8.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk")))) + "14sgm3ia7jj5jckysqkljrffafg6rl8i7fgzsxv8ycnrwbd05d09")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -17354,14 +17756,14 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.6.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0")))) + "0zmiaixknwxv72l4fygrn0qr3mvl7kqfbqgflnavs0wxx6xdjqgn")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments @@ -17388,14 +17790,14 @@ Bioconductor-friendly.") (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d")))) + "13l5shmiiv4wl9m5xnwzagjxqrchjg9znvcgf7hv8f263l2yc8qm")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) @@ -17418,14 +17820,14 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1")))) + "08ahz3v2xbhwfh89dbnhhcdm0x5qv4hibi8wknlqf5x8gqm5j5w6")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs @@ -17463,14 +17865,14 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n")))) + "0728fpj05bvna5lpm29pdbn4slfmq16nz35as086ddbl2hhc9ni1")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs @@ -17492,14 +17894,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g")))) + "1yzb7m7vk50f9x1g8yb95wlmpccj3n4qgczz46lvhsk7hkifybzq")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") @@ -17512,14 +17914,14 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz")))) + "1xclmwxps7yvqnaw8kn6z4mlpx6v8xfzyly4cadsjaj2qm535xxk")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs @@ -17534,14 +17936,14 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln")))) + "0n026b744ah5kcnipsyiqqs7vlz5n5im1kgv35i2pgxyzvf7a8sn")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs @@ -17559,14 +17961,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp")))) + "10nwgp8a9chn33p5k7cdp920rraiw187xfrylyd9bq010c7vp7xh")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs @@ -17615,14 +18017,14 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm")))) + "12c6m7dzwkdh4bk1c5xmzm5ajrsba7v62mag1f3rrpmrapdh6s0j")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs @@ -17644,14 +18046,14 @@ scoring subnetwork.") (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2")))) + "1h99d6gnqw5v9ha2169zfhw9cvxhyjgkf4zm8qj1i03h2cywapgv")))) (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs @@ -17686,14 +18088,14 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m")))) + "1ssxsxdm8vmlrmvvdz5p98apd3xsal1h3ss8556g83kgw830zsxf")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs @@ -17712,14 +18114,14 @@ optimised for high performance.") (define-public r-biotip (package (name "r-biotip") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6")))) + "1n90n4vz0cwz8irwpmrkm9qcyvk5rssl2v6wrzny4zwhzjkmvlni")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs @@ -17742,14 +18144,14 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22")))) + "1sbwbz0xdws31lsh46mfcijqmi6rm050r1d6vwii65q686x5j43w")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs @@ -17784,14 +18186,14 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5")))) + "0rd0ihr1ai1kvly2zf5y2qx3qyhk3ag2mdsrwqnzs67xkv99glsf")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs @@ -17830,13 +18232,13 @@ visualizing bisulfite sequencing data.") (define-public r-dada2 (package (name "r-dada2") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dada2" version)) (sha256 (base32 - "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x")))) + "1cdfq4qa4kkfkqnkyxyr109hbvj5li396rm3p2b11qm2pxmfd7kc")))) (properties `((upstream-name . "dada2"))) (build-system r-build-system) (propagated-inputs @@ -17867,14 +18269,14 @@ fragments by exact matching.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n")))) + "1zx62lbj0am85p0c1vk06s7qf8294vk8yyh67nkiqc7xgqqwybyk")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs @@ -17913,13 +18315,13 @@ interest on transformed methylation proportions.") (define-public r-omicade4 (package (name "r-omicade4") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "omicade4" version)) (sha256 (base32 - "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj")))) + "1w9fsg0r6ir9nmmpf08b1mh8mnrzxk3f398y1w5dg34fdz4phgpg")))) (properties `((upstream-name . "omicade4"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-biobase r-made4)) @@ -17932,13 +18334,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.4.0") + (version "3.5.25") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni")))) + (base32 "1a0d4vf8i45h1fifswx9lhk6fk0z8sxfnav35psz9kvmxxab9698")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -17958,12 +18360,14 @@ interest on transformed methylation proportions.") r-later r-logger r-magrittr + r-rmarkdown r-progress r-purrr r-rappdirs r-readr r-readxl r-rlang + r-rvest r-stringr r-tibble r-tidyr @@ -17985,14 +18389,14 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr")))) + "1fq2nj0vclpxavqj5qx7jc3ympg00izxn9fpy4mlhyp9l921z13m")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs @@ -18037,13 +18441,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.24.3") + (version "2.25.3") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms")))) + (base32 "0daq7093yipry8pp6fj6pj8x1njxs8j6cz7875qkfmzqkbis4vql")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs @@ -18092,13 +18496,13 @@ starburst plots) in order to easily develop complete analysis pipelines.") (define-public r-tricycle (package (name "r-tricycle") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 - "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln")))) + "0b5agqhywg23zxf0f9s1vfbzs7s7ijf9c716s7hwjprxfdz5znvw")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) (propagated-inputs @@ -18131,14 +18535,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "0hxq5lkrdiz0a3xpl88adrv4m55jr6g46a5m9pamc0w4bxddirr8")))) + "0v1s5ssinyrizpg2i88dn2ckzs4i16hjfg2pzxhal3ypsiw24qna")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs @@ -18172,13 +18576,13 @@ reproducibility.") (define-public r-phyloseq (package (name "r-phyloseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 - (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k")))) + (base32 "07zi059v6zwrm31qwc7fmg35fwqlqfb6c30wwj9q4m2y67srnskk")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6d7097c42c..6c6ff3e25a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de> ;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net> +;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -535,6 +536,42 @@ BED, GFF/GTF, VCF.") and utilities for PacBio C++ applications.") (license license:bsd-3)))) +(define-public r-btools + (let ((commit "fa21d4ca01d37ea4d98b45582453f3bf95cbc2b5") + (revision "1")) + (package + (name "r-btools") + (version (git-version "0.0.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/twbattaglia/btools") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0bca593dnxz6xdywpdi0ipli0paln2b3bfxxj0csnmj55ryrz428")))) + (properties `((upstream-name . "btools"))) + (build-system r-build-system) + (propagated-inputs + (list r-biomformat + r-coin + r-deseq2 + r-dplyr + r-genefilter + r-phyloseq + r-picante + r-plotly + r-reshape2 + r-stringr + r-vegan)) + (home-page "https://github.com/twbattaglia/btools") + (synopsis "R functions for microbial diversity analyses") + (description + "This package provides an assortment of R functions that is suitable +for all types of microbial diversity analyses.") + (license license:expat)))) + (define-public pbbam (package (name "pbbam") diff --git a/gnu/packages/bqn.scm b/gnu/packages/bqn.scm index 984dfbe53e..8cce9564a2 100644 --- a/gnu/packages/bqn.scm +++ b/gnu/packages/bqn.scm @@ -33,7 +33,6 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages llvm) #:use-module (gnu packages java) - #:use-module (gnu packages linux) #:use-module (gnu packages compression)) (define-public dbqn @@ -113,7 +112,7 @@ the same author.") ;; Aside from dbqn above, the main bqn repository is used by other ;; implementations as a "known good" set of sources. CBQN uses dbqn to ;; generate an intermediate bytecode for its own compilation. - (let ((commit "e219af48401473a7bac49bdd8b89d69082cf5dd8")) + (let ((commit "71ce36141aaacfa714edca2e408ca522a3bc5554")) (origin (method git-fetch) (uri (git-reference @@ -121,11 +120,11 @@ the same author.") (commit commit))) (file-name (git-file-name "bqn-sources" commit)) (sha256 - (base32 "0r6pa9lscl2395g4xlvmg90vpdsjzhin4f1r0s7brymmpvmns2yc"))))) + (base32 "060a3r5m7hynzxj4iz1av2kj5jf8w3j8yswzzx9wkx31rdrsiv2c"))))) (define cbqn-bootstrap - (let* ((revision "1") - (commit "9c1cbdc99863b1da0116df61cd832137b196dc5c")) + (let* ((revision "2") + (commit "66584ce1491d300746963b8ed17170348b2a03e6")) (package (name "cbqn-bootstrap") (version (git-version "0" revision commit)) @@ -137,7 +136,7 @@ the same author.") (file-name (git-file-name name version)) (sha256 (base32 - "0w38fhwf20drkyijy6nfnhmc5g5gw0zmzgmy1q605x57znlj85a2")))) + "13gg96aa56b8k08bjvv8i0f5nxrah2sij7g6pg7i21fdv08rd9iv")))) (build-system gnu-build-system) (arguments (list @@ -202,7 +201,6 @@ by APL.") (install-file "libcbqn.so" lib)))))))) (native-inputs (list dbqn bqn-sources - libffi - linux-libre-headers)) + libffi)) (properties `((tunable? . #t))))) diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm index 6583810277..32a8f23f19 100644 --- a/gnu/packages/calendar.scm +++ b/gnu/packages/calendar.scm @@ -34,6 +34,7 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix build-system gnu) + #:use-module (guix build-system go) #:use-module (guix build-system cmake) #:use-module (guix build-system python) #:use-module (gnu packages admin) @@ -45,6 +46,7 @@ #:use-module (gnu packages freedesktop) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) + #:use-module (gnu packages golang) #:use-module (gnu packages gtk) #:use-module (gnu packages icu4c) #:use-module (gnu packages perl) @@ -426,3 +428,38 @@ written in C++ using GTK. Launched once, it pops up a small calendar applet, launched again it closes the running instance. It can additionally be configured to show the current time in different timezones.") (license license:bsd-3)))) + +(define-public hebcal + (let ((commit "2384bb88dc1a41a4a5ae57a29fb58b2dd49a475d") + (revision "0")) + (package + (name "hebcal") + (version (git-version "5.3.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hebcal/hebcal") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "12rv3b51jb7wcjwmmizz9jkw7gh37yklys4xncvpzgxdkkfgmmjx")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/hebcal/hebcal")) + (inputs + (list go-github-com-hebcal-hebcal-go + go-github-com-pborman-getopt)) + (synopsis "Perpetual Jewish Calendar program") + (description + "Hebcal is a program for converting between Hebrew and Gregorian +dates, and generating lists of Jewish holidays for a given year. +Shabbat, holiday candle lighting, and havdalah times are approximated +using your location. + +It can also show daily prayer times, the weekly Torah reading, and +the daily leaf of Talmud. The program can help with counting of the +Omer or with calculation of Hebrew yahrzeits, birthdays, or +anniversaries.") + (home-page "https://github.com/hebcal/hebcal") + (license license:gpl2+)))) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index e3deed573a..e0a9f5fbad 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -317,7 +317,7 @@ ;; run the Blink performance tests, just remove everything to save ~70MiB. '("third_party/blink/perf_tests")) -(define %chromium-version "107.0.5304.110") +(define %chromium-version "107.0.5304.121") (define %ungoogled-revision (string-append %chromium-version "-1")) (define %debian-revision "debian/102.0.5005.61-1") (define %arch-revision "6afedb08139b97089ce8ef720ece5cd14c83948c") @@ -330,7 +330,7 @@ (file-name (git-file-name "ungoogled-chromium" %ungoogled-revision)) (sha256 (base32 - "14z9qi9i9l7kjx7gf74lzs63bpxqyd3wbqqpsvzvqgr2v0cgqahx")))) + "1ns664y7qx0ry8hg8r704z64jmx8j6rpxn2lkliv0xjfwlrbbfx3")))) (define %debian-origin (origin @@ -495,7 +495,7 @@ %chromium-version ".tar.xz")) (sha256 (base32 - "1k7yjsb4i7m8i5mk018v7z25r4x1ypyprz4hnyrn7vk2983lhdfk")) + "12z0fhgxcsdkf6shnsg9maj3v901226cjcy8y2x8m88maw2apc0j")) (modules '((guix build utils))) (snippet (force ungoogled-chromium-snippet)))) (build-system gnu-build-system) diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm index fb4e48ad4d..b78e8b739b 100644 --- a/gnu/packages/ci.scm +++ b/gnu/packages/ci.scm @@ -58,8 +58,8 @@ #:use-module ((guix search-paths) #:select ($SSL_CERT_DIR))) (define-public cuirass - (let ((commit "1fb4b0ac1297e9bd680d0f4a356ce3050b27f913") - (revision "12")) + (let ((commit "1341725f2cbb886e0960c6fad13444e3cfe36c13") + (revision "13")) (package (name "cuirass") (version (git-version "1.1.0" revision commit)) @@ -72,7 +72,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0134klqiykjgyc6lwl165hpil6hgd8xhm62mpxabr6wrvclk8bhm")))) + "0l928hd84ky9l4d1nfdkzc4jvghvxia4j6gflliydvfiyfiw87b3")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) diff --git a/gnu/packages/cluster.scm b/gnu/packages/cluster.scm index 6e4055736a..4db64d5d19 100644 --- a/gnu/packages/cluster.scm +++ b/gnu/packages/cluster.scm @@ -132,7 +132,7 @@ ;; For the documentation. docbook-xml docbook-xml-4.4 ;used by documentation/ra2refentry.xsl - docbook-xsl + docbook-xsl-next libxml2 ;for XML_CATALOG_FILES libxslt ;for xsltproc ruby-asciidoctor)) diff --git a/gnu/packages/coq.scm b/gnu/packages/coq.scm index e4ee1aa882..0d8cb26358 100644 --- a/gnu/packages/coq.scm +++ b/gnu/packages/coq.scm @@ -54,7 +54,7 @@ (define-public coq-core (package (name "coq-core") - (version "8.16.0") + (version "8.16.1") (source (origin (method git-fetch) @@ -64,7 +64,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "1rp4m2yjldsz0kj7p2fsc312n740fr8kg99jlsk8aq3h524qz2h8")) + "0ljpqhh5lfsim29fcfp2xfcvm3j84pf1mb0gnpdr8vcqqw7mqwpf")) (patches (search-patches "coq-fix-envvars.patch")))) (native-search-paths (list (search-path-specification diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3e5d654c5a..ad0657ef3b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -599,6 +599,27 @@ Google. @code{googleVis} makes use of the internal R HTTP server to display the output locally.") (license license:gpl2+))) +(define-public r-gson + (package + (name "r-gson") + (version "0.0.9") + (source (origin + (method url-fetch) + (uri (cran-uri "gson" version)) + (sha256 + (base32 + "065ify3i7zqwi7h5jzr7kdgr358kwgw6xrkvvmrznbl7s9f7d57n")))) + (properties `((upstream-name . "gson"))) + (build-system r-build-system) + (propagated-inputs (list r-jsonlite r-rlang r-tidyr)) + (home-page "https://cran.r-project.org/package=gson") + (synopsis "Base Class and Methods for 'gson' Format") + (description + "This packages proposes a new file format named @code{gson} for storing +gene set and related information, and provides read, write and other utilities +to process this file format.") + (license license:artistic2.0))) + (define-public r-guix-install (package (name "r-guix-install") @@ -709,6 +730,33 @@ allows transformation of geographic coordinates from one projection and/or datum to another.") (license license:gpl2))) +(define-public r-rorcid + (package + (name "r-rorcid") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "rorcid" version)) + (sha256 + (base32 + "1d0s5w48ksyj152nc4xq5w0nsimab8jc5fgspdwnbas2g8a52igr")))) + (properties `((upstream-name . "rorcid"))) + (build-system r-build-system) + (propagated-inputs (list r-crul + r-data-table + r-fauxpas + r-httr + r-jsonlite + r-tibble + r-xml2)) + (home-page "https://github.com/ropensci/rorcid") + (synopsis "Interface to the @url{Orcid.org, https://orcid.org} API") + (description + "This package provides an API for @url{Orcid.org, https://orcid.org}. +Functions include searching for people, searching by DOI, or searching by +Orcid ID.") + (license license:expat))) + (define-public r-waldo (package (name "r-waldo") @@ -1273,13 +1321,13 @@ variables.") (define-public r-ggprism (package (name "r-ggprism") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "ggprism" version)) (sha256 (base32 - "09dh0r8r5s61i5dbk6rswajc2vm7k8wvlqyvzq8wr160676lycjp")))) + "0ycklp7764cw65hqh9r61im8vqfd7sjayyw1gvprxzg7k217gnl3")))) (properties `((upstream-name . "ggprism"))) (build-system r-build-system) (propagated-inputs @@ -1874,6 +1922,30 @@ excellent candidate for labeling of a polygon.") @code{dplyr} and the wider @code{tidyverse} using only @code{base}.") (license license:expat))) +(define-public r-ecosolver + (package + (name "r-ecosolver") + (version "0.5.4") + (source (origin + (method url-fetch) + (uri (cran-uri "ECOSolveR" version)) + (sha256 + (base32 + "0973m346vakgddp92dzqlky0wa196hj341r9y7rz67bc2zl8jx2x")))) + (properties `((upstream-name . "ECOSolveR"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bnaras.github.io/ECOSolveR/") + (synopsis "Embedded conic solver in R") + (description + "This package provides an R interface to the @dfn{Embedded COnic +Solver} (ECOS), an efficient and robust C library for convex problems. +Conic and equality constraints can be specified in addition to integer +and boolean variable constraints for mixed-integer problems. This R +interface is inspired by the Python interface and has similar calling +conventions.") + (license license:gpl3+))) + (define-public r-ecp (package (name "r-ecp") @@ -3603,13 +3675,13 @@ annotation data to keep updated.") (define-public r-ggtern (package (name "r-ggtern") - (version "3.3.5") + (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "ggtern" version)) (sha256 - (base32 "15hhn8msy0l8zbq8ms0zvg1iajn1c28gd77v3hp6dvwwsla8zzbd")))) + (base32 "01j1rvff3vz72vwqsy3bh81aav7gfymg4sbvc267vg0r3a16ywcg")))) (properties `((upstream-name . "ggtern"))) (build-system r-build-system) (propagated-inputs @@ -5639,6 +5711,43 @@ testing framework of Wald are generic and can therefore also be used in other contexts.") (license license:gpl2+))) +(define-public r-cvxr + (package + (name "r-cvxr") + (version "1.0-11") + (source (origin + (method url-fetch) + (uri (cran-uri "CVXR" version)) + (sha256 + (base32 + "0alp1g4bszxqcrjbn54bz1zswg8y10372fwwlbi0jjazycw9cap9")))) + (properties `((upstream-name . "CVXR"))) + (build-system r-build-system) + (propagated-inputs + (list r-bit64 + r-ecosolver + r-gmp + r-matrix + r-osqp + r-r6 + r-rcpp + r-rcppeigen + r-rmpfr + r-scs)) + (native-inputs (list r-knitr)) + (home-page "https://cvxr.rbind.io") + (synopsis "Disciplined convex optimization") + (description + "This package provides an object-oriented modeling language for +@dfn{disciplined convex programming} (DCP) as described in Fu, +Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows +the user to formulate convex optimization problems in a natural way +following mathematical convention and DCP rules. The system analyzes +the problem, verifies its convexity, converts it into a canonical +form, and hands it off to an appropriate solver to obtain the +solution. Interfaces to solvers on CRAN and elsewhere are provided.") + (license license:asl2.0))) + (define-public r-squarem (package (name "r-squarem") @@ -19203,6 +19312,28 @@ authoring books and technical documents with R Markdown.") that accept short and long options.") (license license:gpl2+))) +(define-public r-osqp + (package + (name "r-osqp") + (version "0.6.0.7") + (source (origin + (method url-fetch) + (uri (cran-uri "osqp" version)) + (sha256 + (base32 + "00w2hr0pagnvpsk84z99c7alhv7xvs9wpcmkzbcg3qs14g888rgf")))) + (properties `((upstream-name . "osqp"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-r6 r-rcpp)) + (home-page "https://osqp.org") + (synopsis "Quadratic Programming Solver using the OSQP Library") + (description + "This package provides bindings to the OSQP solver. The OSQP +solver is a numerical optimization package or solving convex quadratic +programs written in C and based on the alternating direction method of +multipliers. See <arXiv:1711.08013> for details.") + (license (list license:asl2.0)))) + (define-public r-kernlab (package (name "r-kernlab") @@ -20947,6 +21078,30 @@ errors and possible semantic issues. It supports on the fly checking of R code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (license license:expat))) +(define-public r-scs + (package + (name "r-scs") + (version "3.0-1") + (source (origin + (method url-fetch) + (uri (cran-uri "scs" version)) + (sha256 + (base32 + "04srf33zw4dxv22b1h5qwjch5yg7hrvk4iq8yvxqnbr8qzp1x26n")))) + (properties `((upstream-name . "scs"))) + (build-system r-build-system) + (home-page "https://github.com/FlorianSchwendinger/scs") + (synopsis "Splitting conic solver") + (description + "This package solves convex cone programs via operator splitting. +It can solve: linear programs, second-order cone programs, +semidefinite programs, exponential cone programs, and power cone +programs, or problems with any combination of those cones. SCS uses +AMD (a set of routines for permuting sparse matrices prior to +factorization) and LDL (a sparse LDL factorization and solve package) +from SuiteSparse.") + (license license:gpl3))) + (define-public r-sctransform (package (name "r-sctransform") diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index e4dde1b22b..862d8bfd62 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1628,17 +1628,24 @@ types are supported, as is encryption.") (sha256 (base32 "1w1q6kh567fd8xismq9i6wr1y893lypd30l452yvydi1qjiq1n6x")) - (snippet '(begin (delete-file "rec-mode.info"))))) + (snippet #~(begin (delete-file "rec-mode.info"))))) (build-system emacs-build-system) (arguments - '(#:phases - (modify-phases %standard-phases - (add-before 'install 'make-info - (lambda _ - (invoke "makeinfo" "--no-split" - "-o" "rec-mode.info" "rec-mode.texi")))))) - (native-inputs - (list texinfo)) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-program-paths + (lambda* (#:key inputs #:allow-other-keys) + (emacs-substitute-variables "rec-mode.el" + ("rec-recfix" (search-input-file inputs "bin/recfix")) + ("rec-recinf" (search-input-file inputs "bin/recinf")) + ("rec-recsel" (search-input-file inputs "bin/recsel"))))) + (add-before 'install 'make-info + (lambda _ + (invoke "makeinfo" "--no-split" + "-o" "rec-mode.info" "rec-mode.texi")))))) + (inputs (list recutils)) + (native-inputs (list texinfo)) (home-page "https://www.gnu.org/software/recutils/") (synopsis "Emacs mode for working with recutils database files") (description "This package provides an Emacs major mode @code{rec-mode} diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 0c7f97b386..e69d1ce83b 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -597,7 +597,7 @@ the position of the variable and allows you to modify its value.") (define-public remake (package (inherit gnu-make) (name "remake") - (version "4.3-1.5") + (version "4.3-1.6") (source (origin (method url-fetch) (uri (let ((upstream-version @@ -609,7 +609,7 @@ the position of the variable and allows you to modify its value.") (file-name (string-append "remake-" version ".tar.gz")) (sha256 (base32 - "0xlx2485y0israv2pfghmv74lxcv9i5y65agy69mif76yc4vfvif")) + "11vvch8bi0yhjfz7gn92b3xmmm0cgi3qfiyhbnnj89frkhbwd87n")) (patches (search-patches "remake-impure-dirs.patch")))) (inputs (modify-inputs (package-inputs gnu-make) diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index 0853eb6d28..8912bb74bc 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -24,6 +24,7 @@ ;;; Copyright © 2021 Justin Veilleux <terramorpha@cock.li> ;;; Copyright © 2014, 2022 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2022 Disseminate Dissent <disseminatedissent@protonmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -835,6 +836,46 @@ hierarchy. It ships with @code{rifle}, a file launcher that is good at automatically finding out which program to use for what file type.") (license license:gpl3))) +(define-public fff + (package + (name "fff") + (version "2.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dylanaraps/fff") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "14ymdw6l6phnil0xf1frd5kgznaiwppcic0v4hb61s1zpf4wrshg")))) + (build-system gnu-build-system) + (inputs + (list bash + file)) + (arguments + (list + #:tests? #f ; no tests + #:make-flags + #~(list + (string-append "PREFIX=" #$output)) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'refer-to-inputs + (lambda* (#:key inputs #:allow-other-keys) + (let ((file (assoc-ref inputs "file"))) + (substitute* "fff" + (("\\bfile [-\"]" match) + (string-append file "/bin/" match)))))) + (delete 'configure)))) ; no configure script + (home-page "https://github.com/dylanaraps/fff") + (synopsis "Simple file manager written in bash") + (description + "@command{fff} (fast file-manager) is a simple, blazing fast and minimal +file manager for Linux, written in bash. It only requires bash and coreutils, +and its highly optimized now for efficient performance.") + (license license:expat))) + (define-public volume-key (package (name "volume-key") diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index ce184aa8dd..21b711d147 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -1013,14 +1013,14 @@ synthesis, and on-the-fly re-configuration.") (define-public knot-resolver (package (name "knot-resolver") - (version "5.4.4") + (version "5.5.3") (source (origin (method url-fetch) (uri (string-append "https://secure.nic.cz/files/knot-resolver/" "knot-resolver-" version ".tar.xz")) (sha256 (base32 - "1sic5ccbbqml4c01dbikkg6qx1gg81nqi76cj79pjdllkqqn92aq")))) + "0bgdbx66dsfik3sdqi4g2imddalqc1p41n444xk7s8vxig35g3x3")))) (build-system meson-build-system) (outputs '("out" "doc")) (arguments diff --git a/gnu/packages/docker.scm b/gnu/packages/docker.scm index 184280b38f..7d109dc94c 100644 --- a/gnu/packages/docker.scm +++ b/gnu/packages/docker.scm @@ -580,7 +580,7 @@ runcexecutor/executor.go" util-linux lvm2 tini - xfsprogs + xfsprogs-5.9 xz)) (native-inputs (list eudev ; TODO: Should be propagated by lvm2 (.pc -> .pc) diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm index 60ef39c77e..8dff0f2ec8 100644 --- a/gnu/packages/ebook.scm +++ b/gnu/packages/ebook.scm @@ -197,6 +197,7 @@ with Microsoft Compiled HTML (CHM) files") python-psutil python-py7zr python-pychm + python-pycryptodome python-pygments python-pyqt-without-qtwebkit python-pyqtwebengine diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 3861c363e7..c0f7778c1c 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -667,7 +667,6 @@ language and very flexible regarding to new or unknown keyboard layouts.") ki18n kiconthemes kitemviews - kqtquickcharts ktextwidgets kwidgetsaddons kwindowsystem diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a92ab71a97..9013e37a54 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -554,6 +554,52 @@ optional baked-in Evil support, antialiased separators, and an easy configuration language which makes it trivial to write your own themes.") (license license:gpl3+)))) +(define-public emacs-inspector + (let ((commit "0e89d28558f57db4519f154bb72ce617a8c6265d") + (revision "0")) + (package + (name "emacs-inspector") + (version (git-version "0.8" revision commit)) + (source + (origin + (uri (git-reference + (url "https://github.com/mmontone/emacs-inspector") + (commit commit))) + (method git-fetch) + (sha256 + (base32 "0n72sqn29b5sya686cicgp40mkk5x5821b7bw4zs6dcl82cyij5n")) + (file-name (git-file-name name version)))) + (build-system emacs-build-system) + (arguments + (list + #:tests? #t + #:test-command #~(list "emacs" "-Q" "--batch" + "-L" "." + "-l" "inspector-tests.el" + "-l" "tree-inspector-tests.el" + "-f" "ert-run-tests-batch-and-exit") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'preserve-emacs-28-compatibility + ;; XXX: `cl-constantly' function is defined in "cl-lib" starting + ;; from Emacs 29+. For now, replace it with its definition. + (lambda _ + (substitute* "tree-inspector.el" + (("cl-constantly") "lambda (_)")))) + (add-before 'check 'skip-failing-test + (lambda _ + (substitute* "tree-inspector-tests.el" + (("\\(ert-deftest inspector-tests--inspect-struct-test.*" all) + (string-append all " (skip-unless nil)")))))))) + (native-inputs (list emacs-ert-runner)) + (propagated-inputs (list emacs-treeview)) + (home-page "https://github.com/mmontone/emacs-inspector") + (synopsis "Inspection tool for Emacs Lisp objects") + (description + "This package provides an introspection tool similar to those found in +Common Lisp or Smalltalk, but for Emacs Lisp.") + (license license:gpl3+)))) + (define-public emacs-terminal-here (package (name "emacs-terminal-here") @@ -576,6 +622,28 @@ Emacs, whose initial working directories are determined in relation to the current buffer.") (license license:gpl3+))) +(define-public emacs-treeview + (let ((commit "d9c10feddf3b959e7b33ce83103e1f0a61162723") + (revision "0")) + (package + (name "emacs-treeview") + (version (git-version "1.1.1" revision commit)) + (source + (origin + (uri (git-reference + (url "https://github.com/tilmanrassy/emacs-treeview") + (commit commit))) + (method git-fetch) + (sha256 + (base32 "14s0b6zbapsvgyxki59lglwb3s8wjsjwkgj5r66af9nj2bgz5ms9")) + (file-name (git-file-name name version)))) + (build-system emacs-build-system) + (home-page "https://github.com/tilmanrassy/emacs-treeview/") + (synopsis "Emacs Lisp framework for tree navigation") + (description + "Abstract Emacs Lisp framework for tree navigation.") + (license license:gpl3+)))) + (define-public emacs-hgignore-mode ;; From 2021-03-14. ;; No releases available. @@ -741,36 +809,31 @@ Emacs package archive}.") (license license:gpl3+))) (define-public emacs-paredit - ;; The last tagged release is from 2014; use the latest commit, which - ;; includes many fixes such as honoring the 'fill-paragraph-function' - ;; variable. - (let ((commit "d0b1a2f42fb47efc8392763d6487fd027e3a2955") - (revision "1")) - (package - (name "emacs-paredit") - (version (git-version "24" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://mumble.net/~campbell/git/paredit.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1x91xxvwb3r3h61ff1kknlaakxm1a40r7zg2lck9j52yiza4f191")))) - (build-system emacs-build-system) - (home-page "http://mumble.net/~campbell/emacs/paredit/") - (synopsis "Emacs minor mode for editing parentheses") - (description - "ParEdit (paredit.el) is a minor mode for performing structured editing + (package + (name "emacs-paredit") + (version "26") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://mumble.net/~campbell/git/paredit.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1hwl2jhv1fhsdrspfhprq77n763i4zsj350q024ajy0m2kaql6ws")))) + (build-system emacs-build-system) + (home-page "http://mumble.net/~campbell/emacs/paredit/") + (synopsis "Emacs minor mode for editing parentheses") + (description + "ParEdit (paredit.el) is a minor mode for performing structured editing of S-expression data. The typical example of this would be Lisp or Scheme source code. -ParEdit helps **keep parentheses balanced** and adds many keys for moving +ParEdit helps keep parentheses balanced and adds many keys for moving S-expressions and moving around in S-expressions. Its behavior can be jarring for those who may want transient periods of unbalanced parentheses, such as when typing parentheses directly or commenting out code line by line.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public emacs-puni ;; No tagged release upstream @@ -826,6 +889,29 @@ of the segments available in that package using icons from information in the mode line.") (license license:expat))) +(define-public emacs-spongebob + (let ((commit "ae8ae6ba0dc57b7357ba87ff0609d27c4a0a5f51") + (revision "0")) + (package + (name "emacs-spongebob") + (version (git-version "0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/dustyweb/spongebob.el") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1agqpp078ij2irn0kb8bgqk0nd47fi20yfd9szn8kbqypfqalvgc")))) + (build-system emacs-build-system) + (home-page "https://gitlab.com/dustyweb/gauche") + (synopsis "Memetically mock a region of text") + (description "This package transforms text using @code{studlify-region} +and inserts a SpongeBob SquarePants ASCII art figure in the current +buffer.") + (license license:gpl3+)))) + (define-public emacs-project (package (name "emacs-project") @@ -2841,6 +2927,34 @@ like. It can be linked with various Emacs mail clients (Message and Mail mode, Rmail, Gnus, MH-E, and VM). BBDB is fully customizable.") (license license:gpl3+))) +(define-public emacs-bbdb-vcard + ;; No release since Dec 1, 2013. + (let ((version "0.4.1") ;3d79fdb4200a64a043e203a3baac95c936095b52, not tagged + (revision "88") + (commit "113c66115ce68316e209f51ebce56de8dded3606")) + (package + (name "emacs-bbdb-vcard") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tohojo/bbdb-vcard") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1sr5kd2gvw1b4hl147yb60cgx6j730vdnpyr09p7vmpw65hzwlwm")))) + (build-system emacs-build-system) + (propagated-inputs (list emacs-bbdb)) + (home-page "https://github.com/tohojo/bbdb-vcard") + (synopsis + "vCard Import and Export for The Insidious Big Brother Database (BBDB)") + (description + "@code{bbdb-vcard.el} imports and exports vCards (version 3.0) as +defined in RFC 2425 and RFC 2426 to/from The Insidious Big Brother Database +(BBDB). Version 2.1 vCards are converted into version 3.0 on import.") + (license license:gpl2+)))) + (define-public emacs-beacon (package (name "emacs-beacon") @@ -3439,7 +3553,7 @@ of bibliographic references.") (define-public emacs-corfu (package (name "emacs-corfu") - (version "0.28") + (version "0.33") (source (origin (method git-fetch) @@ -3448,7 +3562,7 @@ of bibliographic references.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0lmjmaijanhhimkd006y5g1pvpllqgm30wj2y3wf3h4sl7h23rcz")))) + (base32 "0c353k6f4i96gajfw1zvidhlwr2brnhhdr39503hpa5wnp69wak7")))) (build-system emacs-build-system) (arguments `(#:phases @@ -3496,7 +3610,7 @@ be regarded as @code{emacs-company-quickhelp} for @code{emacs-corfu}.") (define-public emacs-cape (package (name "emacs-cape") - (version "0.10") + (version "0.11") (source (origin (method git-fetch) @@ -3505,7 +3619,7 @@ be regarded as @code{emacs-company-quickhelp} for @code{emacs-corfu}.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0kcnyzksj8yglk67g1130wxzscgipm7cz2hs8mvdqpcbz4i38jny")))) + (base32 "0z6ixw7gsx1g7x2xpj5ilslrjrlp6x2ynzh731hs3yf3n281715b")))) (build-system emacs-build-system) (home-page "https://github.com/minad/cape") (synopsis "Completion at point extensions for Emacs") @@ -4626,7 +4740,6 @@ which is restored where possible when the file is loaded again.") (build-system emacs-build-system) (arguments `(#:tests? #t - #:emacs ,emacs ; FIXME: tests fail with emacs-minimal #:test-command '("./run-tests.sh"))) (home-page "https://github.com/magnars/s.el") (synopsis "Emacs string manipulation library") @@ -4999,6 +5112,28 @@ at the current line number or active region. @code{git-link-commit} returns the URL for a commit. URLs are added to the kill ring.") (license license:gpl3+))) +(define-public emacs-frowny + (package + (name "emacs-frowny") + (version "0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/duckwork/frowny.el") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "01ss3js71as1jpqcf0x9hfvapiyyhj9ni4y1n6wvqsghv5dcaiy0")))) + (build-system emacs-build-system) + (home-page "https://github.com/duckwork/frowny.el") + (synopsis "Insert frownies in Emacs :(") + (description "This package ships @code{frowny-mode}, which makes it so that +inserting a single @code{(} when after a @code{:} will not automatically close +the parenthesis, meaning that only @code{:(} is inserted. Works with +@code{electric-pair-mode}, @code{paredit-mode}, and others.") + (license license:public-domain))) + (define-public emacs-apache-mode (package (name "emacs-apache-mode") @@ -6010,6 +6145,30 @@ allrecipes.com.") inline PDF preview in Org buffers by using pdf2svg.") (license license:gpl3+))) +(define-public emacs-org-rainbow-tags + ;; Upstream didn't tag version. + (let ((commit "c6040d228c5e8c5c6d33c7f81fc09d935ad1bcbd")) + (package + (name "emacs-org-rainbow-tags") + (version "0.1-pre") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/KaratasFurkan/org-rainbow-tags") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "006nx01sby8k0fc9lf63ldf0sl94ihldyrvqr9r18fb1gpzvivl6")))) + (build-system emacs-build-system) + (home-page "https://github.com/KaratasFurkan/org-rainbow-tags") + (synopsis "Colorize Org tags automatically") + (description + "This package adds random colors to your Org tags. In order to make +colors random but consistent between same tags, colors are generated from the +hash of the tag names.") + (license license:gpl3+)))) + (define-public emacs-org-rich-yank (package (name "emacs-org-rich-yank") @@ -6105,10 +6264,10 @@ blocks with @code{org-babel} in @code{org-mode}.") (license license:gpl3+)))) (define-public emacs-ob-restclient - (let ((commit "f7449b2068498fe9d8ab9589e0a638148861533f")) + (let ((commit "1b021ce1c67c97fa1aa4d2c0816edb7add129e48")) (package (name "emacs-ob-restclient") - (version (git-version "0.02" "2" commit)) + (version (git-version "0.02" "3" commit)) (source (origin (method git-fetch) @@ -6117,7 +6276,7 @@ blocks with @code{org-babel} in @code{org-mode}.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0s3931w9ab3yfml2pmq71rw21yf6hpg7m3vihxyy3vs6zli1cvmq")))) + (base32 "1bcjj01q5n9w2cch6brbz8pzwnwsmdlgaa4sf5s97b9frmqb2ffg")))) (propagated-inputs (list emacs-restclient)) (build-system emacs-build-system) @@ -6930,7 +7089,7 @@ files which are intended to be packages.") (source (origin (method git-fetch) (uri (git-reference - (url "https://git.sr.ht/~manuel-uberti/flycheck-proselint") + (url "https://git.sr.ht/~manuel-uberti/flymake-proselint") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -6947,11 +7106,9 @@ files which are intended to be packages.") (("\"proselint\"") (string-append "\"" (search-input-file inputs "/bin/proselint") "\"")))))))) - (propagated-inputs - (list emacs-flycheck)) (inputs (list python-proselint)) - (home-page "https://git.sr.ht/~manuel-uberti/flycheck-proselint") + (home-page "https://git.sr.ht/~manuel-uberti/flymake-proselint") (synopsis "Flymake backend for @code{proselint}") (description "This package adds support for @code{proselint} in Flymake.") (license license:gpl3+)))) @@ -10990,10 +11147,36 @@ keybinding style. The provided commands allow for editing Lisp in normal state and will work even without lispy being enabled.") (license license:gpl3+)))) +(define-public emacs-function-args + ;; The latest release is from August 21, 2017. + (let ((commit "beba049751fed78666c87bd146a6f1cf149bb819") + (revision "0")) + (package + (name "emacs-function-args") + (version (git-version "0.6.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/abo-abo/function-args") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1vxrjy6k030hcbclblgcaaw7h6k17kl3n9zla08527525c0gma01")))) + (build-system emacs-build-system) + (propagated-inputs (list emacs-ivy)) + (home-page "https://github.com/abo-abo/function-args") + (synopsis "C/C++ completion for GNU Emacs") + (description + "This package provides a way of showing an inline arguments hint for +the C/C++ function at point.") + (license license:gpl3+)))) + (define-public emacs-lpy ;; There is no proper release/tag. - (let ((commit "ce78a4613458790cc785c1687af7eed8f0d8d66c") - (revision "5")) + (let ((commit "fa95b11e1023704510cc7dd2897bf8bcc3027cbb") + (revision "6")) (package (name "emacs-lpy") (version (git-version "0.1.0" revision commit)) @@ -11003,13 +11186,13 @@ state and will work even without lispy being enabled.") (uri (git-reference (url "https://github.com/abo-abo/lpy") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 - "1vxrjy6k030hcbclblgcaaw7h6k17kl3n9zla08527525c0gma01")) - (file-name (git-file-name name version)))) - (propagated-inputs - (list emacs-zoutline emacs-lispy)) + "1j92ll2afvcp891fxra3sawxg000cs3ra01wxksiil2dg5zpzzkn")))) (build-system emacs-build-system) + (propagated-inputs + (list emacs-function-args emacs-lispy emacs-zoutline)) (home-page "https://github.com/abo-abo/lpy") (synopsis "Modal editing for Python") (description @@ -11763,26 +11946,40 @@ like @code{org-edit-src-code} but for arbitrary regions.") (define-public emacs-projectile (package (name "emacs-projectile") - (version "2.6.0") - (source (origin - (method url-fetch) - (uri (string-append "https://raw.githubusercontent.com/bbatsov" - "/projectile/v" version "/projectile.el")) - (file-name (string-append "projectile-" version ".el")) - (sha256 - (base32 - "12crymgri4sg7fvnh692f96cm0krmmcnz6x3ypxgq8da84rl34p4")))) + (version "2.7.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bbatsov/projectile") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ybd41iss8vd56qv6czpxqq7a99s4h7i3a2r4khy4rf5blj5zdqi")))) (build-system emacs-build-system) + (arguments + (list + #:tests? #t + #:test-command #~(list "buttercup" "-L" ".") + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'fix-failing-test + (lambda _ + (substitute* "test/projectile-test.el" + (("user-emacs-directory") "\".\""))))))) + (native-inputs + (list emacs-buttercup)) (propagated-inputs (list emacs-dash emacs-pkg-info)) (home-page "https://github.com/bbatsov/projectile") (synopsis "Manage and navigate projects in Emacs easily") (description "This library provides easy project management and navigation. The -concept of a project is pretty basic - just a folder containing special file. -Currently git, mercurial and bazaar repos are considered projects by default. -If you want to mark a folder manually as a project just create an empty -.projectile file in it.") +concept of a project is pretty basic: just a folder containing special file. +Currently Git, Mercurial and Bazaar repositories are considered projects by +default. If you want to mark a folder manually as a project just create an +empty @file{.projectile} file in it.") (license license:gpl3+))) (define-public emacs-skeletor @@ -13325,6 +13522,30 @@ Lua programming language}.") news items, openrc and runscripts.") (license license:gpl2+))) +(define-public emacs-ebuku + ;; Upstream has no tagged release. + (let ((revision "1") + (commit "0c6cf404a49bd68800221446df186fffa0139325")) + (package + (name "emacs-ebuku") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/flexibeast/ebuku") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "09fkzmcvzdbdjaa167wiybj0kir7y12pcq2varjywshvq2l7niz4")))) + (build-system emacs-build-system) + (home-page "https://github.com/flexibeast/ebuku") + (synopsis "Emacs interface to the buku Web bookmark manager") + (description + "Ebuku provides a basic interface to the @code{buku} Web bookmark +manager.") + (license license:gpl3+)))) + (define-public emacs-evil ;; Commit message claims this is 1.15.0, but there's no tag for it, so we ;; use full git-version instead @@ -16623,6 +16844,26 @@ for the current file, using the major mode as a hint. It prompts you to enter one if it fails.") (license license:gpl3+))) +(define-public emacs-jarchive + (package + (name "emacs-jarchive") + (version "0.8.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.sr.ht/~dannyfreeman/jarchive") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1fi3y5kmy7ginyqg12q797bma638xmam7lrk74x6yhx84xgzb4fq")))) + (build-system emacs-build-system) + (home-page "https://sr.ht/~dannyfreeman/jarchive") + (synopsis "Jarchive teaches Emacs how to navigate to files inside JARs") + (description "Jarchive makes Emacs handle Java and LSP URIs pointing to + source inside JARs.") + (license license:gpl3+))) + (define-public emacs-eldoc (package (name "emacs-eldoc") @@ -16929,9 +17170,9 @@ formatting, and utility methods for jsonnet files.") (license license:gpl3+))) (define-public emacs-restclient - (let ((commit "ac8aad6c6b9e9d918062fa3c89c22c2f4ec48bc3") + (let ((commit "1fb570643b08ba66eb70831b6f874f52546917f1") (version "0") - (revision "3")) ;Guix package revision, + (revision "4")) ;Guix package revision, ;upstream doesn't have official releases (package (name "emacs-restclient") @@ -16943,7 +17184,7 @@ formatting, and utility methods for jsonnet files.") (commit commit))) (sha256 (base32 - "1a2c7xzy7rsan1zcdskia6m7n6j29xacfkqjlfdhzk6rr1bpzkwk")) + "0npij1p1yw4p1f1yrx6bl8q18nav5p2xvbp7qhzhn7lb2fdn5jqv")) (file-name (git-file-name name version)))) (build-system emacs-build-system) (propagated-inputs @@ -19336,7 +19577,7 @@ match and total match information in the mode-line in various search modes.") (define-public emacs-pg (package (name "emacs-pg") - (version "0.16") + (version "0.19") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/emarsden/pg-el") @@ -19344,7 +19585,7 @@ match and total match information in the mode-line in various search modes.") (file-name (git-file-name name version)) (sha256 (base32 - "1jdnslpgdm16klaga02p33g7c8bjzg164kxz3jd7gs5v9gqa6ppz")))) + "13fkkpimhxh91hmsp551wzrdcic5ws7wj7vjwnh8l83hsrxmxz0y")))) (build-system emacs-build-system) (home-page "https://github.com/emarsden/pg-el") (synopsis "Emacs Lisp interface for PostgreSQL") @@ -19940,7 +20181,7 @@ according to a parsing expression grammar.") (define-public emacs-eldev (package (name "emacs-eldev") - (version "1.2.2") + (version "1.3") (source (origin (method git-fetch) @@ -19949,7 +20190,7 @@ according to a parsing expression grammar.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0d6wbfim0q81sm5m45fjc6n0v6nk32qrgas5nzrs0vslym4bfxna")))) + (base32 "112jv9rz6brglffwsablnhafhhnfnq89k9vh8xzbbi6i4xz2l1ak")))) (build-system emacs-build-system) (arguments (list @@ -20791,8 +21032,8 @@ never confused by comments or @code{foo-bar} matching @code{foo}.") (define-public emacs-crdt ;; XXX: Upstream does not always tag new releases. The commit below ;; corresponds exactly to latest version bump. - (let ((commit "92a7c93a3b4cb4b40f133acd22c89a5fda5cdd30") - (version "0.3.4")) + (let ((commit "e6d42f42c5dedb73560048f4bf6263c63ffa21bb") + (version "0.3.5")) (package (name "emacs-crdt") (version version) @@ -20804,7 +21045,7 @@ never confused by comments or @code{foo-bar} matching @code{foo}.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1vh4d15g62crm4vimc7lgr11ws68g25ylipnvqlrrkvl6qrz3fhj")))) + (base32 "16dpg0d8p4fqjl2nir290iim9bb7f87rwnxs16lx67dasvbfawph")))) (build-system emacs-build-system) (home-page "https://code.librehq.com/qhong/crdt.el") (synopsis "Real-time collaborative editing environment") @@ -21021,22 +21262,22 @@ or expressions with SVG rounded box labels that are fully customizable.") (define-public emacs-kind-icon (package (name "emacs-kind-icon") - (version "0.1.7") + (version "0.1.9") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/kind-icon-" version ".tar")) (sha256 - (base32 "02imi2qj329yrqvs23d4z7fv8bbaz0fvya6zdswb38blpdri4cn1")))) + (base32 "0phssrcpmcidzlwy1577f3f02qwjs6hpavb416302y0n8kkhwvli")))) (build-system emacs-build-system) (propagated-inputs (list emacs-svg-lib)) (home-page "https://github.com/jdtsmith/kind-icon") (synopsis "Completion kind icons in Emacs") - (description "Kind-icon mode adds a colorful icon or text prefix based -on :company-kind for compatible completion UIs. The \"kind\" prefix is -typically used for differentiating completion candidates such as variables, -functions, etc.") + (description "Kind-icon mode adds a colorful icon or text prefix based on +@code{:company-kind} for compatible completion UIs. The ``kind'' prefix is +typically used for differentiating completion candidates such as variables or +functions.") (license license:gpl3+))) (define-public emacs-svg-icon @@ -22589,6 +22830,29 @@ It replaces the standard completions buffer with Ido prompt.") using user-provided rules.") (license license:gpl3+))) +(define-public emacs-on + (let ((commit "83baed07a105c135190d49d7ec77f95e8f38fa54") + (revision "0")) + (package + (name "emacs-on") + (version (git-version "0.1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ajgrf/on.el") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "14ly3w89hf4jgd8wacirxgd8vrgj7vc0hpfn911w5wa4k2a6nzpp")))) + (build-system emacs-build-system) + (home-page "https://github.com/ajgrf/on.el") + (synopsis "Hooks for faster Emacs startup") + (description + "This package exposes a number of utility hooks and functions ported +from Doom Emacs.") + (license license:expat)))) + (define-public emacs-on-screen (package (name "emacs-on-screen") @@ -26123,7 +26387,7 @@ according to their use.") (define-public emacs-detached (package (name "emacs-detached") - (version "0.9.2") + (version "0.10.1") (source (origin (method git-fetch) (uri (git-reference @@ -26132,7 +26396,7 @@ according to their use.") (file-name (git-file-name name version)) (sha256 (base32 - "0bcrqqim6is75d4zadswxp162m9gd34xmb2wxsx9rhvkwq0ln35k")))) + "0dvvyqc0nw9has54vps10f5iv831cb29vqvbvx0m2djv9pacqp17")))) (arguments (list #:tests? #t @@ -28607,8 +28871,7 @@ between \"frame-width\" and \"frame-height\", between \"public\", (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/ediprolog-" - version - ".el")) + version ".tar")) (sha256 (base32 "021jm5zdxrjg7xcja18vgc2v52rk17xi1k7xxw8q802nmixhy0js")))) (build-system emacs-build-system) @@ -30140,39 +30403,40 @@ service, and connect it with Emacs via inter-process communication.") (name "emacs-telega") (build-system emacs-build-system) (arguments - `(#:emacs ,(if (target-64bit?) - emacs-minimal - ;; Require wide-int support for 32-bit platform. - emacs-wide-int) - #:include (cons "^etc\\/" %default-include) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-sources - (lambda* (#:key inputs #:allow-other-keys) - ;; Hard-code paths to `ffplay` and `ffmpeg`. - (let* ((ffplay-bin (search-input-file inputs "/bin/ffplay")) - (ffmpeg-bin (search-input-file inputs "/bin/ffmpeg"))) - (substitute* '("telega-ffplay.el" "telega-vvnote.el") - (("(shell-command-to-string\|concat) \"(ffmpeg\|ffprobe)" - all func cmd) - (string-append func " \"" - (search-input-file - inputs (string-append "/bin/" cmd)))) - (("\\(executable-find \"ffplay\"\\)") - (string-append "(and (file-executable-p \"" ffplay-bin "\")" - "\"" ffplay-bin "\")")) - (("\\(executable-find \"ffmpeg\"\\)") - (string-append "(and (file-executable-p \"" ffmpeg-bin "\")" - "\"" ffmpeg-bin "\")")))))) - (add-after 'unpack 'configure - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* "telega-customize.el" - (("@TELEGA_SERVER_BIN@") - (search-input-file inputs "/bin/telega-server"))) - (substitute* "telega-util.el" - (("@TELEGA_SHARE@") - (string-append (elpa-directory (assoc-ref outputs "out")) - "/etc")))))))) + (list + #:emacs (if (target-64bit?) + emacs-minimal + ;; Require wide-int support for 32-bit platform. + emacs-wide-int) + #:include #~(cons "^etc\\/" %default-include) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-sources + (lambda* (#:key inputs #:allow-other-keys) + ;; Hard-code paths to `ffplay` and `ffmpeg`. + (let* ((ffplay-bin (search-input-file inputs "/bin/ffplay")) + (ffmpeg-bin (search-input-file inputs "/bin/ffmpeg"))) + (substitute* '("telega-ffplay.el" "telega-vvnote.el") + (("(shell-command-to-string\|concat) \"(ffmpeg\|ffprobe)" + all func cmd) + (string-append func " \"" + (search-input-file + inputs (string-append "/bin/" cmd)))) + (("\\(executable-find \"ffplay\"\\)") + (string-append "(and (file-executable-p \"" ffplay-bin "\")" + "\"" ffplay-bin "\")")) + (("\\(executable-find \"ffmpeg\"\\)") + (string-append "(and (file-executable-p \"" ffmpeg-bin "\")" + "\"" ffmpeg-bin "\")")))))) + (add-after 'unpack 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "telega-customize.el" + (("@TELEGA_SERVER_BIN@") + (search-input-file inputs "/bin/telega-server"))) + (substitute* "telega-util.el" + (("@TELEGA_SHARE@") + (string-append (elpa-directory (assoc-ref outputs "out")) + "/etc")))))))) (inputs (list emacs-telega-server ffmpeg)) (native-inputs '()) @@ -30188,13 +30452,14 @@ for the Telegram messaging platform."))) (inherit emacs-telega) (name "emacs-telega-contrib") (arguments - `(#:exclude '("telega-live-location.el") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'enter-subdirectory - (lambda _ (chdir "contrib") #t)) - (add-before 'install-license-files 'leave-subdirectory - (lambda _ (chdir "..") #t))))) + (list + #:exclude #~(list "telega-live-location.el") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'enter-subdirectory + (lambda _ (chdir "contrib"))) + (add-before 'install-license-files 'leave-subdirectory + (lambda _ (chdir "..")))))) (inputs '()) (native-inputs '()) (propagated-inputs @@ -31944,6 +32209,31 @@ ASCII UML sequence diagrams in Emacs, which can be embedded in source code, comments or emails.") (license license:gpl3+)))) +(define-public emacs-ukrainian-holidays + ;; There is no proper release. + ;; The base version is extracted from the source code. + (let ((revision "0") + (commit "e52b0c92843e9f4d0415a7ba3b8559785497d23d")) + (package + (name "emacs-ukrainian-holidays") + (version (git-version "1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri + (git-reference + (url "https://github.com/abo-abo/ukrainian-holidays") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "033v4ck979lhkpwblci5clacfc1xnkq03p5d1m566wff8dp5flwz")))) + (build-system emacs-build-system) + (home-page "https://github.com/abo-abo/ukrainian-holidays") + (synopsis "Ukrainian holidays for Emacs calendar") + (description + "This package provides Ukrainian holidays for Emacs calendar.") + (license license:gpl3+)))) + (define-public emacs-trashed (package (name "emacs-trashed") @@ -32723,14 +33013,14 @@ work on alists, hash-table and arrays. All functions are prefixed with (define-public emacs-xref (package (name "emacs-xref") - (version "1.5.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/xref-" version ".tar")) (sha256 - (base32 "131jxsc1sl8q3r9drhylwyfig9qjjkj3hilv3npidp868pr7xdna")))) + (base32 "0vqs2l4gypdx475yi0yic0mnsg1f9nm698gi90kh7xfcpmkfcgb4")))) (build-system emacs-build-system) (home-page "http://elpa.gnu.org/packages/xref.html") (synopsis "Cross-referencing commands") @@ -32910,7 +33200,7 @@ and preferred services can easily be configured.") (define-public emacs-vertico (package (name "emacs-vertico") - (version "0.28") + (version "0.29") (source (origin (method git-fetch) @@ -32919,7 +33209,7 @@ and preferred services can easily be configured.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0yybwj32k74c5c4rzlpmkq540b8ax0ihn5v7krnri83wn50hr272")))) + (base32 "0gqfq7yni470yys9blarmsinjgf1025azlr09g1842w20hwrs7hc")))) (build-system emacs-build-system) (arguments `(#:phases @@ -33414,7 +33704,7 @@ Fennel code within Emacs.") (define-public emacs-org-modern (package (name "emacs-org-modern") - (version "0.5") + (version "0.6") (source (origin (method git-fetch) @@ -33422,7 +33712,7 @@ Fennel code within Emacs.") (url "https://github.com/minad/org-modern") (commit version))) (sha256 - (base32 "1gny2p3w6ck5sarv6vap2y1lj6h9qaxbh7r7bzszb9qj8rhapk6q")) + (base32 "03zpwb475rpbhq1s6101clj0j9mcxdg033clvvybp0p7hm4inwaz")) (file-name (git-file-name name version)))) (build-system emacs-build-system) (home-page "https://github.com/minad/org-modern") @@ -33471,8 +33761,8 @@ headlines, keywords, tables and source blocks.") (license license:gpl3+)))) ; License is in pyimport.el (define-public emacs-straight-el - (let ((commit "fed215348076ba9182f634e0770a175220474b5a") - (revision "0")) + (let ((commit "f21103d97d180fba0b6e2e86ebb0b6269219ef2c") + (revision "1")) (package (name "emacs-straight-el") (version (git-version "0" revision commit)) @@ -33485,7 +33775,7 @@ headlines, keywords, tables and source blocks.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0z0j670s18mp1bhrsnng0mybcbnlywarhlz7zmrf9399rr513z1x")))) + (base32 "1dqhb7kx4hr3cm4gj6qdk9aav05vc016y4nks2dj1sy88wia6wsv")))) (build-system emacs-build-system) (arguments (list @@ -33622,7 +33912,7 @@ with popups, which also work in the terminal.") (define-public emacs-popon (package (name "emacs-popon") - (version "0.11") + (version "0.12") (source (origin (method git-fetch) @@ -33632,7 +33922,7 @@ with popups, which also work in the terminal.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "14hf1n9d7rqfzr58kjsvjq63v3iamk3szvcn6zms7ry8x70v3lmv")))) + (base32 "0wkydg326ql8cvvmibq1nf6y40d1b0ax0p892pwncmi7awnf20gr")))) (build-system emacs-build-system) (home-page "https://codeberg.org/akib/emacs-popon/") (synopsis "Pop floating text on a window") @@ -33828,16 +34118,16 @@ into the current buffer.") (revision "0")) (package (name "emacs-flymake-mypy") - (version (git-version "0.2.0" revision commit)) + (version "0.3.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/com4/flymake-mypy") - (commit commit))) + (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "124pfa1kwrapwylbrvkzg3jwcmlsvfklg33ms9ki32khvglmff5h")))) + "1zaa2kljsmm13layqmb7dwd7l2x3a5ymzzmzjjhykc67kbyjvvkk")))) (build-system emacs-build-system) (home-page "https://github.com/com4/flymake-mypy") (synopsis "Flymake checker for mypy") @@ -33881,6 +34171,187 @@ using mypy.") process via its IPC interface.") (license license:gpl3+)))) +(define-public emacs-apel-lb + ;; No release since Jun 15, 2010. + (let ((version "10.8") ;tag chise-base-0_25 + (revision "81") + (commit "82eb2325bd149dc57b43a9ce9402c6c6183e4052")) + (package + (name "emacs-apel-lb") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wanderlust/apel") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0qiw19pn1cs8y571irw7bjdygkvwan9ch2i1dg139dri4b6q1il6")))) + (build-system emacs-build-system) + (home-page "https://www.emacswiki.org/emacs/WanderLust") + (synopsis "Library for making portable Emacs Lisp programs") + (description + "A Portable Emacs Library (APEL) is a library for making portable Emacs +Lisp programs. APEL-LB is a variant of APEL, which features supports to +latest Emacs.") + (license license:gpl2+)))) + +(define-public emacs-flim-lb + ;; No release since Nov 28, 2007. + (let ((version "1.14.9") + (revision "133") + (commit "57c6b868aa314717f40a520daed7249665e8d992")) + (package + (name "emacs-flim-lb") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wanderlust/flim") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mf8r5mf3bd0719fnhifb6lfvl7n4m552crcdhkbkkif8srrl6df")))) + (build-system emacs-build-system) + (propagated-inputs (list emacs-apel-lb emacs-oauth2)) + (home-page "https://www.emacswiki.org/emacs/WanderLust") + (synopsis + "Library for basic features about message representation or encoding") + (description + "FLIM is a library to provide basic features about message representation +or encoding. FLIM-LB is a variant of FLIM, which features supports to latest +Emacs.") + (license license:gpl2+)))) + +(define-public emacs-semi-epg + ;; No release since Dec 24, 2003. + (let ((version "1.14.6") + (revision "241") + (commit "ac3e726ca94ed245c25881ec8d7177d0d834ea6a")) + (package + (name "emacs-semi-epg") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wanderlust/semi") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1bg07y6svvg1mmlr455x3j1anjp3wbv27s6b2inp294rbwprm41n")))) + (build-system emacs-build-system) + (propagated-inputs (list emacs-bbdb-vcard emacs-flim-lb)) + (home-page "https://www.emacswiki.org/emacs/WanderLust") + (synopsis "Library to provide MIME feature for GNU Emacs") + (description + "SEMI is a package for GNU Emacs to provide features related with MIME +user interface. SEMI-EPG is a variant of SEMI, which features supports to +EasyPG and latest Emacs.") + (license license:gpl2+)))) + +(define-public emacs-wanderlust + ;; No release since Jan 15, 2010. + ;; FIXME: Building with emacs-next-pgtk would yield a void variable related + ;; macro-expansion failure at runtime, so don't rewrite emacs input of this + ;; package. + (let ((version "2.15.9") + (revision "779") + (commit "f5cb2f0cf5e2c893acf2e669fd549836828dfdfc")) + (package + (name "emacs-wanderlust") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wanderlust/wanderlust") + (commit commit))) + (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet + '(begin (substitute* "WL-CFG" + ((".*WL_PREFIX.*") + (string-append "(setq wl-install-utils t)" "\n" + "(setq WL_PREFIX \"\")" "\n" + "(setq ELMO_PREFIX \"\")" "\n"))) + (substitute* "Makefile" + (("package-user-dir") "NONE")))) + (sha256 + (base32 + "1ijs57wv1vrh33vn311hgkp42vlmjyi998nc4qdrqi7yy9j8hl1h")))) + (build-system emacs-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'expand-load-path 'chdir-elmo + (lambda _ + (chdir "elmo"))) + (add-after 'chdir-elmo 'expand-load-path-elmo + (assoc-ref %standard-phases 'expand-load-path)) + (add-after 'expand-load-path-elmo 'chdir-utils + (lambda _ + (chdir "../utils"))) + (add-after 'chdir-utils 'expand-load-path-utils + (assoc-ref %standard-phases 'expand-load-path)) + (add-after 'expand-load-path-utils 'chdir-wl + (lambda _ + (chdir "../wl"))) + (add-after 'chdir-wl 'expand-load-path-wl + (assoc-ref %standard-phases 'expand-load-path)) + (add-after 'expand-load-path-wl 'change-directory + (lambda _ + (chdir ".."))) + (add-after 'install 'install-via-makefile + (lambda* (#:key inputs #:allow-other-keys) + (let ((emacs (search-input-file inputs "/bin/emacs")) + (lispdir (elpa-directory #$output)) + (infodir (string-append #$output "/share/info"))) + (for-each mkdir-p (list lispdir infodir)) + (substitute* "Makefile" + (("(EMACS\t= )emacs" all m) + (string-append m emacs)) + (("(LISPDIR = )NONE" all m) + (string-append m lispdir)) + (("(PIXMAPDIR = )NONE" all m) + (string-append m lispdir "/icons")) + (("(INFODIR = )NONE" all m) + (string-append m infodir)))) + (invoke "make" "install") + (invoke "make" "install-info")))))) + (propagated-inputs (list emacs-semi-epg)) + (home-page "https://www.emacswiki.org/emacs/WanderLust") + (synopsis "Yet Another Message Interface on Emacsen") + (description + "Wanderlust is an mail/news management system on Emacsen. It supports +IMAP4rev1(RFC2060), NNTP, POP and local message files. + +The main features of Wanderlust: + +@itemize +@item Pure elisp implementation. +@item Supports IMAP4rev1, NNTP, POP(POP3/APOP), MH and Maildir format. +@item Unified access method to messages based on Mew-like Folder Specification. +@item Mew-like Key-bind and mark handling. +@item Manages unread messages. +@item Interactive thread display. +@item Folder Mode shows the list of subscribed folders. +@item Message Cache, Disconnected Operation. +@item MH-like FCC (Fcc: %Backup and Fcc: $Backup is allowed). +@item MIME compliant (by SEMI). +@item Transmission of news and mail are unified by Message transmitting draft. +@item Graphical list of folders. +@item View a part of message without retrieving the whole message (IMAP4). +@item Server-side message look up (IMAP4), multi-byte characters are allowed. +@item Virtual Folders. +@item Supports compressed folder using common archiving utilities. +@item Old articles in folders are automatically removed/archived (Expiration). +@item Automatic re-file. +@item Template function makes it convenient to send fixed form messages. +@end itemize\n") + (license license:gpl2+)))) + (define-public emacs-waveform ;; XXX: Upstream provides no Version keyword. Using 0 as base version. (let ((commit "ee52c6a72b3e9890743e3a6e2fc1f3195f5687b2") diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 21569b07c9..43e23e30a8 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -3310,7 +3310,7 @@ visualization, matrix manipulation.") (define-public prusa-slicer (package (name "prusa-slicer") - (version "2.4.2") + (version "2.5.0") (source (origin (method git-fetch) @@ -3319,7 +3319,7 @@ visualization, matrix manipulation.") (url "https://github.com/prusa3d/PrusaSlicer") (commit (string-append "version_" version)))) (file-name (git-file-name name version)) - (sha256 (base32 "17p56f0zmiryy8k4da02in1l6yxniz286gf9yz8s1gaz5ksqj4af")) + (sha256 (base32 "17ic92ww2ny0frxyv7ajwdwa0fq70ygq562ik8sh94jx67jvxdy0")) (modules '((guix build utils))) (snippet '(begin @@ -3368,10 +3368,12 @@ visualization, matrix manipulation.") hidapi ilmbase libigl + libjpeg-turbo libpng mesa mpfr nlopt + opencascade-occt openvdb pango tbb diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index c8f3ee9d1d..feb533eca7 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -129,10 +129,10 @@ #:use-module (gnu packages xml) #:use-module (gnu packages gnuzilla)) -(define-public bitcoin-core-0.21 +(define-public bitcoin-core-23.0 (package (name "bitcoin-core") - (version "0.21.2") + (version "23.0") (source (origin (method url-fetch) (uri @@ -140,7 +140,7 @@ version "/bitcoin-" version ".tar.gz")) (sha256 (base32 - "17nvir1yc6mf4wr1fn4xsabw49cd5p9vig8wj77vv4anzi8zfij1")))) + "01fcb90pqip3v77kljykx51cmg7jdg2cmp7ys0a40svdkps8nx16")))) (build-system gnu-build-system) (native-inputs (list autoconf @@ -207,23 +207,10 @@ of the bitcoin protocol. This package provides the Bitcoin Core command line client and a client based on Qt.") (license license:expat))) -(define-public bitcoin-core-0.20 - (package - (inherit bitcoin-core-0.21) - (version "0.20.2") - (source (origin - (method url-fetch) - (uri - (string-append "https://bitcoincore.org/bin/bitcoin-core-" - version "/bitcoin-" version ".tar.gz")) - (sha256 - (base32 - "14smp5vmh7baabl856wlg7w7y5910jhx6c02mlkm4hkywf3yylky")))))) - ;; The support lifetimes for bitcoin-core versions can be found in ;; <https://bitcoincore.org/en/lifecycle/#schedule>. -(define-public bitcoin-core bitcoin-core-0.21) +(define-public bitcoin-core bitcoin-core-23.0) (define-public hledger (package @@ -553,7 +540,7 @@ do so.") (define-public electrum (package (name "electrum") - (version "4.2.1") + (version "4.3.2") (source (origin (method url-fetch) @@ -561,7 +548,7 @@ do so.") version "/Electrum-" version ".tar.gz")) (sha256 - (base32 "0w41411zq07kx0351wxkmpn0wr42wd2nx0m6v0iwvpsggx654b6r")) + (base32 "1kbyinm9fnxpx9chkyd11yr9rxvcxvw3ml7kzvxcfa8v7jnl0dmx")) (modules '((guix build utils))) (snippet '(begin @@ -628,7 +615,7 @@ other machines/servers. Electrum does not download the Bitcoin blockchain.") (define-public electron-cash (package (name "electron-cash") - (version "4.2.11") + (version "4.2.12") (source (origin (method git-fetch) @@ -637,7 +624,7 @@ other machines/servers. Electrum does not download the Bitcoin blockchain.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1g0xnb63c52l379zrqkfhxlkg1d2hf2dgjs2swspa0vah845r282")))) + (base32 "1bfnfpdyi3q5zq0zj07dq82aj3cihnr7j82gy4ch97182lsl6nms")))) (build-system python-build-system) (arguments (list @@ -2134,7 +2121,7 @@ and manipulation.") (define-public xmrig (package (name "xmrig") - (version "6.18.0") + (version "6.18.1") (source (origin (method git-fetch) @@ -2142,7 +2129,7 @@ and manipulation.") (url "https://github.com/xmrig/xmrig") (commit (string-append "v" version)))) (file-name (git-file-name name version)) - (sha256 (base32 "1ncnfjpjwjdv29plyiam2nh01bfni49sgfi3qkijygi1450w71dx")) + (sha256 (base32 "0f0kly374pkgnpnx60hac0bg9297a5zhycss6p37iavayn28jg39")) (modules '((guix build utils))) (snippet ;; TODO: Try to use system libraries instead of bundled ones in @@ -2190,7 +2177,7 @@ mining.") (define-public p2pool (package (name "p2pool") - (version "2.2.1") + (version "2.5") (source (origin (method git-fetch) @@ -2199,7 +2186,7 @@ mining.") (commit (string-append "v" version)) (recursive? #t))) (file-name (git-file-name name version)) - (sha256 (base32 "19pn7axj96yvza2x7678rs79c2vgmhl8d7f9ki72v2n6l2630fw8")) + (sha256 (base32 "1kdsxh6f24zp7h7bwkrin2mc81ysfny5wprzgy41h2bc6dpq067w")) (modules '((guix build utils))) (snippet #~(for-each delete-file-recursively diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 696814cc71..e9bb3ed450 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2017 David Craven <david@craven.ch> -;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2017, 2018, 2022 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Vagrant Cascadian <vagrant@debian.org> ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com> @@ -259,19 +259,11 @@ driver.") help2man gettext-minimal)) (inputs (list bash-completion - glib libgudev libxmlb - gusb sqlite - libarchive - libjcat - json-glib - curl polkit eudev - gcab - gnutls libelf tpm2-tss cairo @@ -281,6 +273,15 @@ driver.") mingw-w64-tools libsmbios gnu-efi)) + ;; In Requires of fwupd*.pc. + (propagated-inputs (list curl + gcab + glib + gnutls + gusb + json-glib + libarchive + libjcat)) (home-page "https://fwupd.org/") (synopsis "Daemon to allow session software to update firmware") (description "This package aims to make updating firmware on GNU/Linux @@ -644,7 +645,7 @@ Virtual Machines. OVMF contains a sample UEFI firmware for QEMU and KVM.") (define* (make-arm-trusted-firmware platform #:optional (arch "aarch64")) (package (name (string-append "arm-trusted-firmware-" platform)) - (version "2.6") + (version "2.8") (source (origin (method git-fetch) @@ -655,27 +656,27 @@ Virtual Machines. OVMF contains a sample UEFI firmware for QEMU and KVM.") (file-name (git-file-name "arm-trusted-firmware" version)) (sha256 (base32 - "1j0rn33pwgmksqliwf2npm2px84qmbyma9iq8zpllwfc7dsl6gx9")))) + "0grq3fgxi9xhcljnhwlxjvdghyz15gaq50raw41xy4lm8rkmnzp3")) + (snippet + #~(begin + (use-modules (guix build utils)) + ;; Remove binary blobs which do not contain source or proper license. + (for-each (lambda (file) + (delete-file file)) + (find-files "." "\\.bin$")))))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases (delete 'configure) ; no configure script - ;; Remove binary blobs which do not contain source or proper license. - (add-after 'unpack 'remove-binary-blobs - (lambda _ - (for-each (lambda (file) - (delete-file file)) - (find-files "." ".*\\.bin$")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) - (bin (find-files "." ".*\\.(bin|elf)$"))) + (bin (find-files "." "\\.(bin|elf)$"))) (for-each (lambda (file) (install-file file out)) - bin)) - #t))) + bin))))) #:make-flags (list (string-append "PLAT=" ,platform) ,@(if (and (not (string-prefix? "aarch64" (%current-system))) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 343f736ed2..95e99d5a73 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -35,7 +35,7 @@ ;;; Copyright © 2020 Raghav Gururajan <raghavgururajan@disroot.org> ;;; Copyright © 2020, 2021 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2020 Zhu Zihao <all_but_last@163.com> -;;; Copyright © 2020, 2021 Simen Endsjø <simendsjo@gmail.com> +;;; Copyright © 2020, 2021, 2022 Simen Endsjø <simendsjo@gmail.com> ;;; Copyright © 2020 Tim Van den Langenbergh <tmt_vdl@gmx.com> ;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz> ;;; Copyright © 2021 Antoine Côté <antoine.cote@posteo.net> @@ -1498,7 +1498,7 @@ guix repl <<EOF (ice-9 string-fun) (gnu packages fonts)) -(let ((new-version "15.2.0") +(let ((new-version "16.4.0") (iosevka-hashes #nil) (iosevka-fails #nil)) (for-each (lambda (font) @@ -1532,7 +1532,7 @@ EOF (define-public font-iosevka (package (name "font-iosevka") - (version "15.2.0") + (version "16.4.0") (source (origin (method url-fetch/zipbomb) @@ -1540,7 +1540,7 @@ EOF "/releases/download/v" version "/ttc-iosevka-" version ".zip")) (sha256 - (base32 "0yyz8vmpi8pww0p9na564lvbkwhdhpk4bcyrli91dn5gq0pc1pvv")))) + (base32 "07v98pr0anqbxn1yc55245k5ixxzfk2wmfq67zhz84aa18viqhbc")))) (build-system font-build-system) (home-page "https://be5invis.github.io/Iosevka/") (synopsis "Coders' typeface, built from code") @@ -1563,7 +1563,7 @@ programming. Iosevka is completely generated from its source code.") "/releases/download/v" version "/ttc-iosevka-slab-" version ".zip")) (sha256 - (base32 "1qy86kdl6lgq5k1qb97adibpfjm4vg1wdnxbqizhqka5bc7avyzb")))))) + (base32 "063qk1d75l1jq7gdwzqxd7j8j56g7da0aagsqm0lvwl217l7x48b")))))) (define-public font-iosevka-term (package @@ -1577,7 +1577,7 @@ programming. Iosevka is completely generated from its source code.") "/releases/download/v" version "/ttf-iosevka-term-" version ".zip")) (sha256 - (base32 "15znvvkhldgbl9k04pwrrnvmjnanw2fr92c0zspg7bbw7id2v510")))) + (base32 "17465bvg6fap53xfqwrg2g4fasv01w86wh658n1rf6djs3yzn1gx")))) (arguments `(#:phases (modify-phases %standard-phases @@ -1598,7 +1598,7 @@ programming. Iosevka is completely generated from its source code.") "releases/download/v" version "/" "ttf-iosevka-term-slab-" version ".zip")) (sha256 - (base32 "1rla7kcb94c7daklp4av27gix86cmwsrqg6884zmv5zfnhz0r700")))) + (base32 "00pc4d8awdiziyzncah3fnh0ppvcdvi9cd7vyknl68f6fj283fvm")))) (arguments `(#:phases (modify-phases %standard-phases @@ -1619,7 +1619,7 @@ programming. Iosevka is completely generated from its source code.") "/releases/download/v" version "/ttc-iosevka-aile-" version ".zip")) (sha256 - (base32 "1lciycahvxgvmcniq4h3m1v3rc42nmv8ydb0fpbl9g4sc0qp81hq")))))) + (base32 "03y0xijb7c0kampm3gjb69mv8hikhsgqhlw1w3zfcjhr2vc62g6q")))))) (define-public font-iosevka-curly (package @@ -1633,7 +1633,7 @@ programming. Iosevka is completely generated from its source code.") "releases/download/v" version "/" "ttc-iosevka-curly-" version ".zip")) (sha256 - (base32 "02jvrj7kzd4bx3maj1bq2p9j746b8c5713d8lqkxx4fn9fm0zppq")))))) + (base32 "1i31zj0j8npgx7wn2qibih48s76qjxakz14sa2hgx908p8xyfwq5")))))) (define-public font-iosevka-curly-slab (package @@ -1647,7 +1647,7 @@ programming. Iosevka is completely generated from its source code.") "releases/download/v" version "/" "ttc-iosevka-curly-slab-" version ".zip")) (sha256 - (base32 "1bhvf95xs74wm8srsvl4yxwvl36llk93mpl1y9acc5z9rdcpzjqq")))))) + (base32 "1xijhk5vbgs3c89a7g9cfjqjqv801gimjja4wqpvaficab692jh2")))))) (define-public font-iosevka-etoile (package @@ -1661,12 +1661,12 @@ programming. Iosevka is completely generated from its source code.") "/releases/download/v" version "/ttc-iosevka-etoile-" version ".zip")) (sha256 - (base32 "1zmgfxfsbxv1k4fwnc7g2jlfhmlzp5kap8m3f10fqanpnkd0yf08")))))) + (base32 "1rqagk6gyja15fa4m107ylbjwbhn811gbl9lbr9yzashw4drjpp9")))))) (define-public font-sarasa-gothic (package (name "font-sarasa-gothic") - (version "0.36.8") + (version "0.37.4") (source (origin (method url-fetch) @@ -1674,7 +1674,7 @@ programming. Iosevka is completely generated from its source code.") "/releases/download/v" version "/sarasa-gothic-ttc-" version ".7z")) (sha256 - (base32 "01fn5mzr1rcz0c8nbhabwbv1pq1c3ylf2msxldc9adks1pi45fmh")))) + (base32 "12i8lccl4ysinhz40s2fz6249r9n35in4rqmk3a0fgcjfaby3kfm")))) (build-system font-build-system) (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index d74d6aa935..1c510951e9 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -61,6 +61,7 @@ #:use-module (guix build-system perl) #:use-module (guix build-system python) #:use-module (guix build-system glib-or-gtk) + #:use-module (guix build-system qt) #:use-module (gnu packages) #:use-module (gnu packages acl) #:use-module (gnu packages admin) @@ -73,11 +74,13 @@ #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages cryptsetup) + #:use-module (gnu packages cups) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages disk) #:use-module (gnu packages docbook) #:use-module (gnu packages documentation) + #:use-module (gnu packages fcitx) #:use-module (gnu packages file) #:use-module (gnu packages fontutils) #:use-module (gnu packages gawk) @@ -91,9 +94,12 @@ #:use-module (gnu packages graphviz) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) + #:use-module (gnu packages ibus) #:use-module (gnu packages image) + #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages language) #:use-module (gnu packages libffi) + #:use-module (gnu packages libreoffice) #:use-module (gnu packages libunwind) #:use-module (gnu packages libusb) #:use-module (gnu packages linux) @@ -386,6 +392,81 @@ inappropriate content.") license:gpl2+ license:lgpl2.1+)))) +(define-public maliit-framework + (package + (name "maliit-framework") + (version "2.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/maliit/framework") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1dkjxvfxg56hfy70j6ibfklfyv57jiha4vgc3ggl60r5kjx65s5b")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules + wayland-protocols + pkg-config + doxygen + graphviz + `(,glib "bin"))) ;for gdbus-codegen)) + (inputs (list qtbase-5 + qtdeclarative-5 + qtwayland-5 + wayland + libxkbcommon + dbus + eudev + glib)) + (home-page "https://github.com/maliit/framework") + (synopsis "Core libraries of Maliit") + (description "This package provides Maliit provides a flexible input +method framework.") + (license license:lgpl2.1+))) + +(define-public maliit-keyboard + (package + (name "maliit-keyboard") + (version "2.3.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/maliit/keyboard") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0g89lckl4wzwamc89hs8871fbiyrsjwzk5b6ic4vhc4d1clyqzaw")))) + (build-system cmake-build-system) + (arguments + (list #:tests? #f + #:phases #~(modify-phases %standard-phases + (add-after 'install 'install-schemas + (lambda* (#:key source outputs #:allow-other-keys) + (with-directory-excursion (string-append #$output + "/share/glib-2.0/schemas") + (invoke "glib-compile-schemas" "."))))))) + (native-inputs (list extra-cmake-modules pkg-config gettext-minimal + `(,glib "bin"))) + (inputs (list hunspell + glib + libchewing + libpinyin + maliit-framework + presage + qtbase-5 + qtdeclarative-5 + qtmultimedia-5 + qtquickcontrols2-5)) + (home-page "https://github.com/maliit/keyboard") + (synopsis "Maliit Keyboard") + (description + "This package provides virtual keyboard for Wayland and X11 +display servers. It supports many different languages and emoji.") + (license license:gpl3+))) + (define-public xdg-utils (package (name "xdg-utils") @@ -904,32 +985,37 @@ with localed. This package is extracted from the broader systemd package.") (define-public packagekit (package (name "packagekit") - (version "1.1.13") + (version "1.2.5") (source (origin - (method url-fetch) - (uri (string-append - "https://www.freedesktop.org/software/" - "PackageKit/releases/" - "PackageKit-" version ".tar.xz")) - (sha256 - (base32 - "1dr1laic65ld95abp2yxbwvijnngh0dwyb1x49x4wjm5rhq43dl8")))) - (build-system gnu-build-system) + (method url-fetch) + (uri (string-append "https://www.freedesktop.org/software/" + "PackageKit/releases/" "PackageKit-" version + ".tar.xz")) + (sha256 + (base32 + "09md23m4fw87x264mls1f5isrswk6iw7y9g4hr1nib008wbbk370")))) + (build-system meson-build-system) (arguments - `(#:tests? #f - #:make-flags (list (string-append "BASH_COMPLETIONS_DIR=" - %output "/etc/bash_completion.d")) - #:configure-flags - '("--disable-systemd"))) + (list #:tests? #f + #:configure-flags #~'("-Dsystemd=false" "-Doffline_update=false"))) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper) - ("glib:bin" ,glib "bin"))) + (list bash-completion + docbook-xsl + gettext-minimal + `(,glib "bin") + gobject-introspection + libxml2 ;for XML_CATALOG_FILES + libxslt + pkg-config + python-wrapper + vala)) (inputs - (list glib bash-completion polkit)) - (propagated-inputs - (list sqlite)) + (list glib + gstreamer + gst-plugins-base + gtk+ + polkit)) + (propagated-inputs (list sqlite)) (home-page "https://www.freedesktop.org/software/PackageKit/") (synopsis "API for package management, through D-Bus") (description @@ -1135,6 +1221,29 @@ protocol either in Wayland core, or some other protocol in wayland-protocols.") (base32 "04vgllmpmrv14x3x64ns01vgwx4hriljayjkz9idgbv83i63hly5")))))) +(define-public wayland-utils + (package + (name "wayland-utils") + (version "1.1.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.freedesktop.org/wayland/wayland-utils") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "04k1yhyh7h4xawbhpz9pf6cpfmmp1l862fdgsvvnyp4hg9n3j9aj")))) + (build-system meson-build-system) + (native-inputs (list pkg-config)) + (inputs (list libdrm wayland wayland-protocols-next)) + (home-page "https://wayland.freedesktop.org/") + (synopsis "Display information about the Wayland protocols") + (description "This package provides @code{wayland-info} tool that can be +used to check which Wayland protocols and versions are advertised by the Wayland +compositor.") + (license license:expat))) + (define-public waylandpp (package (name "waylandpp") @@ -2581,6 +2690,42 @@ which uses GTK+ and various pieces of GNOME infrastructure, such as the interfaces.") (license license:lgpl2.1+))) +(define-public xdg-desktop-portal-kde + (package + (name "xdg-desktop-portal-kde") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "0l3lmwihxyl65y0mkyg3afk1k6gc0ldjw2vg92g7yydbgmn39q7k")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list cups + kcoreaddons + kconfig + ki18n + kdeclarative + kio + kirigami + knotifications + plasma-framework + plasma-wayland-protocols + kwayland + kwidgetsaddons + kwindowsystem + kiconthemes + qtdeclarative-5 + qtwayland-5 + wayland)) + (synopsis "Backend implementation for xdg-desktop-portal using Qt/KF5") + (description "This package provides a backend implementation +for xdg-desktop-portal that is using Qt/KF5.") + (home-page "https://invent.kde.org/plasma/xdg-desktop-portal-kde") + (license license:lgpl2.0+))) + (define-public xdg-desktop-portal-wlr (package (name "xdg-desktop-portal-wlr") diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index 7a69e3b4e2..05955ad59a 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -177,14 +177,14 @@ as required.") (define-public libfilezilla (package (name "libfilezilla") - (version "0.37.2") + (version "0.39.2") (source (origin (method url-fetch) (uri (string-append "https://download.filezilla-project.org/" "libfilezilla/libfilezilla-" version ".tar.bz2")) (sha256 - (base32 "1mg2zqmpkkcimx6kq3a1ab26v515zzxw2s8rwhmajsv4cgp404g5")))) + (base32 "1x2rixppmvdpn9m01hmh3yqzpczxbkw301hx27n5bfq0dbnx9aar")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -217,14 +217,14 @@ output. (define-public filezilla (package (name "filezilla") - (version "3.60.1") + (version "3.62.2") (source (origin (method url-fetch) (uri (string-append "https://download.filezilla-project.org/client/" "FileZilla_" version "_src.tar.bz2")) (sha256 - (base32 "1bv643abf8jai552j9fqcl4i54h1yrs5hgn6w0w1ibwccdinryc1")))) + (base32 "04lcffmvl1356iyc14pikq3z6jikj6qn0v0zd57lgsm0biihjrx7")))) (build-system gnu-build-system) (arguments ;; Don't let filezilla phone home to check for updates. diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 5622b9d2ee..66d0ca316f 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -1692,7 +1692,7 @@ robust and compatible with many systems and operating systems.") (define-public mygui (package (name "mygui") - (version "3.2.2") + (version "3.4.1") (source (origin (method git-fetch) @@ -1702,7 +1702,7 @@ robust and compatible with many systems and operating systems.") (file-name (git-file-name name version)) (sha256 (base32 - "1wk7jmwm55rhlqqcyvqsxdmwvl70bysl9azh4kd9n57qlmgk3zmw")))) + "1gyd4bzm6qqpqw6is065qs5c729gl6rp989bnkygha6q4s371vz6")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; No test target @@ -1734,10 +1734,8 @@ of use.") (define-public mygui-gl ;; Closure size is reduced by some 800 MiB. - (package - (inherit mygui) + (package/inherit mygui (name "mygui-gl") - (version "3.2.2") (arguments (substitute-keyword-arguments (package-arguments mygui) ((#:configure-flags _) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 357dee69d0..9d79efbe94 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -880,14 +880,14 @@ Quizzes: arithmetic and quiz.") (define-public bzflag (package (name "bzflag") - (version "2.4.24") + (version "2.4.26") (source (origin (method url-fetch) (uri (string-append "https://download.bzflag.org/bzflag/source/" version "/bzflag-" version ".tar.bz2")) (sha256 - (base32 "1i73ijlnxsz52fhqgkj2qcvibfgav3byq1is68gab2zwnyz330az")))) + (base32 "050h933lmcdf4bw9z3c6g3k8c9sch9f6kq57jp2ivb96zw2h90q1")))) (build-system gnu-build-system) (arguments (list @@ -6137,21 +6137,21 @@ starting a decryption sequence to reveal the original plaintext characters.") "1ffck3ii1wp5k3nn5p0ga06jgp7pzk4zw0xln3xim2w7qrxzdzh9")))) (build-system cmake-build-system) (inputs - `(("curl" ,curl) - ("fontconfig" ,fontconfig) - ("ftgl" ,ftgl) - ("glew" ,glew) - ("libjpeg-turbo" ,libjpeg-turbo) - ("megaglest-data" ,megaglest-data) - ("mesa" ,mesa) - ("miniupnpc" ,miniupnpc) - ("openal" ,openal) - ("libircclient" ,libircclient) - ("libpng" ,libpng) - ("libvorbis" ,libvorbis) - ("lua" ,lua) - ("sdl2" ,sdl2) - ("wxwidgets" ,wxwidgets))) + (list curl + fontconfig + ftgl + glew + libjpeg-turbo + megaglest-data + mesa + miniupnpc + openal + libircclient + libpng + libvorbis + lua + sdl2 + wxwidgets)) (native-inputs (list cppunit pkg-config)) (arguments @@ -6159,8 +6159,8 @@ starting a decryption sequence to reveal the original plaintext characters.") (list "-DCMAKE_CXX_FLAGS=-fcommon" "-DCMAKE_C_FLAGS=-fcommon" (string-append "-DCUSTOM_DATA_INSTALL_PATH=" - (assoc-ref %build-inputs "megaglest-data") - "/share/megaglest") + (search-input-directory %build-inputs + "share/megaglest")) "-DBUILD_MEGAGLEST_TESTS=ON") #:phases (modify-phases %standard-phases @@ -6239,7 +6239,7 @@ emerges from a sewer hole and pulls her below ground.") (define-public cdogs-sdl (package (name "cdogs-sdl") - (version "0.8.0") + (version "1.4.0") (source (origin (method git-fetch) @@ -6248,7 +6248,7 @@ emerges from a sewer hole and pulls her below ground.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0vx37zb2iw7sfw5a2bs97ydlmb301nvy485ybdm8g46c5hn9s13c")))) + (base32 "1505z8rli59i1ych4rzwbf4dvhv72icdj22n1xarb8xfyz0wyp3b")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -10451,14 +10451,14 @@ get high scores.") (define-public burgerspace (package (name "burgerspace") - (version "1.9.4") + (version "1.9.5") (source (origin (method url-fetch) (uri (string-append "http://perso.b2b2c.ca/~sarrazip/dev/" "burgerspace-" version ".tar.gz")) (sha256 - (base32 "1xb4immzmd419aa08lgkzf7ibxa6ax238zb2l5iw9nkgvzlh1v6l")))) + (base32 "1r2albqv2ygs58rwcldsx1mp2vy96j7k4yw5jjmvwgnxjmddq7wr")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index f8163b1e37..0f777c7f9b 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -2123,7 +2123,7 @@ exchanged form one Spatial DBMS and the other.") (define-public opencpn (package (name "opencpn") - (version "5.6.0") + (version "5.6.2") (source (origin (method git-fetch) @@ -2132,11 +2132,10 @@ exchanged form one Spatial DBMS and the other.") (commit (string-append "Release_" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0g5x45wv3djfjmigk6kgs0i63yp8rs1fbmm4pb15wb3z6dml624y")))) + (base32 "16hb0ycp0kbx2h8fx08rqkgrlz48kaym0d6wqvpjrcfa2r4myss8")))) (build-system cmake-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) + (list gettext-minimal pkg-config)) (inputs (list alsa-utils bzip2 diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm index d606acf798..5df30c4be3 100644 --- a/gnu/packages/gettext.scm +++ b/gnu/packages/gettext.scm @@ -120,13 +120,19 @@ "coreutils-gnulib-tests.patch"))))) '()) + #$@(if (hurd-target?) + #~((substitute* + "gettext-tools/gnulib-tests/Makefile.in" + ;; See 'coreutils' for the rationale. + ((" test-tls\\$\\(EXEEXT\\) ") " "))) + '()) + #t))))) ;; When tests fail, we want to know the details. #:make-flags #~'("VERBOSE=yes" #$@(if (hurd-target?) - ;; Linking to libgettextlib.so makes test-raise fail - '("XFAIL_TESTS=test-raise") + '("XFAIL_TESTS=test-perror2") '())))) (home-page "https://www.gnu.org/software/gettext/") (synopsis diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm index 68c751ace5..01ab6135a4 100644 --- a/gnu/packages/gl.scm +++ b/gnu/packages/gl.scm @@ -587,30 +587,29 @@ from software emulation to complete hardware acceleration for modern GPUs.") (source (mesa-demos-source version)) (build-system gnu-build-system) (inputs - `(("mesa" ,mesa) - ("glut" ,freeglut) - ("glew" ,glew))) + (list mesa freeglut glew)) (native-inputs (list pkg-config)) (arguments - '(#:phases - (modify-phases %standard-phases - (replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (mkdir-p (string-append out "/bin")) - (for-each - (lambda (file) - (copy-file file (string-append out "/bin/" (basename file)))) - '("src/xdemos/glxdemo" "src/xdemos/glxgears" - "src/xdemos/glxinfo" "src/xdemos/glxheads")) - #t)))))) + (list + #:phases + #~(modify-phases %standard-phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out #$output)) + (mkdir-p (string-append out "/bin")) + (for-each (lambda (file) + (copy-file file + (string-append out "/bin/" + (basename file)))) + '("src/xdemos/glxdemo" "src/xdemos/glxgears" + "src/egl/opengl/eglinfo" + "src/xdemos/glxinfo" "src/xdemos/glxheads")))))))) (home-page "https://mesa3d.org/") (synopsis "Utility tools for Mesa") (description - "The mesa-utils package contains several utility tools for Mesa: glxdemo, -glxgears, glxheads, and glxinfo.") + "The mesa-utils package contains several utility tools for Mesa: eglinfo, +glxdemo, glxgears, glxheads, and glxinfo.") ;; glxdemo is public domain; others expat. (license (list license:expat license:public-domain)))) diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index 61040c91e7..f85d5e3225 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> ;;; Copyright © 2020 Arthur Margerit <ruhtra.mar@gmail.com> ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be> +;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -67,6 +68,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages sqlite) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) @@ -76,6 +78,7 @@ #:use-module (guix build-system perl) #:use-module (guix build-system python) #:use-module (guix download) + #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) @@ -758,6 +761,59 @@ translated.") by GDBus included in Glib.") (license license:gpl2))) ; or Academic Free License 2.1 +(define-public libaccounts-glib + (package + (name "libaccounts-glib") + (version "1.25") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/accounts-sso/libaccounts-glib") + (commit (string-append "VERSION_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "19rhk9f97m736d5ia26vfcbjp5kgi454558yhf9mrwm4iw5d9pk4")))) + (build-system meson-build-system) + (native-inputs (list dbus + `(,glib "bin") + gobject-introspection + gtk-doc + pkg-config + vala)) + (inputs (list check python python-pygobject)) + (propagated-inputs (list glib libxml2 sqlite)) + (arguments + (list #:tests? #f ;one test fails. + #:imported-modules `((guix build python-build-system) + ,@%meson-build-system-modules) + #:modules '(((guix build python-build-system) + #:select (python-version)) + (guix build meson-build-system) + (guix build utils)) + ;; don't try installing to python store path. + #:configure-flags + #~(list (string-append "-Dpy-overrides-dir=" + #$output "/lib/python" + (python-version #$(this-package-input + "python")) + "/site-packages/gi/overrides")) + #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "dbus-run-session" "--" "meson" "test" + "--print-errorlogs"))))))) + (home-page "https://accounts-sso.gitlab.io/") + (synopsis "Accounts SSO (Single Sign-On) management library for GLib +applications") + (description + "Accounts SSO is a framework for application developers who +wish to acquire, use and store web account details and credentials. It +handles the authentication process of an account and securely stores the +credentials and service-specific settings.") + (license license:lgpl2.1+))) + (define libsigc++ (package (name "libsigc++") diff --git a/gnu/packages/gnome-xyz.scm b/gnu/packages/gnome-xyz.scm index b7e10100fb..0368ccc223 100644 --- a/gnu/packages/gnome-xyz.scm +++ b/gnu/packages/gnome-xyz.scm @@ -55,6 +55,7 @@ #:use-module (gnu packages bash) #:use-module (gnu packages build-tools) #:use-module (gnu packages check) + #:use-module (gnu packages freedesktop) #:use-module (gnu packages gettext) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) @@ -304,6 +305,59 @@ and products. Plots is designed to integrate well with the GNOME desktop and takes advantage of modern hardware using OpenGL.") (license license:gpl3+))) +(define-public portfolio + (package + (name "portfolio") + (version "0.9.14") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tchx84/Portfolio") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0h09v8lhz3kv6qmwjhx3gr7rp6ccfhrzm54gjnaixl4dcg9zddls")))) + (arguments + (list #:glib-or-gtk? #t + #:imported-modules `(,@%meson-build-system-modules + (guix build python-build-system)) + #:modules '((guix build meson-build-system) + ((guix build python-build-system) + #:prefix python:) + (guix build utils)) + #:phases #~(modify-phases %standard-phases + (add-after 'install 'rename-executable + (lambda _ + (with-directory-excursion (string-append #$output + "/bin") + (symlink "dev.tchx84.Portfolio" "portfolio")))) + (add-after 'glib-or-gtk-wrap 'python-and-gi-wrap + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (search-input-file outputs + "bin/dev.tchx84.Portfolio") + `("GUIX_PYTHONPATH" = + (,(getenv "GUIX_PYTHONPATH") ,(python:site-packages + inputs + outputs))) + `("GI_TYPELIB_PATH" = + (,(getenv "GI_TYPELIB_PATH"))))))))) + (build-system meson-build-system) + (inputs (list bash-minimal python-pygobject gtk+ libhandy)) + (native-inputs + (list desktop-file-utils + gettext-minimal + `(,glib "bin") + `(,gtk+ "bin") + python)) + (home-page "https://github.com/tchx84/Portfolio") + (synopsis "Minimalist file manager for Linux mobile devices") + (description + "Portfolio is a minimalist file manager for those who want to use Linux +mobile devices. Tap to activate and long press to select, to browse, open, +copy, move, delete, or edit your files.") + (license license:gpl3+))) + (define-public gnome-shell-extension-unite-shell (package (name "gnome-shell-extension-unite-shell") diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 78e65d7400..f81b44cca2 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -2594,6 +2594,11 @@ GNOME Desktop.") python-wrapper)) ;for tests (propagated-inputs (list gcr)) + + ;; XXX: There are concerning test failures on i686-linux and other 32-bit + ;; platforms: <https://gitlab.gnome.org/GNOME/gnome-keyring/-/issues/124>. + (supported-systems %64bit-supported-systems) + (home-page "https://www.gnome.org") (synopsis "Daemon to store passwords and encryption keys") (description @@ -4956,6 +4961,57 @@ GLibproxyResolver, and a GNOME GProxyResolver that uses the proxy information from the GSettings schemas in gsettings-desktop-schemas.") (license license:lgpl2.1+))) +(define-public raider + (package + (name "raider") + (version "1.3.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ADBeveridge/raider/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ll9220d6qf9m7wdi5xhq69p8h8whs7l5h5nzdhlbn99qh5388bz")))) + (build-system meson-build-system) + (arguments + (list #:meson meson-0.63 + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "data/com.github.ADBeveridge.Raider.gschema.xml" + (("/usr/bin/shred") + (which "shred"))))) + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (string-append (assoc-ref outputs "out") + "/bin/raider") + `("GSETTINGS_SCHEMA_DIR" = + (,(string-append (assoc-ref outputs "out") + "/share/glib-2.0/schemas"))))))))) + (native-inputs + (list gettext-minimal + pkg-config + cmake + `(,glib "bin") + desktop-file-utils + itstool + gobject-introspection + blueprint-compiler + `(,gtk "bin"))) + (inputs + (list libadwaita + gtk)) + (home-page "https://github.com/ADBeveridge/raider") + (synopsis "Securely delete your files") + (description + "Raider is a simple shredding program built for GNOME. Also known as +File Shredder, it uses the GNU Core Utility called shred to securely delete +files.") + (license license:gpl3+))) + (define-public rest (package (name "rest") diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 210b1ab8b3..064b775ab1 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -431,6 +431,19 @@ and every application benefits from this.") (properties '((ftp-server . "ftp.gnupg.org") (ftp-directory . "/gcrypt/gpgme"))))) +;; TODO: Merge with gpgme in the next rebuild cycle. +(define-public gpgme-1.18 + (package + (inherit gpgme) + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnupg/gpgme/gpgme-" + version ".tar.bz2")) + (sha256 + (base32 + "17hfigfnq6xz45b5xrp299f68b5mwx0aysd51sx5v4nf8yp4w79n")))))) + (define-public qgpgme (package (inherit gpgme) @@ -459,6 +472,16 @@ QGpgME was originally developed as part of libkleo and incorporated into gpgpme starting with version 1.7.") (license license:gpl2+))) ;; Note: this differs from gpgme +;; TODO: Merge with qgpgme in the next rebuild cycle. +(define-public qgpgme-1.18 + (package + (inherit qgpgme) + (version (package-version gpgme-1.18)) + (source (package-source gpgme-1.18)) + (inputs + (modify-inputs (package-inputs qgpgme) + (replace "gpgme" gpgme-1.18))))) + (define-public guile-gcrypt (package (name "guile-gcrypt") diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 2ed4c7a73c..b7c0acb9f6 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -2107,6 +2107,29 @@ writers can be supplied for alternate environments.") "The datacounter package provides counters for Go readers and writers.") (license license:expat))) +(define-public go-github-com-emersion-go-textwrapper + (package + (name "go-github-com-emersion-go-textwrapper") + (version "0.0.0-20200911093747-65d896831594") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/go-textwrapper") + (commit (go-version->git-ref version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1lh9d7zvj6gm1rr6sv5xlagklgx9d666hq5srd37a4sdcjkbiqmq")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/emersion/go-textwrapper")) + (home-page "https://github.com/emersion/go-textwrapper") + (synopsis "Text-wrapping writer for Go") + (description + "The textwrapper package provides a writer that wraps long text lines to +a specified length.") + (license license:expat))) + (define-public go-github-com-aki237-nscjar (let ((commit "e2df936ddd6050d30dd90c7214c02b5019c42f06") (revision "0")) @@ -2485,6 +2508,101 @@ web framework @end itemize") (license license:expat))) +(define-public go-github-com-nathan-osman-go-sunrise + (let ((commit "c8f9f1eb869135f07378e7e3c5ec7a005f806c73") + (revision "0")) + (package + (name "go-github-com-nathan-osman-go-sunrise") + (version (git-version "1.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nathan-osman/go-sunrise") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "017zwzx05r5spxcs07dp6bnh7waknzsd819k7aqd8kr819v3x9in")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/nathan-osman/go-sunrise")) + (home-page "https://github.com/nathan-osman/go-sunrise") + (synopsis "Calculate sunrise and sunset times in Go") + (description + "This package provides a Go library for calculating sunrise and +sunset times from geographical coordinates and a date.") + (license license:expat)))) + +(define-public go-github-com-hebcal-gematriya + (let ((commit "fe3043f73e415eb82727701d10f2fb40f87675e9") + (revision "0")) + (package + (name "go-github-com-hebcal-gematriya") + (version (git-version "1.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hebcal/gematriya") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xmnb2i80dy380yv8c4pd04bbyqgbc7c40p8hz1vqj2lhbm6jabf")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/hebcal/gematriya")) + (home-page "https://github.com/hebcal/gematriya") + (synopsis "Print numbers as Hebrew letters in Go") + (description + "This package provides a Go library for printing numbers as +Hebrew letters.") + (license license:bsd-2)))) + +(define-public go-github-com-hebcal-hebcal-go + (let ((commit "d42e881860cfc9e8249fc79f268091c3c4d36b0d") + (revision "0")) + (package + (name "go-github-com-hebcal-hebcal-go") + (version (git-version "0.9.11" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hebcal/hebcal-go") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1m9akb8pwxchpaci05gambshrzw626gsrfhl25f36vjl7mq5292n")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/hebcal/hebcal-go" + ;; Source-only package + #:tests? #f + #:phases + #~(modify-phases %standard-phases + ;; Source-only package + (delete 'build)))) + (native-inputs + (list go-github-com-stretchr-testify)) + (propagated-inputs + (list go-github-com-hebcal-gematriya + go-github-com-nathan-osman-go-sunrise)) + (home-page "https://github.com/hebcal/hebcal-go") + (synopsis "Go library for the Hebcal perpetual Jewish calendar") + (description + "This package provides a library for conversion between Hebrew +and Gregorian dates, and generation of lists of Jewish holidays for +a given year. Shabbat and holiday candle lighting and havdalah times +are approximated based on location. + +Torah readings, Daf Yomi, and counting of the Omer can also be +specified. Algorithms are included to calculate yahrzeits, birthdays, +and anniversaries.") + (license license:gpl2+)))) + (define-public go-github-com-aws-sdk (package (name "go-github-com-aws-sdk") @@ -2547,6 +2665,32 @@ termination.") (home-page "https://gopkg.in/tomb.v2") (license license:bsd-3)))) +(define-public go-gopkg-in-tomb-v1 + (package + (inherit go-gopkg.in-tomb.v2) + (name "go-gopkg-in-tomb-v1") + (version "1.0.0-20141024135613-dd632973f1e7") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gopkg.in/tomb.v1") + (commit (go-version->git-ref version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1lqmq1ag7s4b3gc3ddvr792c5xb5k6sfn0cchr3i2s7f1c231zjv")))) + (arguments + (list #:import-path "gopkg.in/tomb.v1" + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-test + (lambda* (#:key import-path #:allow-other-keys) + (substitute* (string-append "src/" import-path + "/tomb_test.go") + (("t.Fatalf\\(`Killf\\(\"BO%s") + "t.Fatalf(`Killf(\"BO%%s"))))))) + (home-page "https://gopkg.in/tomb.v1"))) + (define-public go-gopkg-in-natefinch-lumberjack.v2 (package (name "go-gopkg-in-natefinch-lumberjack.v2") @@ -2775,6 +2919,37 @@ for the Go language.") (home-page "https://go.googlesource.com/crypto/") (license license:bsd-3)))) +(define-public go-github-com-protonmail-go-crypto + (package + (name "go-github-com-protonmail-go-crypto") + (version "0.0.0-20220623141421-5afb4c282135") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ProtonMail/go-crypto") + (commit (go-version->git-ref version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "05qxdbn8wdk901z5kw2r3jdrag58nxlcsy0p8xd6rq0d71sw94wy")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/ProtonMail/go-crypto" + #:tests? #f ; Source-only package. + #:phases + #~(modify-phases %standard-phases + ;; Source-only package. + (delete 'build)))) + (propagated-inputs (list go-golang-org-x-crypto)) + (home-page "https://github.com/ProtonMail/go-crypto") + (synopsis "Fork of x/crypto with up-to-date OpenPGP implementation") + (description + "This package provides cryptography for Go. This version of the +package is a fork that adds a more up-to-date OpenPGP implementation. +It is completely backwards compatible with @code{golang.org/x/crypto}, +the official package.") + (license license:bsd-3))) + (define-public go-golang-org-x-net (let ((commit "ba9fcec4b297b415637633c5a6e8fa592e4a16c3") (revision "4")) @@ -3896,6 +4071,30 @@ application's http.Handlers.") (description "File system notifications for Go") (license license:bsd-3))) +(define-public go-github-com-nxadm-tail + (package + (name "go-github-com-nxadm-tail") + (version "1.4.8") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nxadm/tail") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1j2gi485fhwdpmyzn42wk62103fclwbfywg42p275z1qv2bsz1rc")))) + (build-system go-build-system) + (arguments (list #:import-path "github.com/nxadm/tail")) + (propagated-inputs (list go-gopkg-in-tomb-v1 + go-github-com-fsnotify-fsnotify)) + (home-page "https://github.com/nxadm/tail") + (synopsis "Go implementation of the functionality of @command{tail -f}") + (description + "This package provides a Go library for reading from continuously +updating files, like @command{tail -f}.") + (license license:expat))) + (define-public go-github-com-magiconair-properties (package (name "go-github-com-magiconair-properties") @@ -5894,6 +6093,33 @@ without requiring a real database connection.") golang's database/sql package.") (license license:mpl2.0))) +(define-public go-github-com-syndtr-goleveldb-leveldb + (package + (name "go-github-com-syndtr-goleveldb-leveldb") + (version "1.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/syndtr/goleveldb") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "042k0gbzs5waqpxmd7nv5h93mlva861s66c3s9gfg1fym5dx4vmd")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/syndtr/goleveldb/leveldb" + #:unpack-path "github.com/syndtr/goleveldb")) + (propagated-inputs (list go-github-com-onsi-gomega + go-github-com-onsi-ginkgo + go-github-com-golang-snappy)) + (home-page "https://github.com/syndtr/goleveldb") + (synopsis "LevelDB implementation in Go") + (description + "This package provides a Go implementation of the LevelDB key/value +storage system.") + (license license:bsd-2))) + (define-public go-github-com-lucasb-eyer-go-colorful (package (name "go-github-com-lucasb-eyer-go-colorful") @@ -5948,6 +6174,30 @@ standard @code{Text} package, including some for dealing with I/O streams from non-UTF-friendly sources.") (license license:expat))) +(define-public go-github-com-cention-sany-utf7 + (package + (name "go-github-com-cention-sany-utf7") + (version "0.0.0-20170124080048-26cad61bd60a") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cention-sany/utf7") + (commit (go-version->git-ref version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1jy15ryfcln1iwchrksqyrnyfy41gisymm4f9sr1d73ja029bznm")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/cention-sany/utf7")) + (propagated-inputs (list go-golang-org-x-text)) + (home-page "https://github.com/cention-sany/utf7") + (synopsis "UTF-7 for Go") + (description + "The utf7 package provides support for the obsolete UTF-7 text +encoding in Go.") + (license license:bsd-3))) + (define-public go-github-com-gdamore-tcell (let ((commit "aaadc574a6ed8dc3abe56036ca130dcee1ee6b6e") (version "1.1.2") @@ -5985,32 +6235,62 @@ systems.") (package (inherit go-github-com-gdamore-tcell) (name "go-github-com-gdamore-tcell") - (version "2.3.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/gdamore/tcell") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0ypbl5080q9sd3irad8mv7zlg4242i8pmg5xyhbyq95kymwibaid")))) + (version "2.5.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gdamore/tcell") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0pvs0gigqxpifc7y7cx82cg95pgqmy8qzxynja3zidplrx2075j3")))) (arguments - `(#:import-path "github.com/gdamore/tcell/v2" - #:phases - (modify-phases %standard-phases - (add-before 'reset-gzip-timestamps 'make-files-writable - (lambda* (#:key outputs #:allow-other-keys) - ;; Make sure .gz files are writable so that the - ;; 'reset-gzip-timestamps' phase can do its work. - (let ((out (assoc-ref outputs "out"))) - (for-each make-file-writable - (find-files out "\\.gz$")))))))) + (list #:import-path "github.com/gdamore/tcell/v2" + #:phases + #~(modify-phases %standard-phases + (add-before 'reset-gzip-timestamps 'make-files-writable + (lambda _ + ;; Make sure .gz files are writable so that the + ;; 'reset-gzip-timestamps' phase can do its work. + (for-each make-file-writable + (find-files #$output "\\.gz$"))))))) (propagated-inputs (modify-inputs (package-inputs go-github-com-gdamore-tcell) (prepend go-golang-org-x-term go-golang-org-x-sys))))) +(define-public go-git-sr-ht-rockorager-tcell-term + (package + (name "go-git-sr-ht-rockorager-tcell-term") + (version "0.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.sr.ht/~rockorager/tcell-term") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "13nfb2mq59846j531j7p2nm8mi0kjw5p90pa89l3fwc0sljkn5p8")))) + (build-system go-build-system) + (arguments + (list #:import-path "git.sr.ht/~rockorager/tcell-term")) + (propagated-inputs + (list go-golang-org-x-sys + go-golang-org-x-term + go-gopkg-in-check-v1 + go-github-com-mattn-go-runewidth + go-github-com-davecgh-go-spew + go-github-com-stretchr-testify + go-github-com-gdamore-tcell-v2 + go-github-com-creack-pty)) + (home-page "https://git.sr.ht/~rockorager/tcell-term") + (synopsis "Terminal widget for @code{tcell}") + (description + "This package provides a virtual terminal widget for the @code{tcell} +Go library.") + (license license:expat))) + (define-public go-github-com-rivo-tview (package (name "go-github-com-rivo-tview") @@ -6447,31 +6727,82 @@ fnmatch gist (https://gist.github.com/kballard/272720).") (define-public go-github-com-emersion-go-imap (package (name "go-github-com-emersion-go-imap") - (version "1.0.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/emersion/go-imap") - (commit (string-append "v" version)))) - (sha256 - (base32 - "1id8j2d0rn9sj8y62xhyygqpk5ygrcl9jlfx92sm1jsvxsm3kywq")) - (file-name (git-file-name name version)))) + (version "1.2.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/go-imap") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ak2ysvfcc9w0g1070msis8x9sh6gzvf0nd65ks594siwbmqddw8")))) (build-system go-build-system) (arguments - '(#:import-path "github.com/emersion/go-imap")) - (native-inputs - (list go-golang-org-x-text)) + (list #:import-path "github.com/emersion/go-imap")) + (propagated-inputs (list go-golang-org-x-text + go-github-com-emersion-go-sasl + go-github-com-emersion-go-message)) (home-page "https://github.com/emersion/go-imap") (synopsis "IMAP4rev1 library written in Go") - (description "This package provides an IMAP4rev1 library written in Go. It -can be used to build a client and/or a server.") + (description + "This package provides an IMAP4rev1 library written in Go. It +can be used to build IMAP clients and servers.") + (license license:expat))) + +(define-public go-github-com-emersion-go-imap-sortthread + (package + (name "go-github-com-emersion-go-imap-sortthread") + (version "1.2.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/go-imap-sortthread") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1cfbgz1l5angnj52v9pxwggai2shx0h78ffcp7j4r4lr7lzflnwz")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/emersion/go-imap-sortthread")) + (propagated-inputs (list go-golang-org-x-text + go-github-com-emersion-go-sasl + go-github-com-emersion-go-imap)) + (home-page "https://github.com/emersion/go-imap-sortthread") + (synopsis "Sorting and threading of messages for the imap package") + (description + "The sortthread package implements message sorting and threading for +@code{go-github-com-emersion-go-imap}.") + (license license:expat))) + +(define-public go-github-com-emersion-go-smtp + (package + (name "go-github-com-emersion-go-smtp") + (version "0.15.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/go-smtp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1vhc0vpjd4yhxk6wrh01sdpi7nprjn98s46yy82xwlkm0cskl0h7")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/emersion/go-smtp")) + (propagated-inputs (list go-github-com-emersion-go-sasl)) + (home-page "https://github.com/emersion/go-smtp") + (synopsis "SMTP implementation for Go") + (description + "This package implements the Simple Mail Transfer Protocol as +defined by RFC 5321.") (license license:expat))) (define-public go-github-com-emersion-go-sasl - (let ((commit "240c8404624e076f633766c16adbe96c7ac516b7") - (revision "0")) + (let ((commit "0b9dcfb154ac3d7515b08bc2691a0332800edfe9") + (revision "1")) (package (name "go-github-com-emersion-go-sasl") (version (git-version "0.0.0" revision commit)) @@ -6481,13 +6812,13 @@ can be used to build a client and/or a server.") (uri (git-reference (url "https://github.com/emersion/go-sasl") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 - "1py18p3clp474xhx6ypyp0bgv6n1dfm24m95cyyqb0k3vibar6ih")) - (file-name (git-file-name name version)))) + "1cbf86wkqrdinfydndgdlnayg4a5mg3d4vqra377j2sfkg7wj0hs")))) (build-system go-build-system) (arguments - '(#:import-path "github.com/emersion/go-sasl")) + (list #:import-path "github.com/emersion/go-sasl")) (home-page "https://github.com/emersion/go-sasl") (synopsis "SASL library written in Go") (description "This package provides a SASL library written in Go.") @@ -6520,6 +6851,106 @@ can be used to build a client and/or a server.") (description "This package provides an IDLE extension for go-imap.") (license license:expat)))) +(define-public go-github-com-emersion-go-maildir + (package + (name "go-github-com-emersion-go-maildir") + (version "0.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/go-maildir") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rs9kbacjpcza25pmdkbm7sdm7r6gq4g44nihi9asyrvspx96zf2")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/emersion/go-maildir")) + (home-page "https://github.com/emersion/go-maildir") + (synopsis "Maildir interface for Go") + (description + "This package provides an interface to mailboxes in the Maildir +format.") + (license license:expat))) + +(define-public go-github-com-emersion-go-milter + (package + (name "go-github-com-emersion-go-milter") + (version "0.3.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/go-milter") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10vpry5gjz2bh9qchcx4p59zm7cc6cb6bfkii2n6vsn4svb950sa")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/emersion/go-milter")) + (propagated-inputs (list go-github-com-emersion-go-message)) + (home-page "https://github.com/emersion/go-milter") + (synopsis "Milter mail filters in Go") + (description + "This package provides an interface for implementing milter mail +filters for Go.") + (license license:bsd-2))) + +(define-public go-github-com-emersion-go-msgauth + (package + (name "go-github-com-emersion-go-msgauth") + (version "0.6.6") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/go-msgauth") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ds8yr4cm9wigcxg1sxc2m0wmy4z9n6gws3mj50dmf2ayij69z9j")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/emersion/go-msgauth" + #:tests? #f ; Source-only package. + #:phases + #~(modify-phases %standard-phases + ;; Source-only package. + (delete 'build)))) + (propagated-inputs (list go-golang-org-x-crypto + go-github-com-emersion-go-milter + go-github-com-emersion-go-message)) + (home-page "https://github.com/emersion/go-msgauth") + (synopsis "Email authentication for Go") + (description + "This package provides a Go library for authenticating emails.") + (license license:expat))) + +(define-public go-github-com-emersion-go-mbox + (package + (name "go-github-com-emersion-go-mbox") + (version "1.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/go-mbox") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0vnadh2khx7sxn0irrd8gz8ra02x7ij0q8zglq3rqffqil06nliv")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/emersion/go-mbox")) + (home-page "https://github.com/emersion/go-mbox") + (synopsis "Go library for handling @code{mbox} files") + (description + "This package provides a library for parsing and formatting +@code{mbox} files.") + (license license:expat))) + (define-public go-github-com-fatih-color (package (name "go-github-com-fatih-color") @@ -7330,6 +7761,34 @@ maps (because they are not addressable using Go reflection).") template functions.") (license license:expat))) +(define-public go-github-com-go-task-slim-sprig + (let ((commit "afa1e2071829e4db655eb448d6c7c16eb0bc5766") + (revision "0")) + (package + (name "go-github-com-go-task-slim-sprig") + (version (git-version "2.20.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/go-task/slim-sprig") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1185y8qygv8gb3wpghx5d945wq68j4dbaiffq3h0dh453g4h1w7a")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/go-task/slim-sprig" + ;; Tests try to access the network. + #:tests? #f)) + (home-page "https://github.com/go-task/slim-sprig") + (synopsis "Various useful template functions for Go") + (description + "Sprig provides over 100 functions that extend the Go template system. +Slim-Sprig is a fork of Sprig that removes all external dependencies to make +the library more lightweight.") + (license license:expat)))) + (define-public go-github-com-bmatcuk-doublestar (package (name "go-github-com-bmatcuk-doublestar") @@ -9125,6 +9584,30 @@ or capture raw audio.") programs that use traditional command lines.") (license license:bsd-3))) +(define-public go-git-sr-ht-sircmpwn-getopt + (package + (name "go-git-sr-ht-sircmpwn-getopt") + (version "1.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.sr.ht/~sircmpwn/getopt") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0f9rammnmhaz21qkmz7qf76r8jlzi323g05ps3j7gwrxlw7442a6")))) + (build-system go-build-system) + (arguments + (list #:import-path "git.sr.ht/~sircmpwn/getopt")) + (propagated-inputs (list go-github-com-stretchr-testify)) + (home-page "https://git.sr.ht/~sircmpwn/getopt") + (synopsis "POSIX getopt for Go") + (description + "This package provides a POSIX-compatible implementation of +@code{getopt} for Go.") + (license license:bsd-3))) + (define-public go-go-uber-org-atomic (package (name "go-go-uber-org-atomic") @@ -10517,6 +11000,31 @@ using shell-style rules for quoting and commenting.") email library.") (license license:gpl3+))) +(define-public go-github-com-emersion-go-message + (package + (name "go-github-com-emersion-go-message") + (version "0.16.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/go-message") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1j5qdhsna28xcs843zsiccw700rld5hin466dl0n3a0ax1w13ay0")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/emersion/go-message")) + (propagated-inputs (list go-golang-org-x-text + go-github-com-emersion-go-textwrapper)) + (home-page "https://github.com/emersion/go-message") + (synopsis "Internet messages and MIME for Go") + (description + "The message package implements the Internet Message Format and Multipurpose +Internet Mail Extensions in Go.") + (license license:expat))) + (define-public go-github-com-jaytaylor-html2text (package (name "go-github-com-jaytaylor-html2text") @@ -10545,6 +11053,97 @@ email library.") text-only mail clients to display them.") (license license:expat))) +(define-public go-github-com-jhillyerd-enmime + (package + (name "go-github-com-jhillyerd-enmime") + (version "0.9.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jhillyerd/enmime") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "124dqm598phbmalyx2gmxk201z9kq4ckvvdq8rc0akjlp24nxqbb")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/jhillyerd/enmime")) + (propagated-inputs (list go-golang-org-x-text + go-golang-org-x-net + go-github-com-stretchr-testify + go-github-com-ssor-bom + go-github-com-rivo-uniseg + go-github-com-pkg-errors + go-github-com-olekukonko-tablewriter + go-github-com-mattn-go-runewidth + go-github-com-gogs-chardet + go-github-com-jaytaylor-html2text + go-github-com-go-test-deep + go-github-com-cention-sany-utf7)) + (home-page "https://github.com/jhillyerd/enmime") + (synopsis "MIME encoder and decoder for Go") + (description + "The enmime package implements a MIME encoding and decoding +library geared towards parsing MIME encoded emails.") + (license license:expat))) + +(define-public go-github-com-emersion-go-pgpmail + (package + (name "go-github-com-emersion-go-pgpmail") + (version "0.2.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emersion/go-pgpmail") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ar26b0apw5bxn58qfn1a79cxigbmrqm1irh1rb7x57fydihc7wm")))) + (build-system go-build-system) + (arguments + (list ;; tests don't support our version of protonmail/go-crypto; see + ;; <https://github.com/emersion/go-pgpmail/issues/12> + #:tests? #f + #:import-path "github.com/emersion/go-pgpmail")) + (propagated-inputs (list go-golang-org-x-text + go-golang-org-x-crypto + go-github-com-emersion-go-message + go-github-com-protonmail-go-crypto)) + (home-page "https://github.com/emersion/go-pgpmail") + (synopsis "PGP mail encryption for Go") + (description + "The pgpmail package implements PGP encryption for e-mail messages.") + (license license:expat))) + +(define-public go-github-com-gatherstars-com-jwz + (package + (name "go-github-com-gatherstars-com-jwz") + (version "1.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gatherstars-com/jwz") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1h37h5w139d3rhvp1n7kz2jm5zhk4pjzf3sip04v48nphkika60c")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/gatherstars-com/jwz")) + (propagated-inputs (list go-github-com-rivo-tview + go-github-com-jhillyerd-enmime + go-github-com-gdamore-tcell-v2)) + (home-page "https://github.com/gatherstars-com/jwz") + (synopsis "Implementation in Go of the email threading algorithm +originally invented for Netscape Mail") + (description + "The jwz package provides an implementation of the email threading +algorithm originally designed for use in Netscape Mail 2.0 for Go.") + (license license:asl2.0))) + (define-public go-github-com-creack-pty (package (name "go-github-com-creack-pty") @@ -10688,6 +11287,180 @@ array or reader.") ICU to Go.") (license license:expat))) +(define-public go-github-com-go-test-deep + (package + (name "go-github-com-go-test-deep") + (version "1.0.8") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/go-test/deep") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mmw2w3by7y24jjpjwmf2gfl08c65jihn3si9m0sswmagmdsk8q0")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/go-test/deep")) + (home-page "https://github.com/go-test/deep") + (synopsis "Human-friendly deep variable equality in Go") + (description + "The deep package provides the deep.Equal function which is like +reflect.DeepEqual but returns a list of differences. This is helpful +when comparing complex types like structures and maps.") + (license license:expat))) + +(define-public go-github-com-niemeyer-pretty + (package + (name "go-github-com-niemeyer-pretty") + (version "0.0.0-20200227124842-a10e7caefd8e") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/niemeyer/pretty") + (commit (go-version->git-ref version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1jmazh4xzaa3v6g46hz60q2z7nmqs9l9cxdzmmscn3kbcs2znq4v")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/niemeyer/pretty" + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'int-to-string-with-rune + (lambda* (#:key import-path #:allow-other-keys) + (with-directory-excursion (string-append "src/" import-path) + (substitute* "formatter.go" + (("s \\+= string\\(i\\)") + "s += string(rune(i))")))))))) + (propagated-inputs (list go-github-com-kr-text)) + (home-page "https://github.com/niemeyer/pretty") + (synopsis "Pretty-print Go values") + (description + "The pretty package provides pretty-printing for Go values. This is +useful during debugging, to avoid wrapping long output lines in the +terminal.") + (license license:expat))) + +(define-public go-github-com-arran4-golang-ical + (package + (name "go-github-com-arran4-golang-ical") + (version "0.0.0-20220517104411-fd89fefb0182") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/arran4/golang-ical") + (commit (go-version->git-ref version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0bxs0b5yg26liiifc0cc41l307r0wc93hp8iygv8dgpc60yzncaw")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/arran4/golang-ical")) + (propagated-inputs (list go-gopkg-in-yaml-v3 + go-gopkg-in-check-v1 + go-github-com-stretchr-testify + go-github-com-niemeyer-pretty + go-github-com-kr-text + go-github-com-davecgh-go-spew)) + (home-page "https://github.com/arran4/golang-ical") + (synopsis "Handle iCalenders in Go") + (description + "The @code{ical} package provides an ICS/iCalender parser and +serialiser for Go.") + (license license:asl2.0))) + +(define-public go-github-com-lithammer-fuzzysearch + (package + (name "go-github-com-lithammer-fuzzysearch") + (version "1.1.5") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/lithammer/fuzzysearch") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1b036sm42cf64diwlqhx24vxy6g5afrmfbdfyqhpg8zrii3lpwns")))) + (build-system go-build-system) + (propagated-inputs (list go-golang-org-x-text)) + (arguments + (list #:import-path "github.com/lithammer/fuzzysearch" + #:tests? #f ; Source-only package. + #:phases + #~(modify-phases %standard-phases + ;; Source-only package. + (delete 'build)))) + (home-page "https://github.com/lithammer/fuzzysearch") + (synopsis "Tiny and fast fuzzy search in Go") + (description + "A speedy fuzzy matching package for Go inspired by the JavaScript +library bevacqua/fuzzysearch.") + (license license:expat))) + +(define-public go-github-com-onsi-gomega + (package + (name "go-github-com-onsi-gomega") + (version "1.19.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/onsi/gomega") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "092phwk97sk4sv0nbx5pfhqs6x3x1lnrjwyda1m6b6zwrfmq5c6i")))) + (build-system go-build-system) + (arguments + (list #:import-path "github.com/onsi/gomega" + ;; Unless we disable the tests, we have a circular dependency on + ;; ginkgo/v2. + #:tests? #f)) + (propagated-inputs (list go-github-com-golang-protobuf-proto + go-golang-org-x-net + go-golang-org-x-sys + go-golang-org-x-text + go-google-golang-org-protobuf + go-gopkg-in-yaml-v2)) + (home-page "https://github.com/onsi/gomega") + (synopsis "Matcher library for Ginkgo") + (description + "Gomega is the preferred matcher library for the Ginkgo test framework.") + (license license:expat))) + +(define-public go-github-com-onsi-ginkgo + (package + (name "go-github-com-onsi-ginkgo") + (version "1.16.5") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/onsi/ginkgo") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1hh6n7q92y0ai8k6rj2yzw6wwxikhyiyk4j92zgvf1zad0gmqqmz")))) + (build-system go-build-system) + (arguments (list #:import-path "github.com/onsi/ginkgo")) + (propagated-inputs (list go-golang-org-x-sys + go-golang-org-x-tools + go-github-com-go-task-slim-sprig + go-github-com-nxadm-tail + go-github-com-onsi-gomega)) + (home-page "https://github.com/onsi/ginkgo") + (synopsis "BDD-style testing framework for Go") + (description + "Ginkgo is a Behaviour-Driven Development testing framework for Go. It +builds on top of Go's builtin @code{testing} library and is complemented by the +Gomega matcher library.") + (license license:expat))) + ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index a92588a9e2..e46bf7b741 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -791,6 +791,14 @@ model to base your own plug-in on, here it is.") ;; FIXME: Why is this failing. ((".*elements/dash_mpd\\.c.*") "") + ;; This test is flaky on at least some architectures. + ;; https://gitlab.freedesktop.org/gstreamer/gstreamer/-/issues/1244 + #$@(if (member (%current-system) + '("i686-linux" "aarch64-linux")) + `((("'elements/camerabin\\.c'\\]\\],") + "'elements/camerabin.c'], true, ],")) + '()) + ;; These tests are flaky and occasionally time out: ;; https://gitlab.freedesktop.org/gstreamer/gst-plugins-bad/-/issues/932 ((".*elements/curlhttpsrc\\.c.*") "") diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 56104b2124..ad34dd51ec 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -32,6 +32,7 @@ ;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com> ;;; Copyright © 2022 Benjamin Slade <slade@lambda-y.net> ;;; Copyright © 2022 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org> +;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -117,6 +118,43 @@ #:use-module (srfi srfi-26) #:use-module (ice-9 match)) +(define-public appmenu-gtk-module + (package + (name "appmenu-gtk-module") + (version "0.7.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/vala-panel-project/vala-panel-appmenu") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ywpygjwlbli65203ja2f8wwxh5gbavnfwcxwg25v061pcljaqmm")))) + (build-system meson-build-system) + (arguments + (list + #:glib-or-gtk? #t + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-install-gtk-module + (lambda* _ + (substitute* + "subprojects/appmenu-gtk-module/src/gtk-3.0/meson.build" + (("gtk3.get_pkgconfig_variable\\('libdir'\\)") + #$output))))))) + (native-inputs + (list `(,glib "bin") vala pkg-config)) + (inputs + (list gtk+ libwnck)) + (synopsis "Application Menu applet") + (description + "This package provides a global menu applet for use with desktop panels +such as mate-panel and xfce4-panel.") + (home-page "https://gitlab.com/vala-panel-project/vala-panel-appmenu") + (license (list license:lgpl3)))) + (define-public atk (package (name "atk") diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 62bcfb6a56..b1620618eb 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -4189,7 +4189,7 @@ models and also supports a rich set of boolean query operators.") perl pkg-config)) (propagated-inputs - (list guile-gcrypt)) + (list guile2.2-gcrypt)) (home-page "https://github.com/o-nly/torrent") (synopsis "Torrent library for GNU Guile") (description "This package provides facilities for working with diff --git a/gnu/packages/heads.scm b/gnu/packages/heads.scm index d5e36b9b3c..212849f2a9 100644 --- a/gnu/packages/heads.scm +++ b/gnu/packages/heads.scm @@ -172,6 +172,7 @@ done (build-system trivial-build-system) (arguments `(#:modules ((guix build utils) + (guix build syscalls) (guix cpio)) #:builder (begin (use-modules (guix build utils) diff --git a/gnu/packages/hunspell.scm b/gnu/packages/hunspell.scm index 65ff90b4b9..48df196e17 100644 --- a/gnu/packages/hunspell.scm +++ b/gnu/packages/hunspell.scm @@ -46,7 +46,7 @@ (string-append "libreoffice-" version)))) (file-name (git-file-name "libreoffice-dictionaries" version)) (sha256 - (base32 "1qyn56kcn2scdlssjgi5b33hnsh20mmnd60w78z0gp7bs0mv0wcs")))) + (base32 "115p29ywyn7ncq664gxmcrrz55v23s34asd2hmrg4ahjp7ycrnmy")))) (build-system trivial-build-system) (native-inputs `(("source" ,source))) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 214420c101..aaa5a82d5f 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -51,6 +51,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages databases) #:use-module (gnu packages docbook) + #:use-module (gnu packages ebook) #:use-module (gnu packages flex) #:use-module (gnu packages freedesktop) #:use-module (gnu packages gettext) @@ -62,9 +63,11 @@ #:use-module (gnu packages graphics) #:use-module (gnu packages graphviz) #:use-module (gnu packages gstreamer) + #:use-module (gnu packages gtk) #:use-module (gnu packages image) #:use-module (gnu packages iso-codes) #:use-module (gnu packages kerberos) + #:use-module (gnu packages kde) #:use-module (gnu packages kde-plasma) #:use-module (gnu packages libcanberra) #:use-module (gnu packages libreoffice) @@ -82,10 +85,13 @@ #:use-module (gnu packages qt) #:use-module (gnu packages textutils) #:use-module (gnu packages tls) + #:use-module (gnu packages text-editors) #:use-module (gnu packages version-control) #:use-module (gnu packages video) + #:use-module (gnu packages vulkan) #:use-module (gnu packages web) #:use-module (gnu packages xml) + #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg) #:use-module (srfi srfi-1)) @@ -173,6 +179,39 @@ modules provided by CMake to find common software. In addition, it provides common build settings used in software produced by the KDE community.") (license license:bsd-3))) +(define-public kquickcharts + (package + (name "kquickcharts") + (version "5.96.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/frameworks/" + (version-major+minor version) + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "1sd9mfxk72xfa1kz77s7z312scfm0vwvvgmyi4pypb9cs7d9dq3j")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (system "Xvfb :1 -screen 0 640x480x24 &") + (setenv "DISPLAY" ":1") + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "ctest"))))))) + (inputs (list qtbase-5 qtdeclarative-5 qtquickcontrols2-5 + xorg-server-for-tests)) + (native-inputs (list extra-cmake-modules glslang pkg-config)) + (home-page "https://api.kde.org/frameworks/kquickcharts/html/index.html") + (synopsis "QtQuick plugin providing high-performance charts") + (description + "The Quick Charts module provides a set of charts that can be +used from QtQuick applications for both simple display of data as well as +continuous display of high-volume data.") + (license (list license:lgpl2.1 license:lgpl3)))) + (define-public phonon (package (name "phonon") @@ -194,18 +233,18 @@ common build settings used in software produced by the KDE community.") (inputs (list qtbase-5)) (arguments - `(#:configure-flags - '("-DCMAKE_CXX_FLAGS=-fPIC" - "-DPHONON_BUILD_PHONON4QT5=ON") - #:phases - (modify-phases %standard-phases - (add-before 'install 'patch-installdir - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((regex (string-append "(INSTALL DESTINATION \")" - (assoc-ref inputs "qtbase")))) - (substitute* "cmake_install.cmake" - ((regex all dest) - (string-append dest (assoc-ref outputs "out")))))))))) + (list #:configure-flags + #~'("-DCMAKE_CXX_FLAGS=-fPIC" + "-DPHONON_BUILD_PHONON4QT5=ON") + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'patch-installdir + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((regex (string-append "(INSTALL DESTINATION \")" + #$(this-package-input "qtbase")))) + (substitute* "cmake_install.cmake" + ((regex all dest) + (string-append dest #$output))))))))) (home-page "https://community.kde.org/Phonon") (synopsis "KDE's multimedia library") (description "KDE's multimedia library.") @@ -228,8 +267,7 @@ common build settings used in software produced by the KDE community.") (native-inputs (list extra-cmake-modules pkg-config qttools-5)) (inputs - (list qtbase-5 - phonon + (list phonon qtbase-5 qtx11extras gstreamer @@ -254,7 +292,7 @@ Phonon-GStreamer is a backend based on the GStreamer multimedia library.") (define-public attica (package (name "attica") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -263,7 +301,7 @@ Phonon-GStreamer is a backend based on the GStreamer multimedia library.") name "-" version ".tar.xz")) (sha256 (base32 - "1xlg2sbfd45p9dw0sprpk0fancasp4idxacsf5xksf2ddn2crzp7")))) + "0w1w6w2jia1q32jnn2dhyxmkq64ha1dcbsqj233v4f224rp3aknp")))) (build-system cmake-build-system) (arguments `(#:phases @@ -294,7 +332,7 @@ http://freedesktop.org/wiki/Specifications/open-collaboration-services/") (define-public bluez-qt (package (name "bluez-qt") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -303,26 +341,24 @@ http://freedesktop.org/wiki/Specifications/open-collaboration-services/") name "-" version ".tar.xz")) (sha256 (base32 - "0yc7mq9bnanp5dfv43vp8wpqw5l8qh4aahqpi9sid7jmd6sbywl2")))) + "0h2k2qiskn921cpni5rs7x5ahric6dlllwsrk77akpi4xcsrip2g")))) (build-system cmake-build-system) (native-inputs (list dbus extra-cmake-modules)) (inputs - ;; TODO: qtdeclarative-5 (yields one failing test) - (list qtbase-5)) + (list qtdeclarative-5 + qtbase-5)) (arguments (list #:configure-flags #~(list (string-append "-DUDEV_RULES_INSTALL_DIR=" #$output "/lib/udev/rules.d")) - ;; TODO: Make tests pass: DBUS_FATAL_WARNINGS=0 still yields 7/8 tests - ;; failing. When running after install, tests hang. - #:phases - '(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "DBUS_FATAL_WARNINGS" "0") - (invoke "dbus-launch" "ctest"))))))) + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "DBUS_FATAL_WARNINGS" "0") + (invoke "dbus-launch" "ctest" "-E" "bluezqt-qmltests"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "QML wrapper for BlueZ") (description "bluez-qt is a Qt-style library for accessing the bluez @@ -332,24 +368,33 @@ Bluetooth stack. It is used by the KDE Bluetooth stack, BlueDevil.") (define-public breeze-icons (package (name "breeze-icons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) - (uri (string-append - "mirror://kde/stable/frameworks/" - (version-major+minor version) "/" - name "-" version ".tar.xz")) + (uri (string-append "mirror://kde/stable/frameworks/" + (version-major+minor version) + "/" name "-" version ".tar.xz")) (sha256 (base32 - "1ij723qy6xfkys8a9vp2ll2z2yp7667hfw559gi8cxn825hjx823")))) + "0a3zvmhcfsnxv0jpyjny3sl769p99psadl1872v0qlkax47pvsjp")))) (build-system cmake-build-system) (native-inputs - (list extra-cmake-modules fdupes - python python-lxml)) ;; For 24x24 icon generation - (inputs - (list qtbase-5)) - (arguments ;; fails because duplicate icons exist. TODO: try fix this. - `(#:tests? #f)) + (list extra-cmake-modules + fdupes + `(,gtk+ "bin") + python + python-lxml)) ;for 24x24 icon generation + (inputs (list qtbase-5)) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'install 'update-cache + (lambda* _ + (invoke "gtk-update-icon-cache" + (string-append #$output + "/share/icons/breeze")) + (invoke "gtk-update-icon-cache" + (string-append #$output + "/share/icons/breeze-dark"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "Default KDE Plasma 5 icon theme") (description "Breeze provides a freedesktop.org compatible icon theme. @@ -362,7 +407,7 @@ It is the default icon theme for the KDE Plasma 5 desktop.") (define-public kapidox (package (name "kapidox") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -371,7 +416,7 @@ It is the default icon theme for the KDE Plasma 5 desktop.") name "-" version ".tar.xz")) (sha256 (base32 - "1w5h4xwscix0yjn8d0rcjd7hlmrnbmkjg20diqjabb5wcxsrjiwi")))) + "1k2qk8ibv5dqdhkn2992n8rlmslpmngz83hxb7zrh3pkphdg8v2n")))) (build-system python-build-system) (arguments `(#:tests? #f ; has no test target @@ -402,26 +447,30 @@ documentation.") (define-public karchive (package (name "karchive") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) - (uri (string-append - "mirror://kde/stable/frameworks/" - (version-major+minor version) "/" - name "-" version ".tar.xz")) + (uri (string-append "mirror://kde/stable/frameworks/" + (version-major+minor version) + "/" name "-" version ".tar.xz")) (sha256 (base32 - "1bra1q225xhh8dilwmzc0jgnj5m3dmi4nkz4y8f42si97b4xxxf5")))) + "1ipj7j1iw6g56z0qppji38h6qwbs05piiqqbsw8hdbf96l6cdiq2")))) (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" "karchivetest"))))))) (native-inputs - (list extra-cmake-modules)) - ;; pkg-config ;; For zstd + (list extra-cmake-modules pkg-config)) (inputs - (list bzip2 qtbase-5 xz zlib)) - ;; `(,zstd "lib") ;; FIXME: Tests fail with zstd + (list bzip2 qtbase-5 xz zlib `(,zstd "lib"))) (home-page "https://community.kde.org/Frameworks") (synopsis "Qt 5 addon providing access to numerous types of archives") - (description "KArchive provides classes for easy reading, creation and + (description + "KArchive provides classes for easy reading, creation and manipulation of @code{archive} formats like ZIP and TAR. It also provides transparent compression and decompression of data, like the @@ -435,7 +484,7 @@ GZip format, via a subclass of QIODevice.") (define-public kcalendarcore (package (name "kcalendarcore") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -444,7 +493,7 @@ GZip format, via a subclass of QIODevice.") name "-" version ".tar.xz")) (sha256 (base32 - "181yif830v4gg7nw9s15pvgfm98rmm6xwi2xxy3nxg7nkp14vs5k")))) + "16kclspsjzld9n07z1i8li2pc91ihpqhbk46a4s92nsihs2dkayk")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules perl tzdata-for-tests)) @@ -475,7 +524,7 @@ and the older vCalendar.") (define-public kcodecs (package (name "kcodecs") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -484,7 +533,7 @@ and the older vCalendar.") name "-" version ".tar.xz")) (sha256 (base32 - "05266wjxmzf3qpb2xwlm40cr9h266l5r9dqww81m8bq856pf8ivi")))) + "0n10r7s9r25xp7vlym41qi421kld00niig73yark7yghj0r41jcz")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules gperf qttools-5)) @@ -509,7 +558,7 @@ Internet).") (define-public kconfig (package (name "kconfig") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -518,7 +567,7 @@ Internet).") name "-" version ".tar.xz")) (sha256 (base32 - "1xa8xxm2x9783fqb26wyvg1mp6ybjikngznqdhsk9slhaca73yhz")))) + "15m2bggfr682q68dym7nzmvz7q7pwarzijad1wj0r5cs62l3bkjy")))) (build-system cmake-build-system) (native-inputs (list dbus extra-cmake-modules inetutils qttools-5 @@ -614,7 +663,7 @@ many more.") (define-public kdbusaddons (package (name "kdbusaddons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -623,7 +672,7 @@ many more.") name "-" version ".tar.xz")) (sha256 (base32 - "1y0fd0a1nwgchsk3vx8hvvkw96f0l0533g57xakq4j4xkvxd8l3y")))) + "0fwdmlnci2xn5pi1ywgia3xka3zsh6gl6xpx1gvql7lczk1y490a")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules dbus qttools-5)) @@ -631,8 +680,8 @@ many more.") (list qtbase-5 qtx11extras kinit-bootstrap)) ;; kinit-bootstrap: kinit package which does not depend on kdbusaddons. (arguments - `(#:phases - (modify-phases %standard-phases + (list #:phases + #~(modify-phases %standard-phases (add-before 'configure 'patch-source (lambda* (#:key inputs #:allow-other-keys) ;; look for the kdeinit5 executable in kinit's store directory, @@ -640,7 +689,8 @@ many more.") (substitute* "src/kdeinitinterface.cpp" (("<< QCoreApplication::applicationDirPath..") (string-append - "<< QString::fromUtf8(\"" (assoc-ref inputs "kinit") "/bin\")" ))))) + "<< QString::fromUtf8(\"/" (dirname (search-input-file inputs + "bin/kdeinit5")) "\")" ))))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? @@ -657,7 +707,7 @@ as well as an API to create KDED modules.") (define-public kdnssd (package (name "kdnssd") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -666,7 +716,7 @@ as well as an API to create KDED modules.") name "-" version ".tar.xz")) (sha256 (base32 - "1d3jq64gyj3bc3sf46gnpbmjrm809hva47z7fkwkk9i2lmnmy70w")))) + "0wcjq0g1cdjz9npy31i4rqbx85a95f15w71aamhm8x82l8nysv4g")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -712,7 +762,7 @@ replace the other outdated Graphviz tools.") (define-public kguiaddons (package (name "kguiaddons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -721,7 +771,7 @@ replace the other outdated Graphviz tools.") name "-" version ".tar.xz")) (sha256 (base32 - "028kn9lcvzv8f8b17a3clki7013dmhhcp1l9svvf6hydv97vkfbv")))) + "022qf858khdqklq117i223ihpw8mvdcbcfn8cwqmn2cv9qnfxnqj")))) (build-system qt-build-system) ;; TODO: Build packages for the Python bindings. Ideally this will be ;; done for all versions of python guix supports. Requires python, @@ -740,7 +790,7 @@ interfaces in the areas of colors, fonts, text, images, keyboard input.") (define-public kholidays (package (name "kholidays") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -748,7 +798,7 @@ interfaces in the areas of colors, fonts, text, images, keyboard input.") (version-major+minor version) "/" name "-" version ".tar.xz")) (sha256 - (base32 "0rcd8k2x1w6jszxj18pkzimn5q4v2k7zs9x1pfwszn7xl59b3n4k")))) + (base32 "0ysw52wiyxrkprn0gis85nphpfl1wdb4439i66dfmg7s9nyqpzp0")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -763,7 +813,7 @@ other special events for a geographical region.") (define-public ki18n (package (name "ki18n") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -772,7 +822,7 @@ other special events for a geographical region.") name "-" version ".tar.xz")) (sha256 (base32 - "1jry8bdjgxkcqln7awkj3k8996lh76vya2mf5kwpyxagk6vmr0gy")))) + "0b3r53v2ybhlyqpkjv98dv2w9q49yqqxk9qzbyc4mm7ypq4hvl47")))) (build-system cmake-build-system) (propagated-inputs (list gettext-minimal python)) @@ -804,7 +854,7 @@ translation scripting.") (define-public kidletime (package (name "kidletime") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -813,7 +863,7 @@ translation scripting.") name "-" version ".tar.xz")) (sha256 (base32 - "13piv607n9hmlbd7kkhl7b1wcxj1jq2b5386c6pxrz5caxjwgnmd")))) + "1jdbjkishqnlzz1qrzyg92xnlsl7w89dmrh0zhzaj9bnr5a3icck")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -833,7 +883,7 @@ or user activity.") ;; plasma-framework which is tier 3. (package (name "kirigami") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -842,7 +892,7 @@ or user activity.") "kirigami2-" version ".tar.xz")) (sha256 (base32 - "12ir4q9njl60b242j9raj1xsjs0cizsk7bixwb1hssfn6fzpzqkv")))) + "1l0ggwrprmg5n5y3gxv7h4593fg87d7naxkf30603kkavq0hgks6")))) (properties `((upstream-name . "kirigami2"))) (build-system cmake-build-system) (native-inputs @@ -868,7 +918,7 @@ of applications that follow the Kirigami Human Interface Guidelines.") (define-public kitemmodels (package (name "kitemmodels") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -877,7 +927,7 @@ of applications that follow the Kirigami Human Interface Guidelines.") name "-" version ".tar.xz")) (sha256 (base32 - "1j6kffvgbd07zzzv0kab8mbwa69fmw4b8jczd0wzvmp56idsfc2v")))) + "1z9swjmll833jxy2ym63zzgi9vl8ld79mgypndqszsrd4mfsbs16")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -918,7 +968,7 @@ model to observers (define-public kitemviews (package (name "kitemviews") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -927,7 +977,7 @@ model to observers name "-" version ".tar.xz")) (sha256 (base32 - "1wr62z6jwlg40m8kl9bpiyzkyjmsqx0fhgwc01192k58nl2696lb")))) + "176gqlinsvdgkbg7kr4qd97mnvcnbymrkcs9kg6hm75qzxcaj8dj")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -943,7 +993,7 @@ to flat and hierarchical lists.") (define-public kplotting (package (name "kplotting") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -952,7 +1002,7 @@ to flat and hierarchical lists.") name "-" version ".tar.xz")) (sha256 (base32 - "1yqx260r3dzcinp8s685yzp5f2ihc0s1csckb9zv7z1bzljkn3h9")))) + "0hnzyl1x6acv1psdgsa9prpvnm12j71x6w6wbs1b0fl9bv5zw222")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -970,7 +1020,7 @@ pixel units.") (define-public ksyntaxhighlighting (package (name "ksyntaxhighlighting") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -979,7 +1029,7 @@ pixel units.") "syntax-highlighting-" version ".tar.xz")) (sha256 (base32 - "176prghxfrb7i68jacmq9vkl7j9arsn6gnkzyc2hlkph35js3zqs")))) + "092ilbhhs8xaqblc9w1xksapdzvqyazz8lj011wz4762p1nagiq2")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules perl qttools-5 @@ -1037,7 +1087,7 @@ protocols used in KDE Plasma.") (define-public kwayland (package (name "kwayland") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1047,12 +1097,17 @@ protocols used in KDE Plasma.") (patches (search-patches "kwayland-skip-flaky-test.patch")) (sha256 (base32 - "0dcnsiippwxvwvf1gvp75lx97c4nydzn3x1l8lfy86w9lfslw7zb")))) + "0c0953gm63xhrqb7aspvf28wi7x31mrgaid23dw5gqphkbgis5qw")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config)) (inputs - (list qtbase-5 plasma-wayland-protocols qtwayland-5 wayland wayland-protocols)) + (list libxkbcommon + plasma-wayland-protocols + qtbase-5 + qtwayland-5 + wayland + wayland-protocols)) (arguments (list ;; Tests spawn Wayland sessions that cannot run in parallel. @@ -1075,7 +1130,7 @@ represented by a QPoint or a QSize.") (define-public kwidgetsaddons (package (name "kwidgetsaddons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1084,7 +1139,7 @@ represented by a QPoint or a QSize.") name "-" version ".tar.xz")) (sha256 (base32 - "1igbkrn8qaalan0lyn8r2gqv5v3rwbmb3xv3w26yw77vwp0n789r")))) + "117wki4w2bs1d2pjhi5qpb2b3qhhva6fq9gikba5fb6980kmdayr")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5 xorg-server-for-tests)) @@ -1110,7 +1165,7 @@ configuration pages, message boxes, and password requests.") (define-public kwindowsystem (package (name "kwindowsystem") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1119,7 +1174,7 @@ configuration pages, message boxes, and password requests.") name "-" version ".tar.xz")) (sha256 (base32 - "1ilb3zl3mlndfrqz6gi28x6qqqs45l65d0wmy3lk07lppcw3wxzx")))) + "02l7xmxcilmrxpkkid4m9srl0d8ymqgwpw5j80w3g57p0rahwjl1")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules @@ -1137,13 +1192,6 @@ configuration pages, message boxes, and password requests.") (arguments `(#:phases (modify-phases %standard-phases - (add-before 'check 'blacklist-failing-tests - (lambda _ - ;; Blacklist a failing test-functions. FIXME: Make it pass. - (with-output-to-file "autotests/BLACKLIST" - (lambda _ - (display "[testGroupLeader]\n*\n") - (display "[testClientMachine]\n*\n"))))) ;; requires network (replace 'check (lambda* (#:key tests? #:allow-other-keys) ;; The test suite requires a running window anager @@ -1155,8 +1203,7 @@ configuration pages, message boxes, and password requests.") (system "openbox &") (setenv "CTEST_OUTPUT_ON_FAILURE" "1") (setenv "DBUS_FATAL_WARNINGS" "0") - (invoke "dbus-launch" "ctest" "-E" - "kwindowsystem-kwindowsystemplatformwaylandtest"))))))) + (invoke "dbus-launch" "ctest"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "KDE access to the windowing system") (description "KWindowSystem provides information about and allows @@ -1174,7 +1221,7 @@ lower level classes for interaction with the X Windowing System.") (define-public modemmanager-qt (package (name "modemmanager-qt") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1183,7 +1230,7 @@ lower level classes for interaction with the X Windowing System.") name "-" version ".tar.xz")) (sha256 (base32 - "1rbiqh1sj328cy7flz9pw6vbvgiy3vyv6xp3fk4xv91sxviz1mhd")))) + "0gk4jy3r1451a2dajhnz6lin4lfawc4qdlxp7n7m43ca4d89h13k")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules dbus pkg-config)) @@ -1211,7 +1258,7 @@ messages.") (define-public networkmanager-qt (package (name "networkmanager-qt") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1220,7 +1267,7 @@ messages.") name "-" version ".tar.xz")) (sha256 (base32 - "1gyvgy0wl00asg9bkhjgvqnz32xmazvazcarh3p0640jy2fjrzfz")))) + "0s1h02v9k8nyl30mw7gayzvpb8bnzzp9crcfqpry7rf02rxv9idw")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules dbus pkg-config)) @@ -1249,7 +1296,7 @@ which are used in DBus communication.") (define-public oxygen-icons (package (name "oxygen-icons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1258,7 +1305,7 @@ which are used in DBus communication.") name "5" "-" version ".tar.xz")) (sha256 (base32 - "1f3fj6zr5iygb3s6f8vq2ayy749gxlx5j9h6v2zmkbf4m96sfmq5")))) + "03wk52hqrgj0r73nb4yiq7rnmdn4rrqzrj3cdzbg3flkw5r7wbbq")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules fdupes)) @@ -1273,7 +1320,7 @@ which are used in DBus communication.") (define-public prison (package (name "prison") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -1281,7 +1328,7 @@ which are used in DBus communication.") (version-major+minor version) "/" name "-" version ".tar.xz")) (sha256 - (base32 "1kzl8rbyj9ik83p1qb8jl32vr06vkzzvr1hpasj50sg3ajq8a9xs")))) + (base32 "1ppqm1f06q8fc1ncvzn9a133npmvlh1qxgvvbpwn6m0a8cr7ac6w")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1323,7 +1370,7 @@ libpulse.") (define-public qqc2-desktop-style (package (name "qqc2-desktop-style") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1332,7 +1379,7 @@ libpulse.") name "-" version ".tar.xz")) (sha256 (base32 - "0ff9vd34wss9na2m3gzm8wc2bwq0flda6bv6yqygv5iallw2lz88")))) + "1af7izd4k220dzngf1nwgcw0bi7vl772lpjrqd9fp9rijh74dx7d")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -1344,7 +1391,9 @@ libpulse.") kirigami qtbase-5 qtdeclarative-5 - qtquickcontrols2-5)) + qtquickcontrols2-5 + qtx11extras ; optional + sonnet)) ; optional (home-page "https://community.kde.org/Frameworks") (synopsis "QtQuickControls2 style that integrates with the desktop") (description "This is a style for QtQuickControls2 which is using @@ -1356,7 +1405,7 @@ feel.") (define-public solid (package (name "solid") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1365,7 +1414,7 @@ feel.") name "-" version ".tar.xz")) (sha256 (base32 - "0j64glc1g7mwy2ysaj09w5f7sd2992h91ncknk9gpfsrxhpm814i")))) + "14bf2k40skhyhrmgyyscg7psm1a8klf4z696pimlwjjhnawjfr06")))) (build-system cmake-build-system) (arguments `(#:phases @@ -1390,7 +1439,7 @@ system.") (define-public sonnet (package (name "sonnet") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1399,7 +1448,7 @@ system.") name "-" version ".tar.xz")) (sha256 (base32 - "0i0gksdkfyl8hfbqgrgklqanbvfm3h9gjnv42p2qq40b0zjj0sh4")))) + "0j4p91xx1scg3jmvq6km7bwfjz5ihafk76yf1byb6aqyw50h3bm3")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config qttools-5)) @@ -1418,7 +1467,7 @@ ASpell and HUNSPELL.") (define-public threadweaver (package (name "threadweaver") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1427,7 +1476,7 @@ ASpell and HUNSPELL.") name "-" version ".tar.xz")) (sha256 (base32 - "0ljjnbwmc2zz4q0q1njqny43cj6xdf976vrvijcsqdsril5wzdbq")))) + "1pwinpz5kscx64kc7dn4qf76m64kxzp92zjk8j2a2s1mx0s0vk2s")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1448,7 +1497,7 @@ uses a job-based interface to queue tasks and execute them in an efficient way." (define-public kactivities (package (name "kactivities") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1457,7 +1506,7 @@ uses a job-based interface to queue tasks and execute them in an efficient way." name "-" version ".tar.xz")) (sha256 (base32 - "0g16k3v6i20rc6h0js4pk00d6yg236bs0kxj88q21d5c934hbksk")))) + "0n7r88y1b8mph5al2xh8fbw5ckdzdmdzjipf205y20ib35bskd9i")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1493,7 +1542,7 @@ with other frameworks.") (define-public kauth (package (name "kauth") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1502,7 +1551,7 @@ with other frameworks.") name "-" version ".tar.xz")) (sha256 (base32 - "1hi36504bbr0266wl08kqiq61xysl3dw3kpgjfbgx169m0m3gmx9")))) + "0nzdvx2mibpq1cgzpll9ffjr46vch1qvriaywyqih0iybx6mx5z6")))) (build-system cmake-build-system) (native-inputs (list dbus extra-cmake-modules qttools-5)) @@ -1537,7 +1586,7 @@ utilities.") (define-public kcompletion (package (name "kcompletion") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1546,7 +1595,7 @@ utilities.") name "-" version ".tar.xz")) (sha256 (base32 - "1jmrd2mfz27qfn6dq1mk6bcqlagmifbf9vnayi1mkqa9jsj4dwdj")))) + "191vid00zskvhl6dgj6yz9iyvwdcmg35l5gq68ggjr17cj59acsf")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -1562,16 +1611,18 @@ integrated it into your application's other widgets.") (define-public kcontacts (package (name "kcontacts") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/frameworks/" (version-major+minor version) "/" name "-" version ".tar.xz")) + (patches + (search-patches "kcontacts-incorrect-country-name.patch")) (sha256 (base32 - "075mw7clqf7qycngly21q3m0js3g8pcgqc2x3alp28f4zq3c8m21")))) + "0g3lg1i9rg7hjw7xjx9228sy54dy35lgwghcjds5cawszl5yi106")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules xorg-server)) ; for the tests @@ -1593,14 +1644,8 @@ integrated it into your application's other widgets.") (setenv "HOME" (getcwd)) (system "Xvfb :1 -screen 0 640x480x24 &") (setenv "DISPLAY" ":1") - ;; testrounddrip fail inconsistently. - ;; addresstest produces wrong value: - ;;Actual (address.formattedAddress(QStringLiteral("Jim Knopf"))): - ;;"Jim Knopf\nLummerlandstr. 1\n12345 Lummerstadt\n\nGERMANY" - ;;Expected (result) : - ;;"Jim Knopf\nLummerlandstr. 1\n12345 Lummerstadt\n\nGERMANIA" (invoke "ctest" "-E" - "(kcontacts-addresstest|kcontacts-emailtest|kcontacts-phonenumbertest|kcontacts-soundtest|kcontacts-secrecytest|kcontacts-geotest|kcontacts-keytest|kcontacts-testroundtrip|kcontacts-impptest|kcontacts-birthdaytest|kcontacts-addresseetest)"))))))) + "(kcontacts-birthdaytest|kcontacts-testroundtrip|kcontacts-addresstest)"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "API for contacts/address book data following the vCard standard") (description "This library provides a vCard data model, vCard @@ -1612,7 +1657,7 @@ localized country name to ISO 3166-1 alpha 2 code mapping and vice verca. (define-public kcrash (package (name "kcrash") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1621,7 +1666,7 @@ localized country name to ISO 3166-1 alpha 2 code mapping and vice verca. name "-" version ".tar.xz")) (sha256 (base32 - "05sw3lh4lw5jgl7gvxvpyl6nims9j4b1hjsn365fa2p48qmsx6v5")))) + "03ba3x9jgp15dxgwbjnv5s98f5di2z4ncp4hiv1qkyiibqqfx6kf")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1636,7 +1681,7 @@ application crashes.") (define-public kdoctools (package (name "kdoctools") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1645,7 +1690,7 @@ application crashes.") name "-" version ".tar.xz")) (sha256 (base32 - "04nk87dbmnf9840401s40mxlsfh9is1l1mqky9xi5mcghbp0308b")))) + "0ygpjasdynsmb3c8rdwnc5jminl5f34cmqnihsig831xsq8z6chs")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1691,7 +1736,7 @@ from DocBook files.") (define-public kfilemetadata (package (name "kfilemetadata") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1700,7 +1745,7 @@ from DocBook files.") name "-" version ".tar.xz")) (sha256 (base32 - "0sh3malq6007fp5m4hica20ha8z5abqzq5ifcmrpm8zqmm5aa2bq")))) + "1nsvslhs2kiff3r5ji8z931lh6srvjzzvwnv9cs0j74sr46c6rkn")))) (build-system cmake-build-system) (arguments `(#:phases @@ -1715,9 +1760,11 @@ from DocBook files.") (native-inputs (list extra-cmake-modules pkg-config)) (inputs (list attr - ;; TODO: EPub http://sourceforge.net/projects/ebook-tools + ebook-tools karchive + kconfig kcoreaddons + kdegraphics-mobipocket ki18n qtmultimedia-5 qtbase-5 @@ -1739,7 +1786,7 @@ by applications to write metadata.") (define-public kimageformats (package (name "kimageformats") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1748,7 +1795,7 @@ by applications to write metadata.") name "-" version ".tar.xz")) (sha256 (base32 - "0dbl2varirp5f1bd8173jlhmkc3ql16yg0d6w04nc56hy973bkm5")))) + "0v4jr1lh2qjk453q8mpz94cd98k4kmjrykn8kxrd7zvrkaa4snfy")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -1791,7 +1838,7 @@ formats.") (define-public kjobwidgets (package (name "kjobwidgets") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1800,7 +1847,7 @@ formats.") name "-" version ".tar.xz")) (sha256 (base32 - "1w1h9vnlq1j72812558cl5dlq7f80nnh5i30qmkpbvv49xhhq2dl")))) + "0f87n5d3h2f9y1z2imfd0jj9108wbcxg7dg4k1c53zar2lrfx4wc")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -1815,7 +1862,7 @@ asynchronous jobs.") (define-public knotifications (package (name "knotifications") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1824,10 +1871,10 @@ asynchronous jobs.") name "-" version ".tar.xz")) (sha256 (base32 - "11fbqylchzvm0pfw8bvy03px5zcg4jbch39vzcvnl6si7vikm4qj")))) + "10whr3wjldaxdvbj6i250rqgsy2m1n606ja1yka571f1fz7laqcd")))) (build-system cmake-build-system) (native-inputs - (list extra-cmake-modules dbus qttools-5)) + (list extra-cmake-modules dbus pkg-config qttools-5)) (inputs (list kcodecs kconfig @@ -1858,7 +1905,7 @@ covers feedback and persistent events.") (define-public kpackage (package (name "kpackage") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1867,7 +1914,7 @@ covers feedback and persistent events.") name "-" version ".tar.xz")) (sha256 (base32 - "0gsxizpqa47apbvchga3f0w86v4jh8z1vyf0kifipz17fay4ws8d")))) + "1234jq9qqhq2z5afkkniz6w5s1ab9r4x9wamq3c9y08nzjq634py")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1914,7 +1961,7 @@ were traditional plugins.") (define-public kpty (package (name "kpty") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1923,7 +1970,7 @@ were traditional plugins.") name "-" version ".tar.xz")) (sha256 (base32 - "15swvv6qhvc654wyvxzbjbnzrd2vwn0mr4lby1x6x5f4c9br0cip")))) + "0arxbdxldwnrcg5x1vpvkwdd4hayrpqvn08jz6r7zb4s9h1582ww")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1949,7 +1996,7 @@ and communicating with them using a pty.") (define-public kunitconversion (package (name "kunitconversion") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1958,7 +2005,7 @@ and communicating with them using a pty.") name "-" version ".tar.xz")) (sha256 (base32 - "1qls3319gwn1nzaq04wrqjhbchk0s0pfx97m4za63yzvapvym73g")))) + "0lhyg1d1k25kqk94lzy8mb06p4c17limmcrzirnsnxjvhjrc6r05")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ;; Requires network. (native-inputs @@ -1976,7 +2023,7 @@ gallons).") (define-public syndication (package (name "syndication") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -1985,7 +2032,7 @@ gallons).") name "-" version ".tar.xz")) (sha256 (base32 - "1q60dznlkbncqqgjnp3lq3x0f6r7wvz141ajkymmxlgfq3wdpcd4")))) + "04py880hxkvidydsqcyjbkq0wv9cp42d7svkdgf74fmzfyfrmrax")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -2008,7 +2055,7 @@ between feed formats.") (define-public baloo (package (name "baloo") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2017,7 +2064,7 @@ between feed formats.") name "-" version ".tar.xz")) (sha256 (base32 - "1icpxmmxhvgdr6zxpz0wybc82nyy595cmr09067i82kh7v5dj66l")))) + "0x515lnvrzlnsv5i924q17mzi88k00krj90myad17s0g7p5pi1rw")))) (build-system cmake-build-system) (propagated-inputs (list kcoreaddons kfilemetadata)) @@ -2070,7 +2117,7 @@ maintaining an index of the contents of your files.") (define-public kactivities-stats (package (name "kactivities-stats") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2079,7 +2126,7 @@ maintaining an index of the contents of your files.") name "-" version ".tar.xz")) (sha256 (base32 - "0lfanv55b7zx5s0a7gh4r41w9yb641j1zjjcvdjfrj7pdh52576s")))) + "0zvw3km1wf91wl9xbjvawjia0847kbs3js4nbf3d0z87l5h6rbx8")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -2096,7 +2143,7 @@ by which applications, and what documents have been linked to which activity.") (define-public kbookmarks (package (name "kbookmarks") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2105,7 +2152,7 @@ by which applications, and what documents have been linked to which activity.") name "-" version ".tar.xz")) (sha256 (base32 - "131yng8wmxrnf3x1i6gg60q3rrya19yk4jnzi5ylafvaw7q2r8b4")))) + "1rpjqz2xnpb2wp2k3pjdclbkb0p96y48x6h8l056nr93alxyrqvi")))) (build-system cmake-build-system) (propagated-inputs (list kwidgetsaddons)) @@ -2137,7 +2184,7 @@ using the XBEL format.") (define-public kcmutils (package (name "kcmutils") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2146,7 +2193,7 @@ using the XBEL format.") name "-" version ".tar.xz")) (sha256 (base32 - "0vff93kja9dq8rf1aapxpfgjxsinm75f5nydxqcihskp8girz0c8")))) + "0jqkg4i16jnxricrhi1cbvv7gjjj7ry3z36mzh11h48ml7rl05qx")))) (build-system cmake-build-system) (propagated-inputs (list kconfigwidgets kservice)) @@ -2192,7 +2239,7 @@ KCModules can be created with the KConfigWidgets framework.") (define-public kconfigwidgets (package (name "kconfigwidgets") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2201,7 +2248,7 @@ KCModules can be created with the KConfigWidgets framework.") name "-" version ".tar.xz")) (sha256 (base32 - "045j6gkp5sf1lc12zwlkr1dz0fd89yrg5b31j4ybk3dyc8jz90hl")))) + "05bwldqc5k6dlzsxjby5565sch6i0mh7jg5cbyjz24xb1fpj0d7b")))) (build-system qt-build-system) (propagated-inputs (list kauth kcodecs kconfig kwidgetsaddons)) @@ -2224,7 +2271,7 @@ KCModules can be created with the KConfigWidgets framework.") (("^\\s*(QDirIterator it\\(.*, QDirIterator::Subdirectories)(\\);)" _ a b) (string-append a " | QDirIterator::FollowSymlinks" b))) (substitute* "CMakeLists.txt" - (("5\\.90\\.0") "5.96.0")))) + (("5\\.90\\.0") "5.98.0")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? @@ -2240,7 +2287,7 @@ their settings.") (define-public kdeclarative (package (name "kdeclarative") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2249,7 +2296,7 @@ their settings.") name "-" version ".tar.xz")) (sha256 (base32 - "1x4r231g0l5im4ala21m5fz5q6nixbx0z6lfia5zjinzlp7x5534")))) + "0y5scmcnzhwvyb7x6fdb59xgdhghw8v9i3r05gx1x7g1gfsw0wh6")))) (build-system cmake-build-system) (propagated-inputs (list kconfig kpackage qtdeclarative-5)) @@ -2303,7 +2350,7 @@ that offer bindings to some of the Frameworks.") (define-public kded (package (name "kded") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2312,7 +2359,7 @@ that offer bindings to some of the Frameworks.") name "-" version ".tar.xz")) (sha256 (base32 - "0x40yvcx2gjb4pngyk2vfrn3z7dbyvksbj1h3ck04fyyma8z3gb3")))) + "1k8yxdnihfvvdjmw7lmd62vi5k1hpvjdcwd7njqxz6178iq7dd75")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -2335,7 +2382,7 @@ started on demand.") (define-public kdesignerplugin (package (name "kdesignerplugin") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2344,7 +2391,7 @@ started on demand.") name "-" version ".tar.xz")) (sha256 (base32 - "0cddad1rdi06l28iiwizfds78dplbvv7j40vphww0ix7cmsh3rh9")))) + "17b0javl6k5zcmx04aqzmh3qdgwvzhf62x603m4pg6xbl3zns67g")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools qttools-5)) @@ -2364,7 +2411,7 @@ ini-style description files.") (define-public kdesu (package (name "kdesu") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2373,7 +2420,7 @@ ini-style description files.") name "-" version ".tar.xz")) (sha256 (base32 - "1wjjjwpfjr7sx10x0236zqjx3jrw6mz60724s5qg269dwfbpahvj")))) + "15fbb7zifk4lhnlwvqhs9svzb80qwms03zbrjfnsc1n1wyyfk7v2")))) (build-system cmake-build-system) (propagated-inputs (list kpty)) @@ -2391,7 +2438,7 @@ with su and ssh respectively.") (define-public kdewebkit (package (name "kdewebkit") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2400,7 +2447,7 @@ with su and ssh respectively.") name "-" version ".tar.xz")) (sha256 (base32 - "0l8nnar4s84igxih5w0fhwd9nvccp7zm53jy2gk6lfbj6gqarfbf")))) + "03bwwgzh1xfj4w7q2cvr7712yrjgf9qhqkqgzypcdb49gpvaq164")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -2423,7 +2470,7 @@ engine WebKit via QtWebKit.") (define-public kemoticons (package (name "kemoticons") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2432,7 +2479,7 @@ engine WebKit via QtWebKit.") name "-" version ".tar.xz")) (sha256 (base32 - "03b5axwvd6ayw1kbl1jv6h04cihp1y1pa835gs3m1qx2ivgj7f75")))) + "0f3d0jmpnqkrjn95sbvjzda923rfdgrlxd4k58pmzd0bblxkcxh2")))) (build-system cmake-build-system) (propagated-inputs (list kservice)) @@ -2459,7 +2506,7 @@ emoticons coming from different providers.") (define-public kglobalaccel (package (name "kglobalaccel") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2468,7 +2515,7 @@ emoticons coming from different providers.") name "-" version ".tar.xz")) (sha256 (base32 - "1sx4fmy8xy22im0i3dw0xdmxrgw2jhnk2wsfy2xw74dsj3adg2iq")))) + "1vr6k7lpxsxa6in60ld2wcdqfpaan5xgbmwm3xyr584x6pv737cl")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config qttools-5)) @@ -2492,7 +2539,7 @@ window does not need focus for them to be activated.") (define-public kiconthemes (package (name "kiconthemes") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2501,7 +2548,7 @@ window does not need focus for them to be activated.") name "-" version ".tar.xz")) (sha256 (base32 - "0w9m956xfpfxp7a63a5v2y10lb9zp2gqfjyfvq3ksxfl961g4hsg")))) + "1qmld8xgabmwx2dh5395pll0a0jgirxhlbqv6aph76jg4lvynkqx")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules qttools-5 shared-mime-info)) @@ -2516,18 +2563,20 @@ window does not need focus for them to be activated.") kitemviews kwidgetsaddons qtbase-5 + qtdeclarative-5 qtsvg-5)) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'check-setup - (lambda* (#:key inputs #:allow-other-keys) - (setenv "XDG_DATA_DIRS" - (string-append (assoc-ref inputs "shared-mime-info") - "/share")) - (setenv "HOME" (getcwd)) - ;; make Qt render "offscreen", required for tests - (setenv "QT_QPA_PLATFORM" "offscreen")))))) + (list #:phases + #~(modify-phases %standard-phases + (add-before 'check 'check-setup + (lambda* (#:key inputs #:allow-other-keys) + (setenv "XDG_DATA_DIRS" + (string-append #$(this-package-native-input + "shared-mime-info") + "/share")) + (setenv "HOME" (getcwd)) + ;; make Qt render "offscreen", required for tests + (setenv "QT_QPA_PLATFORM" "offscreen")))))) (home-page "https://community.kde.org/Frameworks") (synopsis "Icon GUI utilities") (description "This library contains classes to improve the handling of icons @@ -2537,7 +2586,7 @@ in applications using the KDE Frameworks.") (define-public kinit (package (name "kinit") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2546,21 +2595,23 @@ in applications using the KDE Frameworks.") name "-" version ".tar.xz")) (sha256 (base32 - "1y7x80icm2jv9c8917481w1hs1vm2rvvvnc9drw4q7vrjzfx73dq")) + "04654hz3yipnlhy5gz3bkh988fcfl1lv7608k4xa5qnbsxaqh141")) ;; Use the store paths for other packages and dynamically loaded ;; libs (patches (search-patches "kinit-kdeinit-extra_libs.patch")))) (build-system cmake-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-paths - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Set patched-in values: - (substitute* "src/kdeinit/kinit.cpp" - (("GUIX_PKGS_KF5_KIO") (assoc-ref inputs "kio")) - (("GUIX_PKGS_KF5_PARTS") (assoc-ref inputs "kparts")) - (("GUIX_PKGS_KF5_PLASMA") (assoc-ref inputs "plasma-framework")))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Set patched-in values: + (substitute* "src/kdeinit/kinit.cpp" + (("GUIX_PKGS_KF5_KIO") #$(this-package-input "kio")) + (("GUIX_PKGS_KF5_PARTS") #$(this-package-input "kparts")) + (("GUIX_PKGS_KF5_PLASMA") + #$(this-package-input "plasma-framework")))))))) (native-search-paths (list (search-path-specification (variable "KDEINIT5_LIBRARY_PATH") @@ -2604,7 +2655,7 @@ consumption.") (define-public kio (package (name "kio") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2613,11 +2664,12 @@ consumption.") name "-" version ".tar.xz")) (sha256 (base32 - "0xmvgq7cp1kkicmngxjj4cmijaah91jmfqdzzxziphq1rl23k64m")) + "0z1ikpa3an3qmd26h2v48kxxw1jph21i12x4nawvc4x1dp4vkm1d")) (patches (search-patches "kio-search-smbd-on-PATH.patch")))) (build-system cmake-build-system) (propagated-inputs - (list kbookmarks + (list acl + kbookmarks kconfig kcompletion kcoreaddons @@ -2629,14 +2681,14 @@ consumption.") solid)) (native-inputs (list extra-cmake-modules dbus kdoctools qttools-5)) - (inputs (list ;; TODO: LibACL , <ftp://oss.sgi.com/projects/xfs/cmd_tars> - mit-krb5 + (inputs (list mit-krb5 karchive kauth kcodecs kconfigwidgets kcrash kdbusaddons + kded kguiaddons kiconthemes ki18n @@ -2647,14 +2699,15 @@ consumption.") libxml2 libxslt qtbase-5 + qtdeclarative-5 qtscript qtx11extras sonnet `(,util-linux "lib") ; libmount zlib)) (arguments - `(#:phases - (modify-phases %standard-phases + (list #:phases + #~(modify-phases %standard-phases (add-after 'unpack 'patch (lambda _ ;; Better error message (taken from NixOS) @@ -2669,35 +2722,30 @@ consumption.") (setenv "QT_QPA_PLATFORM" "offscreen") (setenv "DBUS_FATAL_WARNINGS" "0") (invoke "dbus-launch" "ctest" - "-E" ; FIXME: 21/67 tests fail. + "-E" ; FIXME: 17/69 tests fail. (string-append "(kiocore-jobtest" - "|fileitemtest" "|kiocore-kmountpointtest" + "|kiocore-kfileitemtest" "|kiocore-ktcpsockettest" "|kiocore-mimetypefinderjobtest" "|kiocore-krecentdocumenttest" "|kiocore-http_jobtest" "|kiogui-openurljobtest" - "|kiocore-threadtest" "|applicationlauncherjob_forkingtest" "|applicationlauncherjob_scopetest" "|applicationlauncherjob_servicetest" "|commandlauncherjob_forkingtest" "|commandlauncherjob_scopetest" "|commandlauncherjob_servicetest" - "|kiowidgets-kdirlistertest" "|kiowidgets-kdirmodeltest" - "|kiowidgets-kfileitemactionstest" "|kiowidgets-kurifiltertest-colon-separator" - "|kiowidgets-kurifiltertest-space-separator" - "|kiofilewidgets-knewfilemenutest)"))))) + "|kiowidgets-kurifiltertest-space-separator)"))))) (add-after 'install 'add-symlinks ;; Some package(s) (e.g. bluedevil) refer to these service types by ;; the wrong name. I would prefer to patch those packages, but I ;; cannot find the files! (lambda* (#:key outputs #:allow-other-keys) - (let ((kst5 (string-append (assoc-ref outputs "out") - "/share/kservicetypes5/"))) + (let ((kst5 (string-append #$output "/share/kservicetypes5/"))) (symlink (string-append kst5 "kfileitemactionplugin.desktop") (string-append kst5 "kfileitemaction-plugin.desktop")))))))) (home-page "https://community.kde.org/Frameworks") @@ -2714,7 +2762,7 @@ KIO enabled infrastructure.") (define-public knewstuff (package (name "knewstuff") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2723,7 +2771,7 @@ KIO enabled infrastructure.") name "-" version ".tar.xz")) (sha256 (base32 - "0kls40wlqkqirfjhf8kn83saxwahlh4rkm7iypqd81h93gi81fgc")))) + "09mxzpv0l1i5ml963gdnji8rskmi8b2f0hp4rn6ibkcj00z48fgy")))) (build-system cmake-build-system) (propagated-inputs (list attica kservice kxmlgui)) @@ -2768,7 +2816,7 @@ specification.") (define-public knotifyconfig (package (name "knotifyconfig") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2777,7 +2825,7 @@ specification.") name "-" version ".tar.xz")) (sha256 (base32 - "09bcw47zp6rsnk7f83gkmlpylg428a7phn7bbi9mpkdpzc6zvfd2")))) + "1qlmgr5rifygp8zk8qfjwm6k72kfyj8x6hvqwy2a59lfi3wgbm07")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -2810,7 +2858,7 @@ notifications which can be embedded in your application.") (define-public kparts (package (name "kparts") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2819,7 +2867,7 @@ notifications which can be embedded in your application.") name "-" version ".tar.xz")) (sha256 (base32 - "0b68kyi7l3ndw798sll2hrzf6qq6w875n48sc11q6882xilzinh2")))) + "01gcnywbzrgwlk4cws2rr139r95r201yfal1af3jkd7g2x499vgr")))) (build-system qt-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -2860,7 +2908,7 @@ widgets with a user-interface defined in terms of actions.") (define-public kpeople (package (name "kpeople") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2869,7 +2917,7 @@ widgets with a user-interface defined in terms of actions.") name "-" version ".tar.xz")) (sha256 (base32 - "0q3c0ghxa9km5xcq6h0cwa7swfd18h491jpfafy4qgq3nwp0115b")))) + "0wxy8pxkbfqbb4i9v3q912shzck56bk6xra3blhwva82qm9rps0f")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -2896,7 +2944,7 @@ to easily extend the contacts collection.") (define-public krunner (package (name "krunner") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2905,7 +2953,7 @@ to easily extend the contacts collection.") name "-" version ".tar.xz")) (sha256 (base32 - "0wd2nmhw9mb09mm88cnkmirwgxdnvkrkyjvaiqh9k74xqsggnplk")))) + "0kch839xw09h1lddqgdcfwniq6rza5wdyyzcx99hcasn7l60nhsj")))) (build-system cmake-build-system) (propagated-inputs (list plasma-framework)) @@ -2914,7 +2962,8 @@ to easily extend the contacts collection.") ;; For tests. dbus)) (inputs - (list kauth + (list kactivities + kauth kbookmarks kcodecs kcompletion @@ -2935,26 +2984,24 @@ to easily extend the contacts collection.") solid threadweaver)) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-paths-for-test - ;; This test tries to access paths like /home, /usr/bin and /bin/ls - ;; which don't exist in the build-container. Change to existing paths. - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "autotests/runnercontexttest.cpp" - (("/home\"") "/tmp\"") ;; single path-part - (("//usr/bin\"") (string-append (getcwd) "\"")) ;; multiple path-parts - (("/bin/ls") - (search-input-file inputs "/bin/ls"))))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" (getcwd)) - (setenv "QT_QPA_PLATFORM" "offscreen") - (invoke "dbus-launch" "ctest" - "-E" ;; Some tests fail - "(runnercontexttest|dbusrunnertest|\ -runnermanagersinglerunnermodetest|runnermanagertest)"))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-paths-for-test + ;; This test tries to access paths like /home, /usr/bin and /bin/ls + ;; which don't exist in the build-container. Change to existing paths. + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "autotests/runnercontexttest.cpp" + (("/home\"") "/tmp\"") ;; single path-part + (("//usr/bin\"") (string-append (getcwd) "\"")) ;; multiple path-parts + (("/bin/ls") + (search-input-file inputs "/bin/ls"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "dbus-launch" "ctest"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "Framework for Plasma runners") (description "The Plasma workspace provides an application called KRunner @@ -2966,7 +3013,7 @@ typed.") (define-public kservice (package (name "kservice") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -2975,7 +3022,7 @@ typed.") name "-" version ".tar.xz")) (sha256 (base32 - "1zg3a35my8ba5ikmlg9s3wc9r0s5a2x0rggiiv9znhfi3snvi6gd")))) + "0lgwpcdkkbxwq84zp5aymrdwy0iacqxz5ckc89pymcm0bacyhl31")))) (build-system cmake-build-system) (propagated-inputs (list kconfig kcoreaddons kdoctools)) @@ -3017,7 +3064,7 @@ types or handled by application specific code.") (define-public ktexteditor (package (name "ktexteditor") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3026,7 +3073,7 @@ types or handled by application specific code.") "ktexteditor-" version ".tar.xz")) (sha256 (base32 - "071jx26ycyk31bh167cq5fwx8xkr4ldjg8zlhn9dh7wa3rjpp183")))) + "1pazi9rz4v95g31s7d26yla8rcb0cgd08mlmdcasywsaxc8nn7vw")))) (build-system cmake-build-system) (propagated-inputs (list kparts @@ -3034,7 +3081,7 @@ types or handled by application specific code.") (native-inputs (list extra-cmake-modules pkg-config)) (inputs - (list ;; TODO: editor-config + (list editorconfig-core-c karchive kauth kbookmarks @@ -3049,6 +3096,7 @@ types or handled by application specific code.") kitemviews ki18n kjobwidgets + kparts kservice ktextwidgets kwidgetsaddons @@ -3062,23 +3110,23 @@ types or handled by application specific code.") solid sonnet)) (arguments - `(#:phases - (modify-phases %standard-phases + (list #:phases + #~(modify-phases %standard-phases (add-after 'unpack 'setup (lambda* (#:key inputs #:allow-other-keys) (setenv "XDG_DATA_DIRS" ; FIXME build phase doesn't find parts.desktop - (string-append (assoc-ref inputs "kparts") "/share")))) + (string-append #$(this-package-input "kparts") "/share")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? ;; Maybe locale issues with tests? (setenv "QT_QPA_PLATFORM" "offscreen") - (invoke "ctest" "-E" "(completion_test|kateview_test|movingrange_test)")))) + (invoke "ctest" "-E" "(kateview_test|movingrange_test)")))) (add-after 'install 'add-symlinks ;; Some package(s) (e.g. plasma-sdk) refer to these service types ;; by the wrong name. I would prefer to patch those packages, but ;; I cannot find the files! (lambda* (#:key outputs #:allow-other-keys) - (let ((kst5 (string-append (assoc-ref outputs "out") + (let ((kst5 (string-append #$output "/share/kservicetypes5/"))) (symlink (string-append kst5 "ktexteditorplugin.desktop") (string-append kst5 "ktexteditor-plugin.desktop")))))))) @@ -3093,7 +3141,7 @@ library.") (define-public ktextwidgets (package (name "ktextwidgets") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3102,7 +3150,7 @@ library.") name "-" version ".tar.xz")) (sha256 (base32 - "1vab4qmqq9268bwzx6xia2bcz8rdmiwlgjkbkk8nci2pnmhjrzpj")))) + "14ivmpng7x9rsk3x6kyd86jabzqxgjcdrma1im44wacnvisi4llk")))) (build-system qt-build-system) (propagated-inputs (list ki18n sonnet)) @@ -3131,7 +3179,7 @@ It supports rich text as well as plain text.") (define-public kwallet (package (name "kwallet") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3140,8 +3188,16 @@ It supports rich text as well as plain text.") name "-" version ".tar.xz")) (sha256 (base32 - "0rj610c7i66fbv1x0i0sfn9mac8fkqir4vwgaq1ad5i9ca36h1jq")))) + "0kwxkxlk0xlxkjgpjpb40xfl2l9hnhpymb4lxw4zwlxjn81r6sab")))) (build-system cmake-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? ;; Seems to require network. + (invoke "ctest" "-E" + "(fdo_secrets_test)"))))))) (native-inputs (list extra-cmake-modules kdoctools)) (inputs @@ -3162,6 +3218,7 @@ It supports rich text as well as plain text.") libgcrypt phonon qgpgme + qca qtbase-5)) (home-page "https://community.kde.org/Frameworks") (synopsis "Safe desktop-wide storage for passwords") @@ -3173,7 +3230,7 @@ the passwords on KDE work spaces.") (define-public kxmlgui (package (name "kxmlgui") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3182,12 +3239,12 @@ the passwords on KDE work spaces.") name "-" version ".tar.xz")) (sha256 (base32 - "1hiz2fgwpc4mgh2zzir0qi18pjsc3052lf888rc1pgql90faxb1k")))) + "08n5l3zgkh0fxaqwrfx5mk4j5wq9ylkpxd37751qcivpag7l0x45")))) (build-system cmake-build-system) (propagated-inputs (list kconfig kconfigwidgets)) (native-inputs - (list extra-cmake-modules qttools-5)) + (list extra-cmake-modules qttools-5 xorg-server-for-tests)) (inputs (list attica kauth @@ -3204,14 +3261,15 @@ the passwords on KDE work spaces.") qtbase-5 sonnet)) (arguments - `(#:tests? #f ; FIXME: 1/5 tests fail. - #:phases - (modify-phases %standard-phases - (add-before 'check 'check-setup - (lambda _ - (setenv "HOME" (getcwd)) - ;; make Qt render "offscreen", required for tests - (setenv "QT_QPA_PLATFORM" "offscreen")))))) + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") ;; These tests fail + (invoke "ctest" "-E" + "(ktoolbar_unittest|kxmlgui_unittest)"))))))) (home-page "https://community.kde.org/Frameworks") (synopsis "Framework for managing menu and toolbar actions") (description "KXMLGUI provides a framework for managing menu and toolbar @@ -3224,7 +3282,7 @@ descriptions for integrating actions from plugins.") (define-public kxmlrpcclient (package (name "kxmlrpcclient") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3233,7 +3291,7 @@ descriptions for integrating actions from plugins.") name "-" version ".tar.xz")) (sha256 (base32 - "1jrmrzcvnnw7q7pxgfpcz8608jmxqxf89habmgwv71b8kjz3vgaw")))) + "09apfrkgvvzv8zwxyjbi5qb145a9awirk02nx474bshgypfqslpb")))) (build-system cmake-build-system) (propagated-inputs (list kio)) @@ -3267,7 +3325,7 @@ setUrl, setUserAgent and call.") (define-public plasma-framework (package (name "plasma-framework") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3276,7 +3334,7 @@ setUrl, setUserAgent and call.") name "-" version ".tar.xz")) (sha256 (base32 - "14myvv70pixygb20c136sk7prv5f5dca53fgc74dk6c28hwyldh2")))) + "1bmwvk0pj0bnb8qhcl0bz82r63nls6h7lzzmkfkdwcwmjifmiqg4")))) (build-system cmake-build-system) (propagated-inputs (list kpackage kservice)) @@ -3318,11 +3376,6 @@ setUrl, setUserAgent and call.") (arguments `(#:phases (modify-phases %standard-phases - ;; Fix based on https://invent.kde.org/frameworks/plasma-framework/-/issues/13 - (add-after 'unpack 'apply-fix - (lambda* _ - (substitute* "src/scriptengines/qml/CMakeLists.txt" - (("KF5::ConfigQml") "")))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? @@ -3342,7 +3395,7 @@ script engines.") (define-public purpose (package (name "purpose") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3351,7 +3404,7 @@ script engines.") name "-" version ".tar.xz")) (sha256 (base32 - "0gji3dsccbii1gm83dpwry02cqmjrimhj8gnkb6nzvzrnq5xfh3r")))) + "0g9ykhsn9dl3y3qp4wm3r7bkdhpl9mcbg671wa26qx3ba8a2jynr")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -3387,11 +3440,11 @@ need.") (source (origin (inherit (package-source kdbusaddons)) (patches '()))) - (inputs (alist-delete "kinit" (package-inputs kdbusaddons))) + (inputs (modify-inputs (package-inputs kdbusaddons) (delete "kinit"))) (arguments (substitute-keyword-arguments (package-arguments kdbusaddons) ((#:phases phases) - `(modify-phases ,phases + #~(modify-phases #$phases (delete 'patch-source))))))) (define kinit-bootstrap @@ -3408,7 +3461,7 @@ need.") (define-public kde-frameworkintegration (package (name "kde-frameworkintegration") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) (uri (string-append @@ -3417,7 +3470,7 @@ need.") "frameworkintegration-" version ".tar.xz")) (sha256 (base32 - "19piq6h51qh64nbkqnpy6jg91vbl67vg2sh4hlwzsb2lcrmwxgk9")))) + "1mrangjj8lhm4njpkhqna2zwnidkd9crs23gj6kdlwzmiknypi6q")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -3462,7 +3515,7 @@ workspace.") (define-public kdelibs4support (package (name "kdelibs4support") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3471,7 +3524,7 @@ workspace.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "18f99g1g1z1mrkgq3l8kgxjxi60a632p0sg8d46r67b9n008w9m7")))) + (base32 "0hyyrxic1rkw2jrr92rnmbk6bqkfrcnpc917vs7xyansk9799b8f")))) (build-system cmake-build-system) (native-inputs (list dbus @@ -3556,9 +3609,8 @@ workspace.") (with-output-to-file "autotests/BLACKLIST" (lambda _ (display "[testSmb]\n*\n"))) - ;; kuniqueapptest hangs. FIXME: Make this test pass. (invoke "dbus-launch" "ctest" - "-E" "kstandarddirstest|kuniqueapptest")))))) + "-E" "kstandarddirstest")))))) (home-page "https://community.kde.org/Frameworks") (synopsis "KDE Frameworks 5 porting aid from KDELibs4") (description "This framework provides code and utilities to ease the @@ -3579,7 +3631,7 @@ http://community.kde.org/Frameworks/Porting_Notes should help with this.") (define-public khtml (package (name "khtml") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3588,7 +3640,7 @@ http://community.kde.org/Frameworks/Porting_Notes should help with this.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "0lc933z4568962xj7grzy44aj97h76s5vvv1cnj351dzwr5qahpx")))) + (base32 "0bflwrp6i2w6a3fq2m2df655495rpnsmqcm7w1f1dzfndc6yd9i5")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules perl)) @@ -3629,7 +3681,7 @@ technology and using KJS for JavaScript support.") (define-public kjs (package (name "kjs") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3638,7 +3690,7 @@ technology and using KJS for JavaScript support.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "0jhfjjpv5hzbib3p30ngn6ic023fnrvnr8jrbjdzyacjywj69vvp")))) + (base32 "03is1a5b1sfh1nd011lchgir9nrywvax06ilg9y7z0vsn0ick7ik")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules kdoctools perl pkg-config)) @@ -3658,7 +3710,7 @@ support.") (define-public kjsembed (package (name "kjsembed") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3667,7 +3719,7 @@ support.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "1z8h0n4v1qgs2lsxflrzhdfb91jna3y2dxal1qz7i3szjvrf63h0")))) + (base32 "0zb4vr0hp73lzc1gfnpq1grwmlpdvnp8awf3ydx4vqjh9n6jbaf2")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules kdoctools qttools-5)) @@ -3682,7 +3734,7 @@ QObjects, so you can script your applications.") (define-public kmediaplayer (package (name "kmediaplayer") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3691,7 +3743,7 @@ QObjects, so you can script your applications.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "0qqlah4zi0b7b6yb4009kkjqw7fkp1lgvp2mcpxs8vbbshs3376c")))) + (base32 "0wcv99xgg9pxijbjl4cmsgmpwb893ira6wd3ys5ihk2nakbvd09x")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools qttools-5)) @@ -3718,7 +3770,7 @@ KParts instead.") (define-public kross (package (name "kross") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3727,7 +3779,7 @@ KParts instead.") (version-major+minor version) "/portingAids/" name "-" version ".tar.xz")) (sha256 - (base32 "03dvg2jh9587kcp2f9nir727z0qvkcywrgxfi1p1hxq1bx6y8fm2")))) + (base32 "0yjn66r44jxlrm4vz1nf8s64kcw7lmarjpqz1mcgb1n4jc28hs60")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules kdoctools qttools-5)) @@ -3760,7 +3812,7 @@ offers abstract functionality to deal with scripts.") (define-public kdav (package (name "kdav") - (version "5.96.0") + (version "5.98.0") (source (origin (method url-fetch) @@ -3768,7 +3820,7 @@ offers abstract functionality to deal with scripts.") (version-major+minor version) "/" name "-" version ".tar.xz")) (sha256 - (base32 "1zqib8km4fg9aj4gmhx4hm7n7bbrz62l41qb48nz1pc3qia2x1wl")))) + (base32 "02474a3k7yqgnb1sbxbnm6l4cahn88y2631jvkq9xlmcx7xs2dzi")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) diff --git a/gnu/packages/kde-internet.scm b/gnu/packages/kde-internet.scm index 36c60b9fca..cf074452e7 100644 --- a/gnu/packages/kde-internet.scm +++ b/gnu/packages/kde-internet.scm @@ -417,7 +417,7 @@ This package is part of the KDE networking module.") phonon qtbase-5 qtscript - qtwebkit + qtwebengine-5 solid syndication taglib)) diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index 73edce6c33..19066fd289 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -22,12 +22,15 @@ (define-module (gnu packages kde-pim) #:use-module (guix build-system qt) + #:use-module (guix gexp) #:use-module (guix download) + #:use-module (guix gexp) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) #:use-module (gnu packages) #:use-module (gnu packages boost) + #:use-module (gnu packages compression) #:use-module (gnu packages cyrus-sasl) #:use-module (gnu packages databases) #:use-module (gnu packages documentation) @@ -37,31 +40,38 @@ #:use-module (gnu packages kde) #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages openldap) + #:use-module (gnu packages pdf) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages qt) #:use-module (gnu packages search) #:use-module (gnu packages sqlite) + #:use-module (gnu packages tls) #:use-module (gnu packages xml)) (define-public akonadi (package (name "akonadi") - (version "22.04.3") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://kde/stable/release-service/" version - "/src/akonadi-" version ".tar.xz")) - (sha256 - (base32 "0g277jl2ay00p4yhkadvzjn1k2rkriz90ql2qcp5d4fjgs0220ky")) - (patches (search-patches - "akonadi-paths.patch" - "akonadi-timestamps.patch" - "akonadi-not-relocatable.patch")))) + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/akonadi-" version ".tar.xz")) + (sha256 + (base32 + "1yfy0b6kyiq82zkfkx9ldgjlbwg3lgg4di53fqjllmqhzaj1xy91")) + (patches (search-patches "akonadi-paths.patch" + "akonadi-timestamps.patch" + "akonadi-not-relocatable.patch")))) (build-system qt-build-system) (native-inputs - (list extra-cmake-modules qttools-5 shared-mime-info)) + (list dbus + extra-cmake-modules + qttools-5 + shared-mime-info + pkg-config)) (inputs (list boost + libaccounts-qt kconfig kconfigwidgets kcoreaddons @@ -79,33 +89,39 @@ ;; Do NOT add mysql or postgresql to the inputs. Otherwise the binaries ;; and wrapped files will refer to them, even if the user choices none ;; of these. Executables are searched on $PATH then. - qtbase-5 - sqlite)) + signond + qtbase-5)) + (propagated-inputs (list sqlite kaccounts-integration)) (arguments - `(#:tests? #f ;; TODO 135/167 tests fail - #:configure-flags '("-DDATABASE_BACKEND=SQLITE") ; lightweight - #:modules ((ice-9 textual-ports) - ,@%qt-build-system-modules) - #:phases - (modify-phases (@ (guix build qt-build-system) %standard-phases) - (add-before 'configure 'add-definitions - (lambda* (#:key outputs inputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (with-output-to-file "CMakeLists.txt.new" - (lambda _ - (display - (string-append - "add_compile_definitions(\n" - "NIX_OUT=\"" out "\"\n" - ;; pin binaries for mysql backend - ")\n\n")) - (display - (call-with-input-file "CMakeLists.txt" - get-string-all)))) - (rename-file "CMakeLists.txt.new" "CMakeLists.txt"))))))) + (list #:tests? #f + #:configure-flags #~'("-DDATABASE_BACKEND=SQLITE") ;lightweight + #:modules `((ice-9 textual-ports) + ,@%qt-build-system-modules) + #:phases + #~(modify-phases (@ (guix build qt-build-system) %standard-phases) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "PATH" + (string-append (getcwd) "/bin" ":" + (getenv "PATH"))) + (invoke "dbus-launch" "ctest" "-E" + "(AkonadiServer-dbconfigtest|mimetypecheckertest|entitytreemodeltest|akonadi-sqlite-testenvironmenttest|akonadi-sqlite-autoincrementtest|akonadi-sqlite-attributefactorytest|akonadi-sqlite-collectionpathresolvertest|akonadi-sqlite-collectionattributetest|akonadi-sqlite-itemfetchtest|akonadi-sqlite-itemappendtest|akonadi-sqlite-itemstoretest|akonadi-sqlite-itemdeletetest|akonadi-sqlite-entitycachetest|akonadi-sqlite-monitortest|akonadi-sqlite-changerecordertest|akonadi-sqlite-resourcetest|akonadi-sqlite-subscriptiontest|akonadi-sqlite-transactiontest|akonadi-sqlite-itemcopytest|akonadi-sqlite-itemmovetest|akonadi-sqlite-invalidatecachejobtest|akonadi-sqlite-collectioncreatetest|akonadi-sqlite-collectioncopytest|akonadi-sqlite-collectionmovetest|akonadi-sqlite-collectionsynctest|akonadi-sqlite-itemsynctest)")))) + (add-before 'configure 'add-definitions + (lambda* (#:key outputs inputs #:allow-other-keys) + (with-output-to-file "CMakeLists.txt.new" + (lambda _ + (display (string-append + "add_compile_definitions(\n" + "NIX_OUT=\"" + #$output "\"\n" ")\n\n")) + (display (call-with-input-file "CMakeLists.txt" + get-string-all)))) + (rename-file "CMakeLists.txt.new" "CMakeLists.txt")))))) (home-page "https://kontact.kde.org/components/akonadi/") (synopsis "Extensible cross-desktop storage service for PIM") - (description "Akonadi is an extensible cross-desktop Personal Information + (description + "Akonadi is an extensible cross-desktop Personal Information Management (PIM) storage service. It provides a common framework for applications to store and access mail, calendars, addressbooks, and other PIM data. @@ -117,14 +133,14 @@ programs.") (define-public akonadi-calendar (package (name "akonadi-calendar") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akonadi-calendar-" version ".tar.xz")) (sha256 - (base32 "0hcc2hpyhpd7219my7hpjcl24gsr9g8d2bwhlc66da96ray0pzg4")))) + (base32 "1xcnlkipy2rq0bsm811y9khw7dmsgkqxgw18b3lmy29xs7wcsiv5")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -164,14 +180,14 @@ collection and item views.") (define-public akonadi-contacts (package (name "akonadi-contacts") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akonadi-contacts-" version ".tar.xz")) (sha256 - (base32 "080ba08sxb79il7na97m56k3gpwc8pj4bljca3qgw5kwhswj6gnx")))) + (base32 "1mzlv124wa135xfbxl2ghl4n8pi1a6zd64195px1v90qnhjljw28")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -219,14 +235,14 @@ to list and filter contacts.") (define-public akonadi-mime (package (name "akonadi-mime") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akonadi-mime-" version ".tar.xz")) (sha256 - (base32 "1qggacdhj5b5vrhwp1srlrhapl13hcc5d1ff5wlsdip87in4jad1")))) + (base32 "19wbfkvhkyzlz5r49y7rzbn4ay7rm8zyj7d4j3x9j79nprjr4zw0")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules libxslt ;; xslt for generating interface descriptions @@ -269,14 +285,14 @@ with emails through Akonadi easier.") (define-public akonadi-notes (package (name "akonadi-notes") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akonadi-notes-" version ".tar.xz")) (sha256 - (base32 "0ps99717hvsq62fh3zagn5xgw5sc99naiiay5ym9wmfjvhr5slml")))) + (base32 "05sx7h1aw4mx93l4krv4574zpjf63vdrhaiwayqz11wrdpvdq7ww")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -294,14 +310,14 @@ wrapping notes into KMime::Message objects.") (define-public akonadi-search (package (name "akonadi-search") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akonadi-search-" version ".tar.xz")) (sha256 - (base32 "0jpirnnpab6ki2gf5vlzklp04rwm05l8phlzajp2apcddb84lqvm")))) + (base32 "06apb5lx7bs0lfvsnbf8kyxk7yyjrzb1f1wfckfsjaysf0xmdvfg")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules @@ -346,17 +362,71 @@ Akonadi PIM data server. It uses Xapian for indexing and querying.") (license ;; GPL for programs, LGPL for libraries (list license:gpl2+ license:lgpl2.0+)))) +(define-public itinerary + (package + (name "itinerary") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" version ".tar.xz")) + (sha256 + (base32 + "1w1gl4lz8gwf8cmxhsfyp4afiaq9anc8glrxay407bqp28andp3a")))) + (build-system qt-build-system) + (arguments + `(#:tests? #f)) ;Fails 20/27 + (native-inputs (list extra-cmake-modules)) + (inputs (list karchive + kdbusaddons + ki18n + kio + kirigami + kitinerary + kitemmodels + kcoreaddons + kcontacts + kholidays + kmime + knotifications + kpublictransport + kcalendarcore + khealthcertificate + kosmindoormap + kopeninghours + kpkpass + kunitconversion + kwindowsystem + prison + qtdeclarative-5 + qtgraphicaleffects + qtlocation + qtmultimedia-5 + qtquickcontrols2-5 + qqc2-desktop-style + shared-mime-info + solid + sonnet + zlib)) + (home-page "https://invent.kde.org/pim/itinerary") + (synopsis "Itinerary and boarding pass management") + (description + "This package provides a tool for managing itinerary and boarding pass +information.") + (license ;GPL for programs, LGPL for libraries + (list license:gpl2+ license:lgpl2.0+)))) + (define-public kincidenceeditor (package (name "kincidenceeditor") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/incidenceeditor-" version ".tar.xz")) (sha256 - (base32 "0bm25r3l9d1qhlkxz7pd5hmg6xd0y651q8any4q71bd6a023ps0b")))) + (base32 "1znbpqpxkbn79pzhcg5v77bqr345lcmy2h0a6d90rzdmnlh303ln")))) (properties `((upstream-name . "incidenceeditor"))) (build-system qt-build-system) (native-inputs @@ -410,14 +480,14 @@ Akonadi PIM data server. It uses Xapian for indexing and querying.") (define-public kaddressbook (package (name "kaddressbook") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kaddressbook-" version ".tar.xz")) (sha256 - (base32 "18f6xjcmqgslrw12dik9immw3mw0krvzi6y6f0ryr2ry1shqvivb")))) + (base32 "177zgbpgignvglpvbis1q9d36pi1dvyckv3q2gcgd9425gpm0vmb")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -496,17 +566,115 @@ modern blogging web application that provides an XML data interface supports one of the APIs mentioned above.") (license license:lgpl2.0+))) +(define-public kaccounts-integration + (package + (name "kaccounts-integration") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" version ".tar.xz")) + (sha256 + (base32 + "1q1d2a1qknfkgm63gji6ijji35d0b1jy1kvf10a7ac4l1z1fvnpl")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kcmutils + ki18n + kcoreaddons + kdbusaddons + kdeclarative + kwallet + kio + libaccounts-qt + signond)) + (home-page "https://invent.kde.org/network/kaccounts-integration") + (synopsis "Online account management system") + (description "The Kaccounts Integration library provides online account +management system and its Plasma integration components.") + (license license:lgpl2.0+))) + +(define-public kalendar + (package + (name "kalendar") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" version + ".tar.xz")) + (sha256 + (base32 + "0slk9z7p1z5m2kbb8kq05afslxad8w5pjsajxawckcx0mlsd3apj")))) + (build-system qt-build-system) + (arguments + (list #:tests? #f ;All 2 tests fail + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'wrap-script + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (string-append #$output + "/bin/kalendar") + `("PATH" ":" prefix + (,(string-append #$(this-package-input "akonadi") + "/bin")))))) + (delete 'check) + (add-after 'wrap-script 'check-again + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "dbus-launch" "ctest"))))))) + (native-inputs (list dbus extra-cmake-modules)) + (inputs (list akonadi + akonadi-contacts + breeze-icons + grantlee + grantleetheme + kio + kirigami + kdbusaddons + ki18n + kcalendarcore + kcalendarsupport + kconfigwidgets + kwindowsystem + kcoreaddons + kcontacts + kitemmodels + kmime + kidentitymanagement + kpimtextedit + ktextwidgets + akonadi-calendar + keventviews + kcalutils + kxmlgui + kiconthemes + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtsvg-5 + qtquickcontrols-5 + qtgraphicaleffects + qtlocation + qqc2-desktop-style)) + (home-page "https://apps.kde.org/kalendar/") + (synopsis "Calendar application") + (description + "Kalendar is a calendar application using Akonadi to sync with +external services.") + (license license:gpl3+))) + (define-public kcalendarsupport (package (name "kcalendarsupport") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/calendarsupport-" version ".tar.xz")) (sha256 - (base32 "05x5ps15hkbv0cm4am859wzf6r5yiyaadidw3617qcim4sh5smqd")))) + (base32 "09fs15qckydmbs6idl5k1b6gyhjkygsa1r8frlysn1ahhfmxr33p")))) (properties `((upstream-name . "calendarsupport"))) (build-system qt-build-system) (native-inputs @@ -544,14 +712,14 @@ calendaring applications.") (define-public kcalutils (package (name "kcalutils") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kcalutils-" version ".tar.xz")) (sha256 - (base32 "1vv2nv4yc2hwi31b9k0jcxmxgbpaalmdc06jhbcq8qbi20pj70kh")))) + (base32 "1y25csn37lp14ba18gqmw9ssimy4dqi55irx8c89p4p1lypjwfzq")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules libxml2)) ;; xmllint required for tests @@ -582,14 +750,14 @@ functions for accessing calendar data using the kcalcore API.") (define-public kdepim-runtime (package (name "kdepim-runtime") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kdepim-runtime-" version ".tar.xz")) (sha256 - (base32 "1lhkcfdjnxlm8amfczw4pi41grlq951pd67cj1z51whs6b84an27")))) + (base32 "1g6bq27s7nf9rmrbl5kwycl4lzjpp3m088mji3p7qrrv01ywp4mn")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules dbus kdoctools libxslt shared-mime-info)) @@ -677,14 +845,14 @@ package.") (define-public keventviews (package (name "keventviews") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/eventviews-" version ".tar.xz")) (sha256 - (base32 "1346k5fvjdgxhfjhf0mbc7s559ampxc2vfg0i4wk1a6n6d4jpmcr")))) + (base32 "0bkidva045q85z4ymhj4m9ayfbsckjl4cl7nncl48yk2dmanfg51")))) (properties `((upstream-name . "eventviews"))) (build-system qt-build-system) (native-inputs @@ -726,14 +894,14 @@ package.") (define-public kgpg (package (name "kgpg") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kgpg-" version ".tar.xz")) (sha256 - (base32 "196xgbvc68jzacal4wwxgdrwxyiyr49hq0h2dwpzq5yhpfh3fcrw")))) + (base32 "1xs0w6lxwq3hzs8r1cwmygcjilbgwa8zpjxwj6zz1wmbg04gqk36")))) (build-system qt-build-system) (arguments `(#:phases @@ -781,17 +949,51 @@ for applying cryptography to short pieces of text, and can also quickly apply cryptography to the contents of the clipboard.") (license license:gpl2+))) +(define-public khealthcertificate + (package + (name "khealthcertificate") + (version "22.09") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" + (version-major+minor version) + "/khealthcertificate-" version ".tar.xz")) + (sha256 + (base32 + "16vkjpyxwx34pvdpnci0l6mx2bdjialiscjvbdx53xbsq9ff701k")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" + "(icaovdsparsertest|nlcoronacheckparsertest)"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list karchive + kcodecs + ki18n + openssl + qtdeclarative-5 + zlib)) + (home-page "https://api.kde.org/khealthcertificate/html/index.html") + (synopsis "Digital vaccination and recovery certificate library") + (description + "This package provides a library for arsing of digital vaccination, +test and recovery certificates.") + (license license:lgpl2.0))) + (define-public kidentitymanagement (package (name "kidentitymanagement") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kidentitymanagement-" version ".tar.xz")) (sha256 - (base32 "0z1ixwlrdm7dzfxszphf2wma0gjprr0143c46li79g5gzvcrid8w")))) + (base32 "1h76c8k6lvf4dlh9awd4z71hkikm7x71760gljybd6fkygxpm992")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -822,14 +1024,14 @@ cryptography to the contents of the clipboard.") (define-public kimap (package (name "kimap") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kimap-" version ".tar.xz")) (sha256 - (base32 "1k5h7jmzxg8wq58iqk0f1gx5r45pr2895vl7y5ihyav9w0qfqcn0")))) + (base32 "1a3wwzwlp0zsj4brhs22sygfxh65slikapa4iipxjw78mkwhiq8h")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -850,17 +1052,62 @@ easier to do so.") (license ;; GPL for programs, LGPL for libraries (list license:gpl2+ license:lgpl2.0+)))) +(define-public kitinerary + (package + (name "kitinerary") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://invent.kde.org/pim/kitinerary/-/archive/v" + version "/kitinerary-v" version ".tar.gz")) + (sha256 + (base32 + "1gpy5siaw9k4332ii6a87rq162dbmyfkqp1l1k8bmldg1755v3jz")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "dbus-launch" "ctest" "-E" + "(jsonlddocumenttest|mergeutiltest|locationutiltest|knowledgedbtest|airportdbtest|extractorscriptenginetest|pkpassextractortest|postprocessortest|calendarhandlertest|extractortest)"))))))) + (native-inputs (list dbus extra-cmake-modules)) + (inputs (list kpkpass + kcalendarcore + karchive + ki18n + kcoreaddons + kcontacts + kmime + knotifications + shared-mime-info + openssl + poppler + qtbase-5 + qtdeclarative-5 + qtlocation + qtquickcontrols2-5 + libxml2 + zlib)) + (home-page "https://apps.kde.org/itinerary/") + (synopsis + "Data Model and Extraction System for Travel Reservation information") + (description "This package provides a library containing itinerary data +model and itinerary extraction code.") + (license license:lgpl2.0))) + (define-public kldap (package (name "kldap") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kldap-" version ".tar.xz")) (sha256 - (base32 "024xgjffz5n8zz6js06i78pf8s3nd5sbmvhzz7bm3qc05xqxyp75")))) + (base32 "0hqvf939d2sqb2frizw9pnhgpc8vi627882d30ssymw5p5nm58il")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -878,21 +1125,21 @@ protocol for querying and modifying directory services running over TCP/IP.") (define-public kleopatra (package (name "kleopatra") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kleopatra-" version ".tar.xz")) (sha256 - (base32 "1dp421hniyknggirpqqdb7pmsrbidz9qshmd3qnsqvcr9pz301d5")))) + (base32 "1vay6cdrx1l7qyg0rrc7z7rwv1jjpwksqzadka7rpshfqhf3r9y8")))) (build-system qt-build-system) (native-inputs (list dbus extra-cmake-modules gnupg ;; TODO: Remove after gpgme uses fixed path kdoctools)) (inputs (list boost - gpgme + gpgme-1.18 kcmutils kcodecs kconfig @@ -912,7 +1159,7 @@ protocol for querying and modifying directory services running over TCP/IP.") libassuan libkleo breeze-icons ;; default icon set - qgpgme + qgpgme-1.18 qtbase-5)) (arguments `(#:phases @@ -932,14 +1179,14 @@ and retrieving certificates from LDAP servers.") (define-public kmail (package (name "kmail") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kmail-" version ".tar.xz")) (sha256 - (base32 "0x2d8w8hlb62h9q9qkh3cwyg7pwwl7px1rf89vyfp9arfbs030dq")))) + (base32 "1q7d2jazc6792dhwxb2zx66bghdnn43sw6lvdg44a7d9zgik1qzb")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules dbus kdoctools)) @@ -949,7 +1196,7 @@ and retrieving certificates from LDAP servers.") akonadi-mime akonadi-search boost - gpgme + gpgme-1.18 grantlee grantleetheme kbookmarks @@ -996,7 +1243,7 @@ and retrieving certificates from LDAP servers.") libkleo libksieve breeze-icons ; default icon set, required for tests - qgpgme + qgpgme-1.18 qtbase-5 qtdeclarative-5 qtkeychain @@ -1032,14 +1279,14 @@ manager from KDE.") (define-public kmailcommon (package (name "kmailcommon") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/mailcommon-" version ".tar.xz")) (sha256 - (base32 "0vir2p7akihfzb86iwspz3k6j3psc6xxyak4x738dw3lhn22nfzb")))) + (base32 "1lpnfcj2p58lhgcjg6ray5b9ygz7gpb8xh8qkakn4m7cpjhgcj5j")))) (properties `((upstream-name . "mailcommon"))) (build-system qt-build-system) (native-inputs @@ -1086,6 +1333,8 @@ manager from KDE.") libxslt phonon qgpgme + qtwebchannel-5 + qtwebengine-5 qtbase-5)) (arguments `(#:tests? #f)) ;; TODO: 12/62 tests fail @@ -1099,14 +1348,14 @@ dealing with email.") (define-public kmailimporter (package (name "kmailimporter") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/mailimporter-" version ".tar.xz")) (sha256 - (base32 "0hb4ba8vr7wrw8mcrc7hicl8f9r6ihsbwkxxr1qkzk0310yjmcbf")))) + (base32 "1k7gwagcvhj733c48ayxwi1gf37y6w5g6n2b9fknhfs40kqpdri9")))) (properties `((upstream-name . "mailimporter"))) (build-system qt-build-system) (native-inputs @@ -1146,14 +1395,14 @@ e-mail client programs into KMail and KDE PIM.") (define-public kmailtransport (package (name "kmailtransport") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kmailtransport-" version ".tar.xz")) (sha256 - (base32 "0fcgwln40d9h3r4m58mp4m79k425hianjz0ambqckdzp0aspkhzp")))) + (base32 "0hhd1m1kfagyiwwfmsxhpin5c25dsiwbzg188khppn6fp2dh79dg")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -1188,14 +1437,14 @@ mail transport.") (define-public kmbox (package (name "kmbox") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kmbox-" version ".tar.xz")) (sha256 - (base32 "0d3i36zkn3apcjqkbsq633mgrk382xgx8knfg6fkyyc8i55p3dig")))) + (base32 "0n49xqgyx40hml9554zvnycff26qki9fdy32awx9v9l8jbnrmm6p")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1210,14 +1459,14 @@ using a Qt/KMime C++ API.") (define-public kmessagelib (package (name "kmessagelib") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/messagelib-" version ".tar.xz")) (sha256 - (base32 "06vsba8r9sh94y59hmkh8nbg8xhib83sv80qnfw4g9fv5gfjppjh")))) + (base32 "0xq1a064g3h3igrqanfald9n21nnrsg16a4kmn9vn1k03qv1vlp2")))) (properties `((upstream-name . "messagelib"))) (build-system qt-build-system) (native-inputs @@ -1296,14 +1545,14 @@ kwebengineviewer.") (define-public kmime (package (name "kmime") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kmime-" version ".tar.xz")) (sha256 - (base32 "1k9lvq3a728015laj7rklg136hgg256l4snarnc5cw97ijqdm5ng")))) + (base32 "1vz5gw33ncc5lx8fx2nnp8ayxpdhfjwwx226gwa94vhxxkfcnmh4")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1331,14 +1580,14 @@ information in non-ASCII character sets.") (define-public knotes (package (name "knotes") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/knotes-" version ".tar.xz")) (sha256 - (base32 "1bbrcr2s5am7gq3im5s9kk63nrsgz0kfkm3qzhasafnz06zhf1vf")))) + (base32 "076rwgkwx67rn6z0mj0sj77h1jngcpbvrwka3ijg2309r9f2wg8h")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools libxslt)) @@ -1401,14 +1650,14 @@ Features: (define-public kontactinterface (package (name "kontactinterface") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kontactinterface-" version ".tar.xz")) (sha256 - (base32 "0npaxlrvgpg2p8wdaqs03k2gyppbid81k64q6cawin6wrn6zzc9m")))) + (base32 "0j7cck262j8z7m7fm55qa5i936x81ljn3cijrk5c5h881152h4fs")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1429,14 +1678,14 @@ application \"Parts\" to be embedded as a Kontact component (or plugin).") (define-public korganizer (package (name "korganizer") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/korganizer-" version ".tar.xz")) (sha256 - (base32 "0ypscdr0la4pdxz491mryjmg535d0g7c4r62y0l7an5g1ribrjq9")))) + (base32 "0pcyij50k96mrm9vkq0pzr7n0nrgy1d51zrcb3hly7fpl4gvkx4x")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules dbus qttools-5 kdoctools)) @@ -1547,17 +1796,37 @@ and exchanging calendar data, vCalendar and iCalendar.") Virtual Contact File}) files to the KPeople contact management library.") (license license:lgpl2.1+))) +(define-public kpkpass + (package + (name "kpkpass") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" version + "/src/kpkpass-" version ".tar.xz")) + (sha256 + (base32 + "09l6c7nsgfnffgkm0yzjhsfkm79fv9izasislrlzdvca5xninrgb")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list karchive qtbase-5 shared-mime-info)) + (home-page "https://invent.kde.org/pim/kpkpass") + (synopsis "Apple Wallet Pass reader") + (description "This package provides library to deal with Apple Wallet +pass files.") + (license license:lgpl2.0+))) + (define-public kpimcommon (package (name "kpimcommon") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/pimcommon-" version ".tar.xz")) (sha256 - (base32 "1xns3qc5n5fig898bsj3kzda6484n0r406km43gicnly1m7jpar9")))) + (base32 "00gxv1028xdp7ag44z9h6cpmlw55f3rk7i6msymga3pdq639c19y")))) (properties `((upstream-name . "pimcommon"))) (build-system qt-build-system) (native-inputs @@ -1613,14 +1882,14 @@ Virtual Contact File}) files to the KPeople contact management library.") (define-public libgravatar (package (name "libgravatar") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libgravatar-" version ".tar.xz")) (sha256 - (base32 "1zik4y1micgqyz2y6cj5w5sjccm69d49svl72bdjcj5n3r6xl9iq")))) + (base32 "1yhmxl2gqwrn5flr5qm56aqg6rgmqbgcr3pyb4d0vshdfksjr4rc")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) (inputs (list kconfig @@ -1644,14 +1913,14 @@ unnecessary network operations.") (define-public kpimtextedit (package (name "kpimtextedit") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kpimtextedit-" version ".tar.xz")) (sha256 - (base32 "1gb0n8nrx673ya3mgkjs6khjlz7472a932lgpy5pwir48mc57g1d")))) + (base32 "1dxdlspqssxnvha202bgh9yaszs77cph5qd9wcbd45xj07dqgbw1")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -1685,14 +1954,14 @@ text in the text edit to all kinds of markup, like HTML or BBCODE.") (define-public ksmtp (package (name "ksmtp") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/ksmtp-" version ".tar.xz")) (sha256 - (base32 "1l0w7yxmmvkj2wbv49yf73b2ca7k0yxrishkdqgm3q5crahg8l4z")))) + (base32 "13ybnr39pim3r83p56wj98fwj0yk1rspd9g24a8d0qykmnbx57l3")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1724,14 +1993,14 @@ standard protocols for e-mail transmission.") (define-public ktnef (package (name "ktnef") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/ktnef-" version ".tar.xz")) (sha256 - (base32 "0nvvaakjhciqdn0v1697d559p0py5v41iyd0ix2z8sqgw7lb7nkh")))) + (base32 "05rcs0m4dr4p4wxigcnhjmmp15nlf36ka85v8b8gd8630v61w6y6")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1756,14 +2025,14 @@ and allows one to view/extract message formatted text in Rich Text Format.") (define-public libkdepim (package (name "libkdepim") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libkdepim-" version ".tar.xz")) (sha256 - (base32 "1r6hbj3rgma1q1fxmi982widvnq1dajslhwmd21aknnnryspfx7s")))) + (base32 "07ihnps983x3sp74yq5glsq3h3jw4k80mnc4xxzm6ps2vgswah12")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -1803,14 +2072,14 @@ and allows one to view/extract message formatted text in Rich Text Format.") (define-public libkgapi (package (name "libkgapi") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libkgapi-" version ".tar.xz")) (sha256 - (base32 "0m47wqr2m147csypzm38i29msm1mcnn6mx3l0nwfhwsmycf6lsr7")))) + (base32 "065441mbl67wyp4nz03jdygkn5wmnmkj4fiql4mnq99k2v80y0ka")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules qttools-5)) @@ -1838,14 +2107,14 @@ various Google services.") (define-public libkleo (package (name "libkleo") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libkleo-" version ".tar.xz")) (sha256 - (base32 "0nk6bi2z4s0rf0qim00xcmvxyzwax4bjn1f4f6iyw5qdfkc6yvnp")))) + (base32 "05ypgrwynm1hr32hj35faj3sxabi46x8slnbs3pxwz2f2z2ry58a")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools qttools-5)) @@ -1855,6 +2124,7 @@ various Google services.") kcodecs kcompletion kconfig + kconfigwidgets kcoreaddons kcrash ki18n @@ -1885,7 +2155,7 @@ KDE using certificate-based crypto.") (define-public libksieve (package (name "libksieve") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) @@ -1893,7 +2163,7 @@ KDE using certificate-based crypto.") "/src/libksieve-" version ".tar.xz")) (sha256 (base32 - "0s5c49vgsqmbpyk1bhwjb04v6v6vb9xlcms8dvc6f3gyjdchk5lc")))) + "1ia1gjx8x9ym3dml3y403kif50jhcsrqmhivn3j5yxf8abc3rnk6")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -1930,7 +2200,7 @@ KDE using certificate-based crypto.") ;; sieveeditorhelphtmlwidgettest fails with `sigtrap` (substitute* "src/ksieveui/editor/webengine/autotests/CMakeLists.txt" - (("^\\s*(add_test|ecm_mark_as_test)\\W" line) + (("^\\s*(add_test|ecm_mark_as_test|set_tests_properties)\\W" line) (string-append "# " line)))))))) (home-page "https://invent.kde.org/pim/libksieve") (synopsis "KDE Sieve library") diff --git a/gnu/packages/kde-plasma.scm b/gnu/packages/kde-plasma.scm index 2b88ea2afe..89405bacaa 100644 --- a/gnu/packages/kde-plasma.scm +++ b/gnu/packages/kde-plasma.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2020 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2022 Brendan Tildesley <mail@brendan.scot> +;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -25,35 +26,101 @@ (define-module (gnu packages kde-plasma) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix gexp) #:use-module (guix build-system cmake) + #:use-module (guix build-system copy) + #:use-module (guix build-system trivial) #:use-module (guix build-system qt) + #:use-module (gnu packages) #:use-module (gnu packages admin) + #:use-module (gnu packages bash) + #:use-module (gnu packages boost) + #:use-module (gnu packages authentication) + #:use-module (gnu packages bash) #:use-module (gnu packages compression) + #:use-module (gnu packages display-managers) + #:use-module (gnu packages firmware) + #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) + #:use-module (gnu packages ghostscript) + #:use-module (gnu packages gnupg) + #:use-module (gnu packages gl) #:use-module (gnu packages glib) + #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) + #:use-module (gnu packages ibus) + #:use-module (gnu packages iso-codes) + #:use-module (gnu packages kde) #:use-module (gnu packages kde-frameworks) + #:use-module (gnu packages kde-pim) + ;; Including this module breaks the build + ;#:use-module ((gnu packages kde-systemtools) #:select (konsole)) + #:use-module (gnu packages libcanberra) #:use-module (gnu packages linux) + #:use-module (gnu packages libusb) + #:use-module (gnu packages networking) + #:use-module (gnu packages maths) + #:use-module (gnu packages messaging) + #:use-module (gnu packages multiprecision) + #:use-module (gnu packages pciutils) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages polkit) + #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) + #:use-module (gnu packages package-management) ; flatpak + #:use-module (gnu packages video) + #:use-module (gnu packages vpn) + #:use-module (gnu packages vulkan) + #:use-module (gnu packages textutils) #:use-module (gnu packages qt) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg) #:use-module (gnu packages web)) +(define-public bluedevil + (package + (name "bluedevil") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "1dsah7rcx2brcd1d5x7bvhrixx5nvwp1fwq9b8k2zc038xzpx6ys")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config qttools-5)) + (inputs (list kcoreaddons + kwidgetsaddons + kdbusaddons + knotifications + kwindowsystem + plasma-framework + ki18n + kio + kdeclarative + bluez-qt + shared-mime-info + qtdeclarative-5)) + (synopsis "Manage the Bluetooth settings from Plasma") + (description + "This package provides Bluetooth manager for Plasma Shell.") + (home-page "https://invent.kde.org/plasma/bluedevil") + (license (list license:lgpl2.1 license:lgpl3)))) + (define-public breeze (package (name "breeze") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/" name "-" version ".tar.xz")) (sha256 (base32 - "0za75ckgfcdxrh2qxgyl2c1273g2xqwmd55njsis1yvwryadypqw")))) + "0m3ggv5znzfcp25afgl7v5w7m27v5hdvv6jw9vrvwbqj8lzq1hlx")))) (build-system qt-build-system) ;; TODO: Warning at /gnu/store/…-kpackage-5.34.0/…/KF5PackageMacros.cmake: ;; warnings during generation of metainfo for org.kde.breezedark.desktop: @@ -93,7 +160,7 @@ the Plasma Desktop. Breeze is the default theme for the KDE Plasma desktop.") (define-public breeze-gtk (package (name "breeze-gtk") - (version "5.19.5") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" @@ -101,7 +168,7 @@ the Plasma Desktop. Breeze is the default theme for the KDE Plasma desktop.") "-" version ".tar.xz")) (sha256 (base32 - "1j2nq9yw1ragmgwrz9f6ca4ifpi86qv1bbprdgd2qm2yh7vb44sj")))) + "0wj8qzy2104ggczxagxm45zwsvvpwd6jjnbv1893mhlr6f2zrbmh")))) (build-system qt-build-system) (arguments '(#:tests? #f)) ;no 'test' target @@ -114,17 +181,186 @@ Breeze is the default theme for the KDE Plasma desktop.") (license (list license:bsd-3 ;cmake/FindSass.cmake license:lgpl2.1+)))) ;<all other files> +(define-public calindori + (package + (name "calindori") + (version "22.09") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" version + "/calindori-" version ".tar.xz")) + (sha256 + (base32 + "1pwgdqznp76mhk0ikzjhy3c67qgk91kgv69ygqwzlh5hwiw5sl4n")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kconfig + kcoreaddons + kdbusaddons + ki18n + kirigami + kcalendarcore + knotifications + kpeople + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtsvg-5 + qtgraphicaleffects)) + (home-page "https://invent.kde.org/plasma-mobile/calindori") + (synopsis "Calendar for Plasma Mobile") + (description + "This package provides a touch friendly calendar application.") + (license license:gpl3+))) + +(define-public discover + (package + (name "discover") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version + "/" + name + "-" + version + ".tar.xz")) + (sha256 + (base32 + "01vdi66c7v60db25p0qi0q73wgqw6dy2kirbk34bvhld41gpxhhv")))) + (build-system qt-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'set-LDFLAGS + (lambda _ + (setenv "LDFLAGS" (string-append "-Wl,-rpath=" #$output + "/lib/plasma-discover")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" "knsbackendtest"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list appstream-qt + attica + fwupd ; optional + flatpak ; optional + kcoreaddons + kconfig + kcrash + kdbusaddons + ki18n + karchive + kxmlgui + kirigami + kuserfeedback + knewstuff + knotifications + kio + kdeclarative + kcmutils + kidletime + packagekit-qt5 + qtdeclarative-5 + qtgraphicaleffects + qtquickcontrols2-5)) + ;; -- The following features have been disabled: + ;; * Ostree, Library to manage ostree repository. Required to build the rpm-ostree backend + ;; * RpmOstree, rpm-ostree binary to manage the system. Required to build the rpm-ostree backend + ;; + ;; -- The following OPTIONAL packages have not been found: + ;; * Snapd, Library that exposes Snapd, <https://www.snapcraft.io> + ;; Required to build the Snap backend + (synopsis "KDE and Plasma resources management GUI") + (description + "This package provides a way to find and install applications, +games, and tools.") + (home-page "https://invent.kde.org/plasma/discover") + (license (list license:gpl2 license:gpl3)))) + +(define-public drkonqi + (package + (name "drkonqi") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0vw4bfld2jdiwm4g3008x8s1lq1ydf87ckb0fvyzsp11hq9nnnk7")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" "connectiontest"))))))) + (native-inputs (list extra-cmake-modules)) + (inputs (list ki18n + kcoreaddons + kconfig + kservice + kdeclarative + kjobwidgets + kio + kcrash + kcompletion + kwidgetsaddons + kwallet + knotifications + kidletime + kwindowsystem + ksyntaxhighlighting + qtdeclarative-5)) + (synopsis "Crash handler for KDE software") + (description "This package provides an automatic handler for crashed apps.") + (home-page "https://invent.kde.org/plasma/drkonqi") + (license license:gpl2+))) + +(define-public kactivitymanagerd + (package + (name "kactivitymanagerd") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0hsllhqi46n25sr27crnad053ghk3hni2w496g6d2qfmi20l3g4n")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list boost + kconfig + kcoreaddons + kwindowsystem + kglobalaccel + kio + kxmlgui + kdbusaddons + ki18n + kcrash)) + (synopsis "System service to manage user's activities") + (description "This package provides components for managing the KDE Activity +concept.") + (home-page "https://invent.kde.org/plasma/kactivitymanagerd") + (license (list license:gpl2 license:gpl3)))) + (define-public kdecoration (package (name "kdecoration") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/kdecoration-" version ".tar.xz")) (sha256 (base32 - "0b6ynqkndmlac89hv339k365m7wykp9y238df62jlq4vpr1r9x9y")))) + "1x3scszz5nfwqciwc3bv0r04wgqlxs0c9j1090zvn6mjjg2nsyb7")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -137,17 +373,326 @@ These window decorations can be used by for example an X11 based window manager which re-parents a Client window to a window decoration frame.") (license license:lgpl3+))) +(define-public kde-cli-tools + (package + (name "kde-cli-tools") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" version ".tar.xz")) + (patches (search-patches "kde-cli-tools-delay-mime-db.patch")) + (sha256 + (base32 + "0i1lnkyb2bdvbhnr2wsgjy2sjichzxxqkvn30ca85rj21cavk2z3")))) + (build-system qt-build-system) + (arguments + (list #:tests? #f ;TODO: Failing sub-tests 3/7 + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-writable-location + (lambda* _ + (substitute* "keditfiletype/tests/filetypestest.cpp" + (("QStandardPaths::writableLocation.QStandardPaths::\ +GenericDataLocation.") + (string-append "\"" (getcwd) "/\""))))) + (add-before 'check 'setup-env + (lambda* _ + (setenv "HOME" (getcwd))))))) + (native-inputs (list extra-cmake-modules pkg-config shared-mime-info)) + (inputs (list kconfig + kdesu + kdoctools + kiconthemes + ki18n + kcmutils + kio + kservice + kwindowsystem + kactivities + kparts + plasma-workspace + qtx11extras + qtsvg-5)) + (synopsis "CLI tools for interacting with KDE") + (description "This package provides command-line tools based on +KDE Frameworks 5 to better interact with the system.") + (home-page "https://invent.kde.org/plasma/kde-cli-tools") + (license license:lgpl2.0+))) + +(define-public kdeplasma-addons + (package + (name "kdeplasma-addons") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "1a5cq0jz69hlcr22wxi2p5mzxv5xcp88220irxmq0dhpk85kywlx")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" + "(converterrunnertest|spellcheckrunnertest)"))))))) + (native-inputs (list extra-cmake-modules)) + (inputs (list karchive + kconfig + kcoreaddons + kdeclarative + kholidays + ki18n + kio + kcmutils + knotifications + krunner + kservice + kunitconversion + knewstuff + plasma-framework + purpose + sonnet + qtdeclarative-5)) + ;qtwebengine-5)) ;; Optional for online dictionary + (synopsis "Add-ons to improve your Plasma experience") + (description + "This package provides multiple addons for the Plasma Desktop.") + (home-page "https://invent.kde.org/plasma/kdeplasma-addons") + (license license:lgpl2.0))) + +(define-public kgamma + (package + (name "kgamma") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "5-" + version ".tar.xz")) + (sha256 + (base32 + "1c305bs50km7bsn0phz7yj4x2168sxwsw9zxbpcgw4q3r53c0ywz")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kauth + kcoreaddons + kconfig + kconfigwidgets + kdoctools + ki18n)) + (synopsis "Adjust monitor gamma settings") + (description + "This package provides a tool to adjust your monitor gamma settings.") + (home-page "https://invent.kde.org/plasma/kgamma5") + (license license:gpl2+))) + +(define-public khotkeys + (package + (name "khotkeys") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "0c9i4vxiiv90dpzsd2hjwavks87cvwplkj63751z8mazax6r95as")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kdbusaddons + kdoctools + kglobalaccel + ki18n + kcmutils + kio + ktextwidgets + kxmlgui + kdelibs4support + plasma-workspace + qtx11extras)) + (synopsis "Trigger actions with the keyboard") + (description + "This package provides a way to trigger actions when certain keys +are pressed.") + (home-page "https://invent.kde.org/plasma/khotkeys") + (license license:lgpl2.0))) + +(define-public kinfocenter + (package + (name "kinfocenter") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "0zvki76yghkn158s7hb5g9drz7xaqxkmp2747404n2n0gmnmsdif")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-systemsettings-symlink + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "CMakeLists.txt" + (("\\$\\{KDE_INSTALL_FULL_BINDIR\\}/systemsettings5") + (search-input-file inputs + "/bin/systemsettings5")))))))) + (native-inputs (list aha extra-cmake-modules kdoctools pkg-config)) + ;; * vulkaninfo + ;; Wayland KCM + (inputs (list dmidecode + ;; fwupdmgr ;; Packaged on master branch already + kconfig + kconfigwidgets + kcoreaddons + kirigami + ki18n + kcmutils + kio + kservice + libusb + kwidgetsaddons + kdeclarative + kpackage + kwayland + mesa-utils + pciutils + plasma-framework + qtbase-5 + solid + util-linux + vulkan-tools + wayland-utils + xdpyinfo)) + (propagated-inputs (list system-settings)) + (home-page "https://invent.kde.org/plasma/kinfocenter") + (synopsis "View information about computer's hardware") + (description "This package provides tool to view information about +computer's hardware.") + (license (list license:gpl2 license:gpl3)))) + +(define-public kmenuedit + (package + (name "kmenuedit") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" version + ".tar.xz")) + (sha256 + (base32 + "0z85w7w207dnsinsz8yg6s408pwfy3l7wjkcsjpyg8aj8s9x6nl7")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools)) + (inputs (list ki18n + kxmlgui + kdbusaddons + kiconthemes + kio + kitemviews + sonnet + kglobalaccel + kwindowsystem)) + (synopsis "Menu Editor for Plasma Workspaces") + (description "This package provides menu editor for Plasma Workspaces.") + (home-page "https://invent.kde.org/plasma/kmenuedit") + (license license:gpl2+))) + +(define-public kongress + (package + (name "kongress") + (version "22.09") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" version + "/kongress-" version ".tar.xz")) + (sha256 + (base32 + "0pjp2s774sgw2dklqib8alm1a9fkixy3s92i2v8v00znx08zf2jz")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + ;; NOTE: Reporting bugs is linked to web browser, better not link it and let + ;; it reslove through xdg-open in the run time + (inputs (list kirigami + kdbusaddons + ki18n + kcalendarcore + kconfigwidgets + kwindowsystem + kcoreaddons + kcontacts + kitemmodels + knotifications + kxmlgui + kiconthemes + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtgraphicaleffects + qtsvg-5)) + (home-page "https://apps.kde.org/kongress/") + (synopsis "Companion application for conferences") + (description "This application provides list of upcoming conferences with +the schedule and venue information.") + (license license:gpl3+))) + +(define-public kscreen + (package + (name "kscreen") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" version + ".tar.xz")) + (sha256 + (base32 + "0361202n0366jiyv61w06jikh2i4s1fzr6x3chmdykx4fgvbqj7s")))) + (build-system cmake-build-system) + (arguments + ;; TODO: All tests fail + (list #:tests? #f)) + (native-inputs (list extra-cmake-modules qttools-5 pkg-config)) + (inputs (list kconfig + kdbusaddons + kdeclarative + kglobalaccel + ki18n + kwindowsystem + kiconthemes + kcoreaddons + kcmutils + kxmlgui + libkscreen + libxi + plasma-wayland-protocols + qtsensors + qtbase-5 + qtx11extras + xcb-util)) + (propagated-inputs (list plasma-framework)) + (home-page "https://invent.kde.org/plasma/kscreen") + (synopsis "Screen management software") + (description "This package provides the screen management software for +KDE Plasma Workspaces.") + (license license:gpl2+))) + (define-public ksshaskpass (package (name "ksshaskpass") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/ksshaskpass-" version ".tar.xz")) (sha256 (base32 - "0sfl77szvfq9c7v0gsv5nnf7h5kxigyy2z2p1cwmhm1pq4n606nk")))) + "0z8pp2mh4s98jh8jkf6r8v014gb6svapmp0m1npzw7zcmr6jvpn6")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -161,17 +706,99 @@ directly, you need to tell @code{ssh-add} about it. @code{ssh-add} will then call it if it is not associated to a terminal.") (license license:gpl2+))) +(define-public ksystemstats + (package + (name "ksystemstats") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "07xm6gn2k3vsl1pkrd2n9w8w8b7jq26h3cpslqha4ipw0by2mlqa")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" "ksystemstatstest"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list glib + kcoreaddons + kdbusaddons + solid + networkmanager-qt + kiconthemes + kio + ki18n + libksysguard + libnl + eudev + `(,lm-sensors "lib") + network-manager)) + (synopsis "Plugin based system monitoring daemon") + (description + "This package provides a daemon that collects statistics about +the running system.") + (home-page "https://invent.kde.org/plasma/ksystemstats") + (license (list license:gpl2 license:gpl3)))) + +(define-public latte-dock + (package + (name "latte-dock") + (version "0.10.8") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/latte-dock/" + "latte-dock-" version ".tar.xz")) + (sha256 + (base32 + "0ali9i0y0y1c5mdaps5ybhk4nqvzzs5jq27wj8rg8xxqjyfvbah0")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list qtbase-5 + qtdeclarative-5 + knotifications + kwindowsystem + kio + plasma-framework + kwayland + kactivities + kcrash + kiconthemes + knewstuff + karchive + kguiaddons + kdbusaddons + kglobalaccel + kirigami + ki18n + kdeclarative + kcoreaddons + xcb-util + qtx11extras + libsm)) + (synopsis "Latte is a dock based on plasma frameworks") + (description + "Latte is a dock based on plasma frameworks that provides +an elegant and intuitive experience for your tasks and plasmoids.") + (home-page "https://github.com/KDE/latte-dock") + (license license:gpl2+))) + (define-public layer-shell-qt (package (name "layer-shell-qt") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/layer-shell-qt-" version ".tar.xz")) (sha256 (base32 - "06rxqm4wh4mcszrwb2dbgpxj3dqfx0rccyyjp091lbsncqm1gib0")))) + "1mvhklq7n9hhjing704jr3ybq58ixwr9fdg3phnqhmdnqc2q3w0l")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -190,14 +817,14 @@ call it if it is not associated to a terminal.") (define-public kscreenlocker (package (name "kscreenlocker") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/kscreenlocker-" version ".tar.xz")) (sha256 (base32 - "1kii3r3j89avwyb00wrw80k5sj0q4wqgmy1q0yxfps9jk729k3wc")))) + "0mivx0l266310iy52qi94b6wi8w2a8nl7cjn5750x66dz81jl3yj")))) (build-system qt-build-system) (arguments `(#:tests? #f ;; TODO: make tests pass @@ -252,27 +879,74 @@ call it if it is not associated to a terminal.") "@code{kscreenlocker} is a library for creating secure lock screens.") (license license:gpl2+))) +(define-public ksysguard + (package + (name "ksysguard") + (version "5.22.0") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/ksysguard/" version + "/ksysguard-" version ".tar.xz")) + (sha256 + (base32 "0bb2aj46v7ig0wn3ir68igryl2gblz2n75cddn8fwamvbx76570g")))) + (build-system qt-build-system) + ;; TODO: No tests found + (native-inputs + (list extra-cmake-modules kdoctools)) + (inputs + (list kconfig + kcoreaddons + kdbusaddons + ki18n + kiconthemes + kinit + kio + kitemviews + knewstuff + knotifications + kwindowsystem + libksysguard + `(,lm-sensors "lib") + qtbase-5)) + (home-page "https://www.kde.org/applications/system/ksysguard/") + (synopsis "Plasma process and performance monitor") + (description "KSysGuard is a program to monitor various elements of your +system, or any other remote system with the KSysGuard daemon (ksysgardd) +installed.") + (license license:gpl2+))) + (define-public libkscreen (package (name "libkscreen") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1mxkrk04wcyw4xbfiyxbp5iwnhqr10yk39zx5bbjd9zag0vdi7z5")))) + (base32 "17f2pbbkpmw3a32nsqlwd0x5xb71l6dzrh7ldwcqv46nvb54yhfa")))) (build-system qt-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (setenv "WAYLAND_DISPLAY" "libkscreen-test-wayland-backend-0") + (invoke "ctest" "-E" + "(kscreen-testscreenconfig|kscreen-testqscreenbackend|kscreen-testkwaylandbackend|kscreen-testkwaylandconfig|kscreen-testkwaylanddpms)"))))))) (native-inputs (list extra-cmake-modules + pkg-config ;; For testing. dbus)) (inputs (list kwayland libxrandr plasma-wayland-protocols qtbase-5 qtwayland-5 wayland qtx11extras)) - (arguments - '(#:tests? #f)) ; FIXME: 55% tests passed, 5 tests failed out of 11 (home-page "https://community.kde.org/Solid/Projects/ScreenManagement") (synopsis "KDE's screen management software") (description "KScreen is the new screen management software for KDE Plasma @@ -283,16 +957,17 @@ basic needs and easy to configure for those who want special setups.") (define-public libksysguard (package (name "libksysguard") - (version "5.25.3") + (version "5.25.5") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/plasma/" version "/libksysguard-" version ".tar.xz")) + (patches (search-patches "libksysguard-qdiriterator-follow-symlinks.patch")) (sha256 - (base32 "1mrrrxjvqmrnkjwafvqrd2hlvl9gr9y4hn7dv0gf70lp5bl06i89")))) + (base32 "1gqsjsdkp25abqqp4f6cv6ih199q9ad7q1a4lkhjgsh4h8jq1856")))) (native-inputs - (list extra-cmake-modules pkg-config qttools-5)) + (list bash-minimal extra-cmake-modules pkg-config qttools-5)) (inputs (list kauth kcompletion @@ -318,18 +993,16 @@ basic needs and easy to configure for those who want special setups.") qtscript qtwebchannel-5 qtwebengine-5 - qtwebkit qtx11extras zlib)) (build-system qt-build-system) (arguments - (list #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - ;; TODO: Fix this failing test-case - (invoke "ctest" "-E" "processtest"))))))) + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-test + (lambda* _ + (substitute* "autotests/processtest.cpp" + (("/bin/sh") + (which "bash")))))))) (home-page "https://userbase.kde.org/KSysGuard") (synopsis "Network enabled task and system monitoring") (description "KSysGuard can obtain information on system load and @@ -337,10 +1010,33 @@ manage running processes. It obtains this information by interacting with a ksysguardd daemon, which may also run on a remote system.") (license license:gpl3+))) +(define-public kwallet-pam + (package + (name "kwallet-pam") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" version + ".tar.xz")) + (sha256 + (base32 + "14w803lc3s2c0f4mqzzdhpfy5qnlz7wv00pbrc3v4k3zv381ci8n")))) + (build-system qt-build-system) + (arguments + (list #:tests? #f)) ;no tests + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list linux-pam kwallet libgcrypt socat)) + (synopsis "PAM Integration with KWallet") + (description "Provide PAM Integration with KWallet to unlock KWallet when +you login.") + (home-page "https://invent.kde.org/plasma/kwallet-pam") + (license (list license:lgpl2.1+)))) + (define-public kwayland-server (package (name "kwayland-server") - (version "5.24.4") + (version "5.24.6") (source (origin (method url-fetch) (uri (string-append @@ -348,7 +1044,7 @@ with a ksysguardd daemon, which may also run on a remote system.") "/" name "-" version ".tar.xz")) (sha256 (base32 - "1279nqhy1qyz84dkn23rvzak8bg71hbrp09jlhv9mkjdb3bhnyfi")))) + "1wwgb1p177g6vvyf4l5jisigwvy5756ray1x355mlp7bi1pfs664")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -386,3 +1082,1444 @@ wayland-server API.") ;; src/server/drm_fourcc.h carries the MIT license. license:expat)))) +(define-public kwayland-integration + (package + (name "kwayland-integration") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "10xl7yrj519b9s5vq0hqqfz3vvg1fdwggw96snzm44iwycqbgss8")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check-after-install + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + ;; https://bugs.gentoo.org/668872 + (invoke "ctest" "-E" "(idleTest-kwayland-test)")))) + (add-before 'check-after-install 'check-setup + (lambda* (#:key outputs #:allow-other-keys) + (setenv "QT_PLUGIN_PATH" + (string-append #$output + "/lib/qt5/plugins:" + (getenv "QT_PLUGIN_PATH")))))))) + (native-inputs (list extra-cmake-modules wayland-protocols pkg-config)) + (inputs (list kguiaddons + kidletime + kwindowsystem + kwayland + libxkbcommon + wayland + qtbase-5 + qtwayland-5)) + (synopsis "KWayland runtime integration plugins") + (description "This package provides Wayland integration plugins for various +KDE Frameworks components.") + (home-page "https://invent.kde.org/plasma/kwayland-integration") + (license (list license:lgpl2.1 license:lgpl3)))) + +(define-public kwin + (package + (name "kwin") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "1dh7ydwxbb9r53p353d53gq7w9vmp7idvsr4s5ldxmah35436v2s")))) + (build-system qt-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("src/plugins/kdecorations/aurorae/src/aurorae.cpp") + (("(^\\s*QDirIterator it.path, QDirIterator::Subdirectories)(\\);)" + _ a b) + (string-append a + " | QDirIterator::FollowSymlinks" b))) + (substitute* + '("autotests/integration/dont_crash_glxgears.cpp" + "autotests/integration/debug_console_test.cpp" + "autotests/integration/x11_window_test.cpp") + (("setProgram\\(QStringLiteral\\(\"glxgears\"\\)") + (string-append + "setProgram(QByteArrayLiteral(\"" (which "glxgears") "\")"))) + (substitute* + '("src/wayland/tests/renderingservertest.cpp" + "src/wayland/tests/waylandservertest.cpp") + (("QByteArrayLiteral\\(\"Xwayland\"\\)") + (string-append + "QByteArrayLiteral(\"" (which "Xwayland") "\")"))) + (substitute* '("src/xwayland/xwaylandlauncher.cpp") + (("(m_xwaylandProcess->setProgram.QStringLiteral..)(Xwayland)(...;)" + _ a Xwayland b) + (string-append a + (which "Xwayland") b))) + (substitute* '("cmake/modules/Findhwdata.cmake") + (("/usr/share") + (string-append #$hwdata:pnp "/share"))))) + (add-after 'install 'add-symlinks + (lambda* (#:key outputs #:allow-other-keys) + (let ((kst5 (string-append #$output + "/share/kservicetypes5/"))) + (symlink (string-append kst5 "kwineffect.desktop") + (string-append kst5 "kwin-effect.desktop")) + (symlink (string-append kst5 "kwinscript.desktop") + (string-append kst5 "kwin-script.desktop"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "HOME" (getcwd)) + (setenv "XDG_DATA_DIRS" + (string-append #$output "/share:" + (getenv "XDG_DATA_DIRS"))) + (setenv "QT_PLUGIN_PATH" + (string-append #$output + "/lib/qt5/plugins:" + (getenv "QT_PLUGIN_PATH"))) + (setenv "DISPLAY" ":1") + (system "Xvfb :1 &") + (sleep 5) + (invoke "ctest" "-E" + "(kwayland-testXdgDecoration|kwin-testLockScreen|kwin-testPointerInput|kwin-testXdgShellWindow|kwin-testXdgShellWindow-waylandonly|kwin-testSceneOpenGLES|kwin-testSceneOpenGLES-waylandonly|kwin-testInputMethod|kwin-testInputMethod-waylandonly|kwin-testNightColor|kwin-testNightColor-waylandonly|kwin-testPlasmaWindow|kwin-testSceneQPainter|kwin-testLibinputDevice)"))))))) + (native-inputs (list extra-cmake-modules + dbus + kdoctools + mesa-utils + pkg-config + qttools-5 + wayland-protocols-next + xorg-server-for-tests)) + (inputs (list breeze + eudev + fontconfig + freetype + `(,hwdata "pnp") + kactivities + kcmutils + kcompletion + kconfig + kconfigwidgets + kcoreaddons + kcrash + kdbusaddons + kdeclarative + kdecoration + kglobalaccel + ki18n + kiconthemes + kidletime + kio + kirigami + knewstuff + knotifications + kpackage + krunner + kscreenlocker + ktextwidgets + kwayland + kwayland-server + kwindowsystem + kxmlgui + libqaccessibilityclient + lcms + libcap + libepoxy + libglvnd ; For OpenGLES + libinput + libxkbcommon + pipewire-0.3 + plasma-framework + plasma-wayland-protocols + qtbase-5 + qtdeclarative-5 + qtmultimedia-5 + qtwayland-5 + qtx11extras + wayland + xcb-util ;fails at build time without this + xcb-util-cursor + xcb-util-keysyms + xcb-util-wm + xcmsdb + xinput ;XXX: Says disabled in configure phase + xorg-server-xwayland + zlib)) + ;; Runtime-only dependency needed for mapping monitor hardware vendor IDs to full names + ;; * QtQuick.Controls-QMLModule, QML module 'QtQuick.Controls' is a runtime dependency. + ;; * org.kde.plasma.core-QMLModule, QML module 'org.kde.plasma.core' is a runtime dependency. + ;; * org.kde.plasma.components-QMLModule, QML module 'org.kde.plasma.components' is a runtime dependency. + (home-page "https://userbase.kde.org/KWin") + (synopsis "KDE Plasma Window Manager") + (description + "KWin is an easy to use, but flexible, composited Window Manager for +Xorg windowing systems (Wayland, X11) on Linux. Its primary usage is in +conjunction with the KDE Plasma Desktop.") + (license license:gpl2+))) + +(define-public kwrited + (package + (name "kwrited") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "03gw3czdgyf35n6x79x416rk6f7w1ayzmy5pb65v9733nx1j34mh")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kcoreaddons ki18n kpty knotifications)) + (home-page "https://invent.kde.org/plasma/kwrited") + (synopsis "System notification daemon") + (description + "This package provides a daemon that listens to system notifications.") + (license license:gpl2+))) + +(define-public lightly + (package + (name "lightly") + (version "0.4.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Luwx/Lightly") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0qkjzgjplgwczhk6959iah4ilvazpprv7yb809jy75kkp1jw8mwk")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kdecoration + kcoreaddons + kguiaddons + kconfigwidgets + kwindowsystem + ki18n + kiconthemes + qtx11extras)) + (home-page "https://github.com/Luwx/Lightly") + (synopsis "Modern style for Qt applications") + (description + "Lightly is a fork of the Breeze theme that aims to be visually modern +and minimalistic.") + (license license:gpl2+))) + +(define-public milou + (package + (name "milou") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0ijdbiq169sy47g0x22pj9x6abldpfxcnski4w1jh9hi9qz1rc25")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kcoreaddons + ki18n + kdeclarative + kitemmodels + kservice + plasma-framework + kwindowsystem + krunner + qtdeclarative-5)) + (synopsis "Dedicated search application built on top of Baloo") + (description "This package provides a dedicated search application built +on top of Baloo.") + (home-page "https://invent.kde.org/plasma/milou") + (license (list license:gpl2+)))) + +(define-public oxygen-sounds + (package + (name "oxygen-sounds") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "04rn3ccqszznknvblz2i8r406m32hk4d3yzma4vzq93jfk57hdf1")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules)) + (home-page "https://community.kde.org/Frameworks") + (synopsis "Sounds for the KDE desktop") + (description "This package provides Oxygen sounds for the KDE desktop.") + (license license:lgpl3+))) + +(define-public plasma + (package + (name "plasma") + (version "5.25.5") + (source #f) + (build-system trivial-build-system) + (arguments + (list #:builder #~(begin + (mkdir #$output)))) + (propagated-inputs (list bluedevil + breeze + breeze-gtk + discover + drkonqi + kactivitymanagerd + kde-cli-tools + ;; kde-gtk-config + kdecoration + kdeplasma-addons + kgamma + khotkeys + kinfocenter + kmenuedit + kscreen + kscreenlocker + ksshaskpass + ksystemstats + kwallet-pam + kwayland-integration + kwin + kwrited + kinit + layer-shell-qt + libkscreen + libksysguard + milou + ;; oxygen + oxygen-sounds + plasma-browser-integration + plasma-desktop + plasma-disks + plasma-firewall + plasma-integration + plasma-nm + plasma-pa + plasma-systemmonitor + ;; plasma-thunderbolt ;; waiting for bolt + plasma-vault + plasma-workspace + plasma-workspace-wallpapers + polkit-kde-agent + powerdevil + sddm + system-settings + xdg-desktop-portal-kde)) + (synopsis "The KDE Plasma desktop environment") + (home-page "https://kde.org/plasma-desktop/") + (description + "KDE Plasma is an advanced graphical desktop system.") + (license license:gpl2+))) + +(define-public plasma-bigscreen + (package + (name "plasma-bigscreen") + (version "5.25.90") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/unstable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "1445j8hzfvh2z91fa8nxrc0z576c67cq5fxcs19pmzpnjjli1ads")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-startplasma + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "bin/plasma-bigscreen-wayland.in" + (("^startplasma-wayland") + (search-input-file inputs + "/bin/startplasma-wayland"))) + (substitute* "bin/plasma-bigscreen-x11" + (("startplasma-x11") + (search-input-file inputs + "/bin/startplasma-x11")))))))) + (native-inputs (list extra-cmake-modules)) + (inputs (list kactivities + kactivities-stats + plasma-framework + ki18n + kirigami + kdeclarative + kcmutils + knotifications + kio + kwayland + kwindowsystem + plasma-workspace + qtbase-5 + qtmultimedia-5)) + (home-page "https://invent.kde.org/plasma/plasma-bigscreen") + (synopsis "Plasma shell for TVs") + (description + "This package provides a big launcher designed for large screens. It +is controllable via voice or TV remote.") + (license license:gpl2+))) + +(define-public plasmatube + (package + (name "plasmatube") + (version "22.09") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" + version "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "00w9p5fcpv4s406lmcdcbrxf19sgkvf9yy8pfjmf1asvvvi8bpnk")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs + (list kconfig + kirigami + ki18n + qtbase-5 + qtdeclarative-5 + qtmultimedia-5 + qtquickcontrols2-5 + qtsvg-5 + youtube-dl)) + (home-page "https://apps.kde.org/plasmatube/") + (synopsis "Kirigami YouTube video player") + (description "This package provides YouTube video player based +on QtMultimedia and @command{yt-dlp}.") + (license license:gpl3+))) + +(define-public plasma-active-window-control +(let ((commit "0b1c091b5662fb21917064d7809b3be8b4a8be47") + (revision "1")) + (package + (name "plasma-active-window-control") + (version (git-version "1.7.3" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/plasma/plasma-active-window-control") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1lns1n7p6b64z7l3bn27hni100pp3k2whzzzg0adr4hiynycdix6")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs + (list kwindowsystem + libsm + plasma-framework + qtdeclarative-5 + qtx11extras)) + (home-page "https://invent.kde.org/plasma/plasma-active-window-control") + (synopsis "Plasma applet for controlling the currently active window") + (description "This package provides window control applet for the current +active window on Plasma Desktop.") + (license (list license:gpl2 license:gpl3))))) + +(define-public plasma-browser-integration + (package + (name "plasma-browser-integration") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "18pbn5ic5l3m8i1y99yprpwd4x4746aq3abqn1f2cq5h2683h2ia")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + ;; TODO: Figure out how to integrate this package into web browsers + ;; CHROMIUM_EXTENSIONS_DIR - extension for chromium + ;; MOZILLA_DIR - extension for firefox + (inputs (list kio + ki18n + kcoreaddons + kconfig + kcrash + kdbusaddons + knotifications + kitemmodels + krunner + kactivities + purpose + kfilemetadata + kjobwidgets + qtdeclarative-5)) + (propagated-inputs (list plasma-workspace)) + (home-page "https://invent.kde.org/plasma/plasma-browser-integration") + (synopsis "Integrate browsers into the Plasma Desktop") + (description + "This package aims to provide better integration of web browsers with +the KDE Plasma 5 desktop.") + (license license:gpl3+))) + +(define-public plasma-desktop + (package + (name "plasma-desktop") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "05s1pkwr4xmkghp8jrwcyrvjm83n68ngmk2694055xcfgi0pxicg")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules + dbus + kdoctools + intltool + pkg-config + qtsvg-5 + qttools-5)) + (inputs (list packagekit-qt5 + signon-plugin-oauth2 + signond + attica + appstream-qt + baloo + breeze + breeze-icons + eudev + fontconfig + glib + ibus + kaccounts-integration + kactivities + kactivities-stats + kauth + karchive + kcmutils + kconfig + kcoreaddons + kcrash + kdbusaddons + kdeclarative + kded + kdesu + kdelibs4support + kglobalaccel + kguiaddons + kholidays + ki18n + kiconthemes + kidletime + kinit + kio + kitemmodels + knewstuff + knotifications + knotifyconfig + kpackage + kpeople + krunner + kscreenlocker + ktexteditor + ktextwidgets + kunitconversion + kuserfeedback + kwallet + kwayland + kwin + layer-shell-qt + libaccounts-qt + libcanberra + libkscreen + libksysguard + libqalculate + gmp + mpfr + libsm + libxi + libxft + libxkbcommon + libxrender + libxtst + networkmanager-qt + phonon + pipewire-0.3 + plasma-framework + plasma-wayland-protocols + pulseaudio + prison + qqc2-desktop-style + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtwayland + qtx11extras + wayland + wayland-protocols + xcb-util + xcb-util-image + xcb-util-keysyms + xdg-user-dirs + + ;; These are needed for Xserver + xf86-input-libinput + xf86-input-evdev + xorg-server + xf86-input-synaptics + xkeyboard-config + libxkbfile + libxcursor + libxkbcommon)) + (propagated-inputs (list iso-codes kirigami plasma-workspace)) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "kcms/keyboard/iso_codes.h" + (("\"/usr/share/xml/iso-codes\"") + (string-append "\"" (search-input-directory + inputs "/share/xml/iso-codes") + "\""))))) + (add-after 'unpack 'patch-qml-import-path + (lambda _ + (substitute* + '("applets/pager/package/contents/ui/main.qml" + "containments/desktop/package/contents/ui/FolderView.qml" + "containments/desktop/package/contents/ui/main.qml" + "containments/panel/contents/ui/main.qml") + (("^import \"(utils|FolderTools|LayoutManager).js\" as " + line mod) + (string-append "import \"../code/" mod + ".js\" as "))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "XDG_CACHE_HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "ctest" "-E" "foldermodeltest"))))))) + (home-page "https://kde.org/plasma-desktop/") + (synopsis "Plasma for the Desktop") + (description + "Plasma Desktop offers a beautiful looking desktop that takes +complete advantage of modern computing technology. Through the use of visual +effects and scalable graphics, the desktop experience is not only smooth but +also pleasant to the eye. The looks of Plasma Desktop not only provide +beauty, they are also used to support and improve your computer +activities effectively, without being distracting.") + (license license:gpl2+))) + +(define-public plasma-disks + (package + (name "plasma-disks") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0vci2cf8vx2lclypys9rmvjb8haakv6ksrvqm5j28pazbq2kskvl")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kcoreaddons + kdbusaddons + knotifications + ki18n + solid + kservice + kio + kauth + kdeclarative + smartmontools)) + (synopsis "Monitors S.M.A.R.T. capable devices for imminent failure") + (description "This package provides interface to S.M.A.R.T. data of disks.") + (home-page "https://invent.kde.org/plasma/plasma-disks") + (license (list license:gpl2 license:gpl3)))) + +(define-public plasma-firewall + (package + (name "plasma-firewall") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0k3pc0dcsjr2hhh4hr8vhsvaddn66s6imm8skrr02icxqvljs6jh")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list iproute + kcoreaddons + kcmutils + ki18n + kdeclarative + python + qtdeclarative-5)) + (synopsis "Control Panel for system firewall") + (description "This package provides interface to system firewall.") + (home-page "https://invent.kde.org/plasma/plasma-firewall") + (license (list license:gpl2 license:gpl3)))) + +(define-public plasma-integration + (package + (name "plasma-integration") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "1pab56cg2zi8fcaar53lhhh98iw7l07f5lkymkqhsh8a5crfc3yr")))) + (build-system qt-build-system) + (arguments + (list #:tests? #f ;TODO: Failing tests + #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "XDG_CACHE_HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "ctest" "-E" + "(frameworkintegration-kdeplatformtheme_unittest|frameworkintegration-kfontsettingsdata_unittest|frameworkintegration-kfiledialog_unittest|qmltests|frameworkintegration-kfiledialogqml_unittest"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list breeze + kconfig + kio + ki18n + kwidgetsaddons + kconfigwidgets + kiconthemes + knotifications + libxcb + libxcursor + plasma-wayland-protocols + qtdeclarative-5 + qtquickcontrols2-5 + qtwayland-5 + qtx11extras + wayland)) + (home-page "https://invent.kde.org/plasma/plasma-integration") + (synopsis + "Qt Platform Theme integration plugins for the Plasma workspaces") + (description + "This package provides a set of plugins responsible for better +integration of Qt applications when running on a KDE Plasma workspace.") + (license license:lgpl2.0))) + +(define-public plasma-nano + (package + (name "plasma-nano") + (version "5.24.3") + (source (origin + (method url-fetch) + (uri (string-append "https://download.kde.org/stable/plasma/" + version "/plasma-nano-" version ".tar.xz")) + (sha256 + (base32 + "13jxhfi3c3dhg7zdyfqnsii661h1am0w9dsv82dalqvwr1mw28l5")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules pkg-config qttools)) + (inputs (list qtbase-5 + qtdeclarative-5 + plasma-framework + kwindowsystem + kwayland + ki18n)) + (home-page "https://plasma-mobile.org/") + (synopsis "Minimal Plasma Shell package") + (description + "This package provides a minimal implementation of Plasma Shell.") + (license license:lgpl2.0+))) + +(define-public plasma-nm + (package + (name "plasma-nm") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" version + ".tar.xz")) + (sha256 + (base32 + "036bx0qjrjanfxy8aiy6ab7rmm2h8l7wlkvlwhzw2hgl1w03xjps")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "-E" "mobileproviderstest"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + (home-page "https://invent.kde.org/plasma/plasma-nm") + (inputs (list kconfigwidgets + kcompletion + kcoreaddons + kdeclarative + kdbusaddons + kio + ki18n + networkmanager-qt + knotifications + kirigami + plasma-framework + modemmanager-qt + network-manager + qca + kservice + solid + prison + kwallet + kwidgetsaddons + kwindowsystem + openconnect + qtdeclarative-5)) + (synopsis "Plasma applet for managing network connections") + (description "This package provides Plasma applet for managing network +connections.") + (license (list license:lgpl2.1 license:lgpl3)))) + +(define-public plasma-mobile + (package + (name "plasma-mobile") + (version "5.24.3") + (source (origin + (method url-fetch) + (uri (string-append "https://download.kde.org/stable/plasma/" + version "/plasma-mobile-" version ".tar.xz")) + (sha256 + (base32 + "1bwmy7xvd8wmh0snqqjh9jjgawib8ks2g30w48sqxwhplhf3da58")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'install 'wrap-script + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (string-append #$output + "/bin/kwinwrapper") + `("PATH" ":" prefix + (,(string-append #$plasma-framework + "/bin"))))))))) + (native-inputs (list extra-cmake-modules pkg-config qttools)) + (inputs (list bash-minimal + kdeclarative + ki18n + kio + knotifications + kwayland + kwin + modemmanager-qt + networkmanager-qt + plasma-framework + qtbase-5)) + (home-page "https://plasma-mobile.org/") + (synopsis + "General UI components for Plasma Phone including shell, containment and applets") + (description "This package provides user-friendly, privacy-enabling and +customizable platform for mobile devices.") + (license (list license:gpl3+ license:lgpl2.1+)))) + +(define-public plasma-mobile-settings + (package + (name "plasma-mobile-settings") + (version "22.02") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" version + "/plasma-settings-" version ".tar.xz")) + (sha256 + (base32 + "0b7lj3r9z9cz2vr0h15sqqxdaa7m07hsk8i2p8nf4a3yh02ywsxy")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list qtbase-5 + qtdeclarative-5 + kio + modemmanager-qt + networkmanager-qt + ki18n + plasma-framework + kdeclarative + kdbusaddons)) + (home-page "https://plasma-mobile.org/") + (synopsis "Settings application for Plasma Mobile") + (description + "This package provides Settings application for Plasma Mobile.") + (license license:gpl2+))) + +(define-public plasma-mobile-sounds + (package + (name "plasma-mobile-sounds") + (version "0.1") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://kde/stable/plasma-mobile-sounds/" + version "/plasma-mobile-sounds-" version ".tar.xz")) + (sha256 + (base32 + "1br6kzicrr45vgg0ciqczxlcid21n5lfjm6zc06rw86ys7fx7bpi")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (home-page "https://plasma-mobile.org/") + (synopsis "Sounds for Plasma Mobile devices") + (description "This package provides sound files for Plasma Mobile.") + (license (list license:cc0 license:cc-by4.0)))) + +(define-public plasma-pa + (package + (name "plasma-pa") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" + version "/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0g06pm1isnzx4hv6380rjpyr22s4j5iw9083s71vnl4npx28npvb")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools pkg-config)) + (inputs (list glib + kcoreaddons + kdeclarative + kglobalaccel + knotifications + kwindowsystem + kirigami + ki18n + qtdeclarative-5)) + (propagated-inputs (list libcanberra pulseaudio plasma-framework)) + (home-page "https://invent.kde.org/plasma/plasma-pa") + (synopsis "Plasma applet for audio volume management using PulseAudio") + (description + "This package provides Plasma applet for audio volume management using +PulseAudio.") + (license (list license:lgpl2.1 license:lgpl3)))) + +(define-public plasma-pass + (package + (name "plasma-pass") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/" name "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "107pd6cnkd46px83pm3q7vbw10g5pd0qsw77jmr0c774k4xv1w01")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list ki18n kitemmodels kwindowsystem oath-toolkit qtdeclarative-5)) + (propagated-inputs (list plasma-framework)) + (home-page "https://invent.kde.org/plasma/plasma-pass") + (synopsis "Plasma applet for the Pass password manager") + (description + "This package provides a Plasma applet for the Pass password manager.") + (license license:lgpl2.1+))) + +(define-public plasma-phonebook + (package + (name "plasma-phonebook") + (version "0.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-phonebook/" + version "/plasma-phonebook-" version + ".tar.xz")) + (sha256 + (base32 + "13nnzdzpganlp319sc9dm9w5hsjhw4f3w8rb80q3nd8q6nyrpky8")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list kpeople + kirigami + kpeoplevcard + kcoreaddons + kcontacts + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://plasma-mobile.org/") + (synopsis "Phonebook for Plasma Mobile devices") + (description "This package provides contacts application which allows +adding, modifying and removing contacts.") + (license license:lgpl2.0+))) + +(define-public plasma-phone-components + (package + (name "plasma-phone-components") + (version "5.23.4") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/plasma-phone-components-" version + ".tar.xz")) + (sha256 + (base32 + "0ml5pyi90nlmx5550sf3x9263f8mypj4jmdskzabzhnz44ck8vy9")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules pkg-config qttools)) + (inputs (list qtbase-5 + qtdeclarative + kactivities + kauth + kbookmarks + kwin + kcodecs + kcompletion + kconfig + kconfigwidgets + kcoreaddons + kdbusaddons + kdeclarative + ki18n + kio + kitemviews + kjobwidgets + knotifications + kpackage + kpeople + kservice + kwayland + kwidgetsaddons + kwindowsystem + kxmlgui + libphonenumber + modemmanager-qt + plasma-framework + solid)) + (home-page "https://plasma-mobile.org/") + (synopsis "Modules providing phone functionality for Plasma") + (description "This package provides user-friendly, privacy-enabling +and customizable platform for mobile devices.") + (license (list license:gpl3+ license:lgpl2.1+)))) + +(define-public plasma-redshift-control + (let ((commit "d9f38a5f0bcf030be16db1776166581c16e802cb") + (revision "1")) + (package + (name "plasma-redshift-control") + (version (git-version "0.1-pre" revision commit)) + (home-page "https://invent.kde.org/plasma/plasma-redshift-control") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1wadxhy6iljhikfw2rbj9dhwb86f2sgwyf62r7sfq6cszcpgp0xi")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list kwindowsystem plasma-framework redshift)) + (synopsis "Adjust color temperature") + (description + "This package provides color temperature control applet for the Plasma +Desktop.") + (license (list license:lgpl2.1 license:lgpl3))))) + +(define-public plasma-vault + (package + (name "plasma-vault") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "15nf4myl6sry0930m8qiixpr1i8bh1g58cy2gf304h029vr2fn5j")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list kio + ki18n + kconfigwidgets + kconfig + kactivities + kdbusaddons + kiconthemes + networkmanager-qt + libksysguard + plasma-framework + qtdeclarative-5)) + (home-page "https://invent.kde.org/plasma/plasma-vault") + (synopsis "Plasma applet and services for creating encrypted vaults") + (description "Provides Plasma applet and services for creating encrypted + vaults.") + (license (list license:gpl2 license:gpl3)))) + +(define-public plasma-systemmonitor + (package + (name "plasma-systemmonitor") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "0rs3avhpmfapzha8dkir9ny60ba2m92bbfv4avsd85vz5kggg29h")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list ki18n + kconfig + kdeclarative + kservice + kiconthemes + kglobalaccel + kio + kdbusaddons + kirigami + knewstuff + ksystemstats + kitemmodels + libksysguard + qtdeclarative-5 + qtquickcontrols2-5)) + (synopsis "System sensors, process information and other system resources +monitor") + (description "This package provides an interface for monitoring system +sensors, process information and other system resources.") + (home-page "https://invent.kde.org/plasma/plasma-systemmonitor") + (license (list license:gpl2 license:gpl3)))) + +(define-public plasma-welcome +(let ((commit "dac7569078782a96f122782c15d34e51737d2b89") ; no tags + (revision "1")) + (package + (name "plasma-welcome") + (version (git-version "0.1-pre" revision commit)) + (home-page "https://invent.kde.org/plasma/plasma-welcome") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1x7ra699r5a9kpa3isdnx6af4j6778kw2pmprnx4s8f1rwk2idhh")))) + (build-system qt-build-system) + (native-inputs + (list extra-cmake-modules pkg-config)) + (inputs + (list kcoreaddons + kdbusaddons + kdeclarative + ki18n + kio + kirigami + knotifications + kservice + kwindowsystem + networkmanager-qt + plasma-framework + qtdeclarative-5 + qtgraphicaleffects + qtsvg-5 + qtquickcontrols2-5 + system-settings)) + (synopsis "Plasma welcome screen") + (description + "This package provides a wizard for Plasma to configure settings.") + (license (list license:gpl2 license:gpl3))))) + +(define-public plasma-workspace + (package + (name "plasma-workspace") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "0pxwg3i07sipfchn4qkmlr6kcgqbhj2s10xq69wi32x1fc13jx5x")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools pkg-config qtsvg-5 + qttools-5)) + (inputs (list appmenu-gtk-module + appstream-qt + baloo + breeze + breeze-icons + dbus + fontconfig + iso-codes + kactivities + kactivities-stats + karchive + kcmutils + kcoreaddons + kcrash + kdbusaddons + kdeclarative + kded + kdesu + kglobalaccel + kguiaddons + kholidays + ki18n + kiconthemes + kidletime + kinit + kio + kio-extras + kio-fuse + kitemmodels + kirigami + knewstuff + knotifications + knotifyconfig + kquickcharts + kpackage + kpeople + krunner + kscreenlocker + ktexteditor + ktextwidgets + kunitconversion + kuserfeedback + kwallet + kwayland + kwin + layer-shell-qt + libkscreen + libksysguard + libqalculate + gmp + mpfr + libsm + libxft + libxkbcommon + libxrender + libxtst + networkmanager-qt + phonon + pipewire-0.3 + plasma-framework + plasma-workspace-wallpapers + plasma-wayland-protocols + prison + qtbase-5 + qtdeclarative-5 + qtquickcontrols2-5 + qtwayland-5 + qtgraphicaleffects + qtx11extras + wayland + wayland-protocols-next + xcb-util + xcb-util-image + xcb-util-keysyms + xrdb + xmessage + xsetroot + zlib)) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-wallpaper + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "sddm-theme/theme.conf.cmake" + (("background=..KDE_INSTALL_FULL_WALLPAPERDIR.") + (string-append "background=" + #$(this-package-input "breeze") + "/share/wallpapers"))))) + (add-after 'unpack 'patch-workspace-bins + (lambda* (#:key inputs #:allow-other-keys) + (let ((xmessage (search-input-file inputs "/bin/xmessage")) + (xsetroot (search-input-file inputs "/bin/xsetroot")) + (xrdb (search-input-file inputs "/bin/xrdb")) + (kinit #$(this-package-input "kinit"))) + (substitute* "startkde/startplasma.cpp" + (("xmessage") xmessage) + (("xsetroot") xsetroot)) + (substitute* (list "kcms/fonts/fontinit.cpp" + "kcms/fonts/fonts.cpp" + "kcms/krdb/krdb.cpp") + (("xrdb") xrdb)) + (substitute* "startkde/plasma-session/startup.cpp" + (("CMAKE_INSTALL_FULL_LIBEXECDIR_KF5..") + (string-append "\"" kinit + "/lib/libexec/kf5"))) + (substitute* (list + "startkde/startplasma-wayland.cpp" + "startkde/startplasma-x11.cpp") + (("kdeinit5_shutdown") + (string-append kinit "/bin/kdeinit5_shutdown")))))) + (delete 'check) + (add-after 'install 'check-after-install + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "XDG_CACHE_HOME" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (setenv "QT_PLUGIN_PATH" + (string-append #$output + "/lib/qt5/plugins:" + (getenv "QT_PLUGIN_PATH"))) + (invoke "ctest" "-E" + "(appstreamtest|lookandfeel-kcmTest|tst_triangleFilter|systemtraymodeltest|testdesktop| screenpooltest)"))))))) + (home-page "https://invent.kde.org/plasma/plasma-workspace") + (synopsis "Plasma workspace components") + (description + "Workspaces provide support for KDE Plasma Widgets, integrated search, +hardware management, and a high degree of customizability.") + (license (list license:gpl2 license:gpl3)))) + +(define-public plasma-workspace-wallpapers + (package + (name "plasma-workspace-wallpapers") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "0pdgg8h6zwyxf1pj241mg3hd94wh38bqxj68af5jfp10xrwkzcyr")))) + (build-system cmake-build-system) + (native-inputs (list extra-cmake-modules)) + (home-page "https://community.kde.org/Frameworks") + (synopsis "Oxygen wallpapers for the KDE desktop") + (description + "This package provides wallpapers for the KDE desktop.") + (license license:lgpl3+))) + +(define-public polkit-kde-agent + (package + (name "polkit-kde-agent") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version "/" + name "-1-" version ".tar.xz")) + (sha256 + (base32 + "1qb9nxlkgcv0c30l2vqgf9xs9d220q5pg7ikpb6zjzvj4wsvlvwd")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list ki18n + kwindowsystem + kdbusaddons + kwidgetsaddons + kcoreaddons + kcrash + kiconthemes + polkit-qt)) + (synopsis "Polkit authentication UI for Plasma") + (description + "This package contains a daemon providing a Polkit authentication +UI for Plasma") + (home-page "https://invent.kde.org/plasma/polkit-kde-agent-1") + (license license:gpl2+))) + +(define-public powerdevil + (package + (name "powerdevil") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/" name "-" version ".tar.xz")) + (sha256 + (base32 + "0anisirn7z8aw442npdnk1csb5ghpzj2hx49gpw4l6ijk70b76pr")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules qttools-5 pkg-config)) + (inputs (list bluez-qt + glib + kauth + kactivities + kscreen + kidletime + kconfig + kdbusaddons + solid + ki18n + kcrash + knotifyconfig + networkmanager-qt + kio + kwayland + kglobalaccel + kcrash + knotifications + kirigami + libcap + libkscreen + network-manager + plasma-workspace + eudev + qtx11extras)) + (synopsis "Manage power consumption") + (description "This package provides the power consumption settings +of a Plasma shell.") + (home-page "https://invent.kde.org/plasma/powerdevil") + (license license:gpl2+))) + +(define-public system-settings + (package + (name "system-settings") + (version "5.25.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma/" version + "/systemsettings-" version ".tar.xz")) + (sha256 + (base32 + "0n7mf6ygi8fgn1m6pk2fadnqj1h58mxqni3h19xbi373wfypq5fl")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kauth + kcrash + kitemviews + kitemmodels + kcmutils + ki18n + kio + kservice + kiconthemes + kwidgetsaddons + kwindowsystem + kxmlgui + kdbusaddons + kconfig + kpackage + kactivities + kactivities-stats + kguiaddons + kirigami + knotifications + krunner + plasma-workspace + qtdeclarative-5)) + (synopsis "Control center to configure Plasma Desktop") + (description "This package provides configuration UI for Plasma Desktop.") + (home-page "https://invent.kde.org/plasma/systemsettings") + (license license:gpl2+))) diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index b2295d184a..2742d6b846 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -22,22 +22,31 @@ (define-module (gnu packages kde-utils) #:use-module (guix build-system qt) + #:use-module (guix gexp) #:use-module (guix download) + #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix utils) #:use-module (gnu packages) #:use-module (gnu packages backup) #:use-module (gnu packages bash) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages crypto) + #:use-module (gnu packages cups) + #:use-module (gnu packages glib) ; dbus for tests #:use-module (gnu packages gnome) + #:use-module (gnu packages gstreamer) #:use-module (gnu packages imagemagick) + #:use-module (gnu packages multiprecision) #:use-module (gnu packages pkg-config) #:use-module (gnu packages kde) #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages kde-plasma) #:use-module (gnu packages qt) #:use-module (gnu packages samba) + #:use-module (gnu packages xdisorg) #:use-module (gnu packages xorg)) (define-public ark @@ -114,6 +123,216 @@ with support for multiple formats, including tar, gzip, bzip2, rar and zip, as well as CD-ROM images.") (license license:gpl2+))) +(define-public atelier + (let ((commit "93d7d440c42f1e49a4933cbbce9f68d5e4ca725a") ; no releases + (revision "1")) + (package + (name "atelier") + (version (git-version "0.1-pre" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/atelier") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00jccpwvksyp2vr3fjxajs8d9d30rspg4zj6rnj8dai96alp303k")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list ki18n + kxmlgui + kconfigwidgets + ktexteditor + libatcore + qt3d-5 + qtbase-5 + qtcharts + qtdeclarative-5 + qtmultimedia-5 + qtserialport)) + (home-page "https://atelier.kde.org") + (synopsis "Desktop interface to control 3D printers powered by AtCore") + (description "Atelier provides interface to control and manage your printer. +@itemize +@item Load and see your GCode File +@item Real time graphic to monitor your bed and hotend temperatures +@item You can log everything that comes and go from your printer +@item Edit gcode file +@end itemize") + (license license:gpl3+)))) + +(define-public basket + (let ((commit "e23a8b3b1198d51f770523c7fb4652750810359a") + (revision "1")) + (package + (name "basket") + (version (git-version "2.49" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/basket") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1i7hrrlwyzzh7mm9xc8hjix24rvy1b2cvvbkhxh9mmdbmphwdhhd")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list breeze-icons + karchive + kcompletion + kconfig + kconfigwidgets + kcoreaddons + kcrash + kdbusaddons + kdoctools + kfilemetadata + kglobalaccel + kguiaddons + ki18n + kiconthemes + kcmutils + kio + knotifications + kparts + kservice + ktextwidgets + kwidgetsaddons + kwindowsystem + kxmlgui + phonon)) + (home-page "https://invent.kde.org/utilities/basket") + (synopsis "Notes and to-dos organizer") + (description "This package provides simple note taking and to-do app.") + (license license:gpl2+)))) + +(define-public fielding + (let ((commit "6b3c5d67b308e9e7e2043dc6072bfd265ec9f3e1") + ;; no releases yet + (revision "1")) + (package + (name "fielding") + (version (git-version "0.1-pre" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/fielding") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1l16am7il7kprmy8irpzj04rb8wbfr84y49wp4i74hspp9xkfick")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kirigami + kcoreaddons + kconfig + ki18n + kdbusaddons + ksyntaxhighlighting + qtdeclarative-5 + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://invent.kde.org/utilities/fielding") + (synopsis "REST API testing tool") + (description + "This package provides a tool for testing REST APIs.") + (license license:lgpl2.1+)))) + +(define-public filelight + (package + (name "filelight") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/filelight-" version ".tar.xz")) + (sha256 + (base32 + "1fqgmpq5dznbn5lalx1j6dyynhylijrcqw3x9hrwxcqwr275h9iw")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kirigami + kquickcharts + kxmlgui + kio + ki18n + kdeclarative + qqc2-desktop-style + qtgraphicaleffects + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://apps.kde.org/filelight/") + (synopsis "Visualize the disk usage") + (description "Filelight is an application to visualize the disk usage on +your computer.") + (license license:lgpl2.1+))) + +(define-public francis + (let ((commit "d2c762ad94170430a667ee57f81ec9dbe498642c") ; no release yet + (revision "1")) + (package + (name "francis") + (version (git-version "0.1-pre" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/francis") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "15bk5iq127mp34n9fzq4d5r3qss3ihk93lqy86z2q3lgwid26s0h")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kirigami + kcoreaddons + kconfig + ki18n + kdbusaddons + knotifications + qtdeclarative-5 + qtgraphicaleffects + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://invent.kde.org/utilities/francis") + (synopsis "Track your time") + (description "This package provides time tracking.") + (license license:lgpl2.1+)))) + +(define-public isoimagewriter + (let ((commit "bd1ef4f0ce179fa874b102689022ebda3e7b4c16") + (revision "1")) + (package + (name "isoimagewriter") + (version (git-version "0.8" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/isoimagewriter") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0dha2y4kmyppi6c0g0hclp53fjj963vq27q7azznpl0bz6zb4042")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kauth + karchive + kcoreaddons + ki18n + kiconthemes + kcrash + solid + kwidgetsaddons)) + (home-page "https://invent.kde.org/utilities/isoimagewriter") + (synopsis "Write hybrid ISO files onto USB disks") + (description + "This package provides a tool to write ISO files to USB disks.") + (license license:gpl3+)))) + (define-public kate (package (name "kate") @@ -180,6 +399,380 @@ Kate's features include: (license ;; GPL for programs, LGPL for libraries (list license:gpl2+ license:lgpl2.0)))) +(define-public kdebugsettings + (package + (name "kdebugsettings") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kdebugsettings-" version + ".tar.xz")) + (sha256 + (base32 + "0l9q7cmzc93zz2zc5ncq3q7q6jil6ai36n2vh70s2wsi8b0gsms8")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kcoreaddons + kconfig + kdbusaddons + ki18n + kwidgetsaddons + kitemviews + kcompletion)) + (home-page "https://invent.kde.org/utilities/kdebugsettings") + (synopsis "Choose which QLoggingCategory are displayed") + (description + "This package allows to select which QLoggingCategory are displayed.") + (license license:lgpl2.0+))) + +(define-public kbackup + (package + (name "kbackup") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kbackup-" version ".tar.xz")) + (sha256 + (base32 + "0c0zdk00j9qssjdb5dg5hwc5mx7h5kvriyszia2xizqjq2m53c3k")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kguiaddons + knotifications + ki18n + kio + kxmlgui + kiconthemes + karchive + kwidgetsaddons + shared-mime-info)) + (home-page "https://apps.kde.org/kbackup/") + (synopsis "Backup program with an easy-to-use interface") + (description + "This package provides tool to backup your data. +@itemize +@item profile for directories and files to be included or excluded from the +backup +@item The backup target can be either a locally mounted device like a ZIP +drive, USB stick, etc +@item Running automated backups without using a graphical user interface +@end itemize") + (license license:gpl2+))) + +(define-public kcalc + (package + (name "kcalc") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kcalc-" version ".tar.xz")) + (sha256 + (base32 + "01rn6qy40q4b90i5mysrygkqh5fzq885dgcd11l6r8s59ijjcjlk")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools)) + (inputs (list gmp + kcoreaddons + kcrash + kconfig + kconfigwidgets + kguiaddons + ki18n + knotifications + kxmlgui + mpfr)) + (home-page "https://apps.kde.org/kcalc/") + (synopsis "Scientific calculator") + (description + "This package provides a scientific calculator.") + (license license:gpl2+))) + +(define-public kcharselect + (package + (name "kcharselect") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kcharselect-" version + ".tar.xz")) + (sha256 + (base32 + "1gs9jkq76dkhjgjqpl5dcsx0l2qi6i0pk122y1qmwgyd6f8af35b")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kbookmarks kcoreaddons kcrash ki18n kwidgetsaddons kxmlgui)) + (home-page "https://apps.kde.org/kcharselect/") + (synopsis "Select and copy special characters from installed fonts") + (description + "This package provides a tool to display various information +about the selected character. This includes not only the Unicode character +name, but also aliases, general notes and cross references to similar +characters.") + (license license:gpl2+))) + +(define-public kdialog + (package + (name "kdialog") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kdialog-" version ".tar.xz")) + (sha256 + (base32 + "1lqzhfn5g16qr6ada9i0i3kshna1zxp1y20ylwmmsa82bgmyblhx")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools)) + (inputs (list ktextwidgets + knotifications + kguiaddons + kiconthemes + kwindowsystem + kio + kdbusaddons)) + (home-page "https://invent.kde.org/utilities/kdialog") + (synopsis "Show dialog boxes from shell scripts") + (description "This package provides tool to show nice dialog boxes from +shell scripts.") + (license license:gpl2+))) + +(define-public keurocalc + (let ((commit "a760d8a7e58b36eb72d15e847f96599c93785194") ; just one release + (revision "1")) + (package + (name "keurocalc") + (version (git-version "1.3.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/keurocalc") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gh5vwl38hwf1405c980j1fj06g5c52am140lf4mxhrjvnmry7kd")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools)) + (inputs (list kconfig + kconfigwidgets + kcoreaddons + ki18n + kio + kwidgetsaddons + kxmlgui)) + (home-page "https://invent.kde.org/utilities/keurocalc") + (synopsis "Currency conversion tool") + (description "This package provides a utility to handle currency +conversions between European currencies.") + (license license:gpl2+)))) + +(define-public keysmith + (package + (name "keysmith") + (version "22.09") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/plasma-mobile/" + (version-major+minor version) "/keysmith-" + version ".tar.xz")) + (sha256 + (base32 + "0w3vvmp9rn6ahly2fm9n6f4glfr7d84bfvj33mrs5pn7n99h7jgy")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list kdbusaddons + kirigami + ki18n + kwindowsystem + libsodium + qtdeclarative-5 + qtgraphicaleffects + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://invent.kde.org/utilities/keysmith") + (synopsis "OTP client for Plasma Mobile and Desktop") + (description + "This package provides OTP client for Plasma Mobile and Desktop +with support for QR scanning.") + (license license:gpl3+))) + +(define-public kfind + (package + (name "kfind") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kfind-" version ".tar.xz")) + (sha256 + (base32 + "0py6ygnj7qxbwrldf2a3hqc1cqd5yvyfi1l0nji0hwn8lvidnjhc")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules kdoctools)) + (inputs (list karchive + kcoreaddons + kfilemetadata + ki18n + kio + kwidgetsaddons)) + (home-page "https://apps.kde.org/kfind/") + (synopsis "File search utility") + (description + "This package provides a file search utility for KDE.") + (license license:gpl2+))) + +(define-public kirogi + (let ((commit "73b009f1fc5ac159c2faba720b302c704f89a806") ; no releases yet + (revision "1")) + (package + (name "kirogi") + (version (git-version "0.1-pre" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/utilities/kirogi") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gncfnwadh11ipynfcrsh1vnk2g02c7scd5wanphi8i95jzak9jd")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-gstreamer + (lambda* _ + (substitute* "CMakeLists.txt" + (("gstreamer-video-1.0") + ""))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + (inputs (list kconfigwidgets + kcoreaddons + ki18n + kirigami + kcrash + kdnssd + qtquickcontrols2-5 + qtgraphicaleffects + qtdeclarative-5 + qtgamepad + qtlocation)) + (propagated-inputs (list gstreamer)) + (home-page "https://apps.kde.org/kirogi/") + (synopsis "Ground control application for drones") + (description "Kirogi is a ground control application for drones. +@itemize +@item Direct flight controls +@item Fly by touch on a Navigation Map +@item Trigger vehicle actions (e.g. flips, trim) +@item Gamepad/joypad support +@item Live video +@item Take photo and record video +@item Configure flight parameters (speed, altitude limits) +@item Support for Parrot (Anafi, Bebop 2) and Ryze Tello drones +@end itemize") + (license ;GPL for programs, LGPL for libraries + (list license:gpl2+ license:lgpl2.0))))) + +(define-public kontrast + (package + (name "kontrast") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/kontrast-" version ".tar.xz")) + (sha256 + (base32 + "03y3y5p29zx4nmqi7hp3abxq2n2bgwbz2knhn9vhl3im3ghp7lmp")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list kirigami + ki18n + kcoreaddons + qtdeclarative-5 + qtgraphicaleffects + qtquickcontrols2-5 + qtsvg-5)) + (home-page "https://apps.kde.org/kontrast/") + (synopsis "Color contrast checker") + (description + "Kontrast is a color contrast checker and tells you if your color +combinations are distinct enough to be readable and accessible.") + (license license:gpl3+))) + +(define-public libatcore + (let ((commit "0de6393ed3e721537dec50b0ad174d83f1207eb6") + (revision "1")) + (package + (name "libatcore") + (version (git-version "1.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://invent.kde.org/libraries/atcore") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1830r6ylpn3l7y2frl8cih5cpjgbkfrib9jq7jklf8aszhlsihf2")))) + (build-system qt-build-system) + (native-inputs (list extra-cmake-modules)) + (inputs (list qtcharts qtdeclarative-5 qtserialport)) + (home-page "https://invent.kde.org/libraries/atcore") + (synopsis "Library for connection and management of 3D printers") + (description + "This package provides a API to manage the serial connection between +the computer and 3D Printers.") + (license (list license:lgpl2.1 license:lgpl3))))) + +(define-public wacomtablet + (package + (name "wacomtablet") + (version "3.2.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/" + name "/" version "/" + name "-" version ".tar.xz")) + (patches (search-patches + "wacomtablet-add-missing-includes.patch" + "wacomtablet-qt5.15.patch")) + (sha256 + (base32 + "197pwpl87gqlnza36bp68jvw8ww25znk08acmi8bpz7n84xfc368")))) + (build-system qt-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "dbus-launch" "ctest" "-E" + "(Test.KDED.DBusTabletService|Test.KDED.TabletHandler|Test.KDED.XInputAdaptor|Test.KDED.XsetWacomAdaptor)"))))))) + (native-inputs (list dbus extra-cmake-modules kdoctools pkg-config)) + (inputs (list kcoreaddons + ki18n + kglobalaccel + kconfig + kxmlgui + kwidgetsaddons + kwindowsystem + knotifications + kdbusaddons + qtx11extras + qtdeclarative-5 + libwacom + xf86-input-wacom + libxi)) + (propagated-inputs (list plasma-framework)) + (home-page "https://invent.kde.org/system/wacomtablet") + (synopsis "KDE GUI for the Wacom Linux Drivers") + (description "Provides KDE GUI for the Wacom Linux Drivers.") + (license license:gpl2+))) + (define-public kmag (package (name "kmag") @@ -456,6 +1049,41 @@ redone.") (license ;; GPL for programs, LGPL for libraries, FDL for documentation (list license:gpl2+ license:lgpl2.0+ license:fdl1.2+)))) +(define-public print-manager + (package + (name "print-manager") + (version "22.08.0") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" version + "/src/print-manager-" version ".tar.xz")) + (sha256 + (base32 "1abwj1ccm70adzx07ykqjlb4f6y55k2rv1j861dl0822187vl799")))) + (build-system qt-build-system) + (native-inputs + (list extra-cmake-modules)) + (inputs + (list cups + kcmutils + kconfig + kconfigwidgets + kcoreaddons + kdbusaddons + kiconthemes + ki18n + kio + knotifications + kwidgetsaddons + kwindowsystem + plasma-framework + qtdeclarative-5)) + (home-page "https://invent.kde.org/utilities/print-manager") + (synopsis "Manage print jobs and printers") + (description + "This package provides printing management for KDE.") + (license license:gpl2+))) + (define-public rsibreak (package (name "rsibreak") diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index f4d36c0f3a..e5ae414b53 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -68,6 +68,7 @@ #:use-module (gnu packages ghostscript) #:use-module (gnu packages gimp) #:use-module (gnu packages gl) + #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gps) #:use-module (gnu packages graphics) @@ -99,14 +100,14 @@ (define-public baloo-widgets (package (name "baloo-widgets") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/baloo-widgets-" version ".tar.xz")) (sha256 - (base32 "0084bnrlbdypdwzxi9gfxcywhyjd1z2cmh7p6gv0zhc9f7h6ffnp")))) + (base32 "02p4v8g4syk908mg7f0l5fpqn7ddsxqji1n8jqghsdkkdsvry7mn")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -123,14 +124,14 @@ This package contains GUI widgets for baloo.") (define-public grantleetheme (package (name "grantleetheme") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/grantleetheme-" version ".tar.xz")) (sha256 - (base32 "50c6s1g3vp5sdhpiciz1j6rsryld7hcc6lvmxdlsvms2bbcmnj7l")))) + (base32 "01ls16x6ngi43lcwffav9qig3afakrs04v4wvyfb8lm7sd65hgf9")))) (build-system qt-build-system) (arguments `(#:tests? #f)) ; unexpected error in the test suite. (native-inputs @@ -151,14 +152,14 @@ This package contains GUI widgets for baloo.") (define-public akregator (package (name "akregator") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/akregator-" version ".tar.xz")) (sha256 - (base32 "08n713271i7ifnbrgwrqmxvcpvj45wfqjiidw8zf9rpwxg2m2m9g")))) + (base32 "01rgyl2hwjprq4z5yjc99j6jk9vrhjy608ha72j470pw6g47ac5s")))) (build-system qt-build-system) (arguments `(#:phases @@ -195,7 +196,7 @@ This package contains GUI widgets for baloo.") kontactinterface kpimcommon kpimtextedit - kqtquickcharts + kquickcharts ktexteditor kuserfeedback libkdepim @@ -220,7 +221,7 @@ browser for easy news reading.") (define-public kdenlive (package (name "kdenlive") - (version "22.04.3") + (version "22.08.1") (source (origin (method git-fetch) @@ -229,7 +230,7 @@ browser for easy news reading.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0v545kd5rm5isy4cx21fp3pi49mvsv1r1ahp0jhim8s6b7ghrh64")))) + (base32 "0xnasi8s8zxh2s4vnn51pc8ni58q8pk70bwh9dfxp1wdmpv3zsrx")))) (build-system qt-build-system) (arguments ;; XXX: there is a single test that spawns other tests and @@ -304,14 +305,14 @@ projects.") (define-public kdevelop (package (name "kdevelop") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kdevelop-" version ".tar.xz")) (sha256 - (base32 "03dwllxy96sy20kdsc3sll0n6bhh6gdmpjl821flsxv0jb5naplv")))) + (base32 "14a80z4sahxyzssrz605zp7ah5xdjbc22ccv0vwcnhr5lzr76v31")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules pkg-config shared-mime-info qttools-5)) @@ -344,7 +345,7 @@ projects.") qtdeclarative-5 qtquickcontrols-5 ;; not checked as requirement qtquickcontrols2-5 ;; not checked as requirement - qtwebkit + qtwebengine-5 threadweaver ;; recommendes astyle @@ -443,6 +444,102 @@ a module for implementing ODF Gantt charts, which are bar charts that illustrate project schedules.") (license license:gpl2+))) +(define-public kio-extras + (package + (name "kio-extras") + (version "22.08.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" + version ".tar.xz")) + (sha256 + (base32 + "0gzna2ps2qd2js28c97kjpcbah7zz8n4s4932faggc2nz5z5wnyn")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "TMPDIR" (getcwd)) + (invoke "ctest" "-E" "testkioarchive"))))))) + (native-inputs (list extra-cmake-modules dbus kdoctools qttools-5)) + (inputs (list karchive + kconfig + kconfigwidgets + kcoreaddons + kdbusaddons + ki18n + kdnssd + kio + solid + kbookmarks + kguiaddons + ksyntaxhighlighting + qtbase-5 + qtsvg-5)) + (home-page "https://community.kde.org/Frameworks") + (synopsis "Additional components to increase the functionality of KIO") + (description + "This package provides additional components to increase +the functionality of the KDE resource and network access abstractions.") + (license license:lgpl2.0+))) + +(define-public kio-fuse + (package + (name "kio-fuse") + (version "5.0.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/" name "/" version "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "1pb62h45c06dq3rml91xbf8j5y2c1l8z8j8lycchxrlgys5rlrv6")))) + (build-system cmake-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" (getcwd)) + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "dbus-launch" "ctest" "-E" + "(fileopstest-cache|fileopstest-filejob)"))))))) + (native-inputs (list dbus extra-cmake-modules pkg-config)) + (inputs (list fuse-3 kio kcoreaddons qtbase-5)) + (home-page "https://community.kde.org/Frameworks") + (synopsis "FUSE Interface for KIO") + (description "This package provides FUSE Interface for KIO.") + (license license:lgpl2.1+))) + +(define-public kirigami-addons + (package + (name "kirigami-addons") + (version "0.3") + (source (origin + (method url-fetch) + (uri (string-append + "https://invent.kde.org/libraries/kirigami-addons/-/archive/v" + version "/kirigami-addons-v" version ".tar.gz")) + (sha256 + (base32 + "1zr8dpc7bzw6g3y0jaxsr2lqlxqwlcphchpk8iah6g1f3n9fq73r")))) + (build-system qt-build-system) + (arguments + (list #:tests? #f)) ; failing test + (native-inputs (list extra-cmake-modules)) + (inputs (list kirigami ki18n qtdeclarative-5 qtquickcontrols2-5)) + (home-page "https://invent.kde.org/libraries/kirigami-addons") + (synopsis "Add-ons for the Kirigami framework") + (description + "This package provides Kirigami components usable by both touch +and desktop experiences.") + (license license:lgpl2.0+))) + (define-public kseexpr (package (name "kseexpr") @@ -581,17 +678,52 @@ the generated @file{massif.out.%pid} in the visualizer. Gzip or Bzip2 compressed massif files can also be opened transparently.") (license license:gpl2+))) +(define-public libqaccessibilityclient + (package + (name "libqaccessibilityclient") + (version "0.4.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/" name + "/libqaccessibilityclient-" version + ".tar.xz")) + (sha256 + (base32 + "0a9lv2jb5gyqxvrkl5xl09gjnlp05b5yfzfb0wmaxz0l8d7qnxhw")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ;TODO: Failing tests + #:phases (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ; + ;; make Qt render "offscreen", required for tests + (setenv "QT_QPA_PLATFORM" "offscreen") + ;; For missing '/etc/machine-id' + (setenv "DBUS_FATAL_WARNINGS" "0") + (setenv "HOME" + (getcwd)) + (invoke "dbus-launch" "ctest"))))))) + (native-inputs (list dbus extra-cmake-modules)) + (inputs (list qtbase-5)) + (home-page "https://invent.kde.org/libraries/libqaccessibilityclient") + (synopsis "Helper library to make writing accessibility tools easier") + (description "This package provides library that is used when writing +accessibility clients such as screen readers.") + (license license:lgpl2.1+))) + (define-public libkomparediff2 (package (name "libkomparediff2") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libkomparediff2-" version ".tar.xz")) (sha256 - (base32 "1vaxbx7c6r7skh3452blxyrngfcsdyjmmvcg6j2wcsn04m01mw8k")))) + (base32 "0hjxxhfv0ds05l821avq787sfdy0afr595xx266c20x8fxgm6kv9")))) (native-inputs (list extra-cmake-modules pkg-config)) (inputs @@ -636,10 +768,70 @@ including SSL/TLS, X.509 certificates, SASL, OpenPGP, S/MIME CMS, and smart cards.") (license license:lgpl2.1+))) +(define-public kopeninghours + (package + (name "kopeninghours") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" version ".tar.xz")) + (sha256 + (base32 + "03hslgx4zgg7gsnz2xhx4wnchvqfc5n8c6ihgwz3972fkxsjfdvq")))) + (build-system cmake-build-system) + (arguments + (list #:phases '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "ctest" "-E" + "(evaluatetest|iterationtest)"))))))) + (native-inputs (list bison extra-cmake-modules flex)) + (inputs (list boost + kholidays + ki18n + osmctools + qtbase-5 + qtdeclarative-5)) + (home-page "https://invent.kde.org/libraries/kopeninghours") + (synopsis "Get opening hours from OpenStreetMap") + (description + "This package provides a library for parsing and evaluating OpenStreetMap +opening hours expressions.") + (license license:lgpl2.0+))) + +(define-public kosmindoormap + (package + (name "kosmindoormap") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kde/stable/release-service/" + version "/src/" name "-" version ".tar.xz")) + (sha256 + (base32 + "042axwxa1497snr8f0m6a61gl9ypdkvllnhnlw4h5ffah7yl5n3s")))) + (build-system cmake-build-system) + (native-inputs (list bison extra-cmake-modules flex)) + (inputs (list ki18n + kopeninghours + kpublictransport + qtbase-5 + qtdeclarative-5 + zlib)) + (home-page "https://invent.kde.org/libraries/kosmindoormap") + (synopsis "Indoor map renderer") + (description + "This package provides facilities for rendering OpenStreetMap +multi-floor indoor maps.") + (license license:lgpl2.0+))) + (define-public kpmcore (package (name "kpmcore") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append @@ -647,7 +839,7 @@ cards.") "/src/" name "-" version ".tar.xz")) (sha256 (base32 - "04qslli4vnbnl329zynbinlwaigxr9xpswra5n0v710p92as0qif")))) + "1y28dnmbnkkjar4kl033fkmcnazgczc3pgdac2q1ry2hjzkcbnpa")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules pkg-config)) @@ -674,6 +866,37 @@ cards.") (description "Library for managing partitions.") (license license:gpl3+))) +(define-public kpublictransport + (package + (name "kpublictransport") + (version "22.08.1") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://kde/stable/release-service/" version + "/src/kpublictransport-" version ".tar.xz")) + (sha256 + (base32 + "0z7zyyiq4815m74s6p841k1c4pxbrss7hnkag8kr5qa3q4264kg9")))) + (build-system qt-build-system) + (arguments + (list #:phases '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "QT_QPA_PLATFORM" "offscreen") + (invoke "ctest" "-E" + "(mergeutiltest|departuretest|journeytest|networkconfigtest|locationhistorymodeltest|navitiaparsertest|otpparsertest|ivvassparsertest|cachetest)"))))))) + (native-inputs (list extra-cmake-modules pkg-config)) + ;; TODO: clipper and osmctools are not detected + (inputs (list clipper osmctools protobuf qtdeclarative-5 zlib)) + (home-page "https://api.kde.org/kdepim/kpublictransport/html/index.html") + (synopsis "Library for accessing realtime public transport data") + (description + "This package provides a library for accessing realtime public +transport data and for performing public transport journey queries.") + (license (list license:lgpl2.0+)))) + (define-public snorenotify (package (name "snorenotify") @@ -703,7 +926,7 @@ different notification systems.") (define-public kdeconnect (package (name "kdeconnect") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) @@ -712,7 +935,7 @@ different notification systems.") version ".tar.xz")) (sha256 (base32 - "015gxglclds2vmjr4bv51yfv840bafzgrl71cnwgnwwy8rrh9x4x")))) + "1yzx49gcm7x2wdk53iznyjz09y2a6mrrhh68xilbcsafyiw3l3zr")))) (build-system qt-build-system) (arguments `(#:configure-flags '("-DBUILD_TESTING=ON" @@ -741,6 +964,7 @@ different notification systems.") kpeoplevcard kwayland libfakekey + plasma-wayland-protocols pulseaudio-qt qca qqc2-desktop-style @@ -847,41 +1071,17 @@ to perform data analysis.") (license (list license:gpl2+ ;labplot license:gpl3+)))) ;liborigin -(define-public kqtquickcharts - (package - (name "kqtquickcharts") - (version "22.04.3") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://kde/stable/release-service/" - version "/src/kqtquickcharts-" version ".tar.xz")) - (sha256 - (base32 - "0bm7rdysvlfnfnvy87ii3kxl238q83vw0ia58zsnwjmkxmlgf6mp")))) - (build-system cmake-build-system) - (native-inputs - (list extra-cmake-modules)) - (inputs - (list qtbase-5 qtdeclarative-5)) - (home-page "https://phabricator.kde.org/source/kqtquickcharts/") - (synopsis "Interactive charts for Qt Quick") - (description - "Kqtquickcharts is a QtQuick plugin to render beautiful and interactive -charts.") - (license license:lgpl2.1+))) - (define-public kdf (package (name "kdf") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kdf-" version ".tar.xz")) (sha256 (base32 - "1m0dwk3inqzk9kjjzgsaam15lnpbhzjfmwrzv8sazfk44scnr2v1")))) + "0p7iqld2phc74pmhyb8bqqg9clnc7l2rh6hd0i6jcsp266cgg205")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -934,14 +1134,14 @@ timers for each task can be started, stopped, changed, or looped.") (define-public kcachegrind (package (name "kcachegrind") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/kcachegrind-" version ".tar.xz")) (sha256 (base32 - "12ckn90hqm2c5c58xqkzgcih64jk4kwkgz4q0f5ns1rxv3pidz5n")))) + "05wcnfqs0fdfhfpagn0pqky0l7014nblv8r9fv1khy4g5mdlm4hs")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules perl python qttools-5 kdoctools)) @@ -968,14 +1168,14 @@ Python, PHP, and Perl.") (define-public libkdegames (package (name "libkdegames") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/libkdegames-" version ".tar.xz")) (sha256 - (base32 "0igq87anam9x2mclb0lkvwhrxk62y1f4xl14a4dhd97mqsc5pbzn")))) + (base32 "1aihbha073fw2bxmdk4l768716kvrlyjd72x2nfx0vvr0ngc5wx9")))) (build-system qt-build-system) (native-inputs (list extra-cmake-modules)) @@ -1014,7 +1214,7 @@ Python, PHP, and Perl.") (define-public marble-qt (package (name "marble-qt") - (version "22.04.3") + (version "22.08.1") (source (origin (method git-fetch) @@ -1024,7 +1224,7 @@ Python, PHP, and Perl.") (file-name (git-file-name name version)) (sha256 (base32 - "1saacnrl0hkl32nq96l1bgn9yrsz455q96jdxzp7ax8iaa5nmdiz")))) + "0pn0mjh5cg7mgjj82bsj8zikzdyq2fmzckdcav2y0msxwi859crl")))) (build-system qt-build-system) (arguments ;; FIXME: libmarblewidget-qt5.so.28 not found. Also enable the @@ -1071,14 +1271,14 @@ creating routes by drag and drop and more.") (define-public okular (package (name "okular") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/" name "-" version ".tar.xz")) (sha256 - (base32 "03jpwgrhjgyx14g1h3lxhnyib88ck0qkqcxh4fpc398xwdr3amkw")))) + (base32 "0f98kfsb6sirpym27j2wwz4qr4p5vl4pbnckxd3gmgyfpz8mszln")))) (build-system qt-build-system) ;; The tests fail because they can't find the proper mimetype plugins: ;; "org.kde.okular.core: No plugin for mimetype '"image/jpeg"'." @@ -1136,7 +1336,7 @@ a variety of formats, including PDF, PostScript, DejaVu, and EPub.") (define-public poxml (package (name "poxml") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri @@ -1144,7 +1344,7 @@ a variety of formats, including PDF, PostScript, DejaVu, and EPub.") "/src/poxml-" version ".tar.xz")) (sha256 (base32 - "1nrp0i3a39pw4pzcanpmjyks3pl1lyfj3zq61ii8xx402xw1ip2w")))) + "13jp5g5la3kq9i3qybdvwfl4vgqz3hxf64qzmh7kl71ykas7s5vi")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules kdoctools)) @@ -1161,14 +1361,14 @@ PO template files.") (define-public kdegraphics-mobipocket (package (name "kdegraphics-mobipocket") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/" name "-" version ".tar.xz")) (sha256 - (base32 "12yrwa22c4qxsf10fv76fzaaj5xlv5lmrwcqvf6qhgr6f9qsw7sj")))) + (base32 "1kxvzgmq83hml10pc4j66r59dsar7h92w2i0cs1nhar781mz666n")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) @@ -1183,14 +1383,14 @@ Mobipocket e-books in Dolphin and other KDE apps.") (define-public libkexiv2 (package (name "libkexiv2") - (version "22.04.3") + (version "22.08.1") (source (origin (method url-fetch) (uri (string-append "mirror://kde/stable/release-service/" version "/src/" name "-" version ".tar.xz")) (sha256 - (base32 "0p43z69yh5jk8m1hn3xynjpgzxpkc89h0dafj5964qx4xp4vxl19")))) + (base32 "0iwpy79ppv4bbsqrszp9kmghgjvkl13gdpnafsbikh4wy1ch4cv9")))) (build-system cmake-build-system) (native-inputs (list extra-cmake-modules)) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 8343f8ffc6..530396213a 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -9,7 +9,7 @@ ;;; Copyright © 2017, 2018, 2019, 2021 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2017, 2018, 2019, 2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com> -;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2018, 2019, 2022 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2018, 2020 Jonathan Brielmaier <jonathan.brielmaier@web.de> ;;; Copyright © 2019 Chris Marusich <cmmarusich@gmail.com> ;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl> @@ -30,6 +30,7 @@ ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. (define-module (gnu packages libreoffice) + #:use-module (guix build-system cmake) #:use-module (guix build-system glib-or-gtk) #:use-module (guix build-system gnu) #:use-module (guix build-system python) @@ -66,6 +67,7 @@ #:use-module (gnu packages gnome) #:use-module (gnu packages gperf) #:use-module (gnu packages gnupg) + #:use-module (gnu packages graphics) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages icu4c) @@ -696,14 +698,14 @@ text documents, vector drawings, presentations and spreadsheets.") (define-public libmwaw (package (name "libmwaw") - (version "0.3.19") + (version "0.3.21") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/libmwaw/libmwaw/libmwaw-" version "/libmwaw-" version ".tar.xz")) (sha256 - (base32 "1bx5xnw8sk5h26x2z7hfac7hfbm68zqg0jilp15qr0pwxqsf4wmj")))) + (base32 "07629xwvlkqj08j13aj9lsq0pwm7r0v7g2zprr1vjqcdlwih2xg8")))) (build-system gnu-build-system) (native-inputs (list doxygen pkg-config)) @@ -1093,6 +1095,45 @@ and to return information on pronunciations, meanings and synonyms.") converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (license license:mpl2.0))) +(define-public dragonbox + (package + (name "dragonbox") + (version "1.1.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jk-jeon/dragonbox") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0qxx94s2kfgnlnyl1gwmbxkksr3dipvb99zdyi5skw3z2bq563sa")))) + (build-system cmake-build-system) + (arguments (list #:tests? #false)) ;no test target + (home-page "https://github.com/jk-jeon/dragonbox") + (synopsis "Float-to-string conversion algorithm") + (description "Dragonbox generates a pair of integers from a floating-point +number: the decimal significand and the decimal exponent of the input +floating-point number. These integers can then be used for string generation +of decimal representation of the input floating-point number, the procedure +commonly called @code{ftoa} or @code{dtoa}.") + (license license:asl2.0))) + +(define-public dragonbox-for-libreoffice + (package + (inherit dragonbox) + (name "dragonbox") + (version "1.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jk-jeon/dragonbox") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "11h9xhpzp61rfyh1nnca5shzi40skgpdql080k5cb6cfy672s1qz")))))) + (define dtoa (origin (method url-fetch) @@ -1105,7 +1146,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (define-public libreoffice (package (name "libreoffice") - (version "7.3.5.2") + (version "7.4.3.2") (source (origin (method url-fetch) @@ -1114,7 +1155,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") "https://download.documentfoundation.org/libreoffice/src/" (version-prefix version 3) "/libreoffice-" version ".tar.xz")) (sha256 - (base32 "14g9873x8m5yakpq7v9f7lhc5fkxh6yhjhgh0pm30cqmxsqhsglv")))) + (base32 "0fyvd4ydh72lmn005h190xa563d4h376pi1fx9lfr5i25qcbpg7z")))) (build-system glib-or-gtk-build-system) (arguments (list @@ -1147,19 +1188,24 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (("GPGMEPP_CFLAGS=-I/usr/include/gpgme\\+\\+") (string-append "GPGMEPP_CFLAGS=-I" (search-input-directory inputs - "include/gpgme++")))) + "include/gpgme++"))) + (("DRAGONBOX_CFLAGS=-I/usr/include/dragonbox-1.0.0") + (string-append "DRAGONBOX_CFLAGS=-I" + (search-input-directory inputs + "include/dragonbox-1.0.0")))) ;; /usr/bin/xdg-open doesn't exist on Guix System. (substitute* '("shell/source/unix/exec/shellexec.cxx" "shell/source/unix/misc/senddoc.sh") (("/usr/bin/xdg-open") - (search-input-file inputs "/bin/xdg-open"))))) + (search-input-file inputs "/bin/xdg-open"))) + (setenv "CPPFLAGS" "-std=c++17"))) (add-after 'install 'reset-zip-timestamps (lambda _ (for-each (lambda (file) (invoke "ziptime" file)) ;; So many different extensions for .zip files. - (find-files #$output "\\.(bau|dat|otp|ott|zip)$")))) + (find-files #$output "\\.(bau|dat|otg|otp|ott|zip)$")))) (add-after 'install 'bin-and-desktop-install ;; Create 'soffice' and 'libreoffice' symlinks to the executable ;; script. @@ -1235,6 +1281,10 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") ;; when our default compiler is >=GCC 6. "--disable-pdfium" "--without-doxygen" + ;; Avoid linker errors about non-virtual thunks on i686-linux. + "--enable-lto" + ;; Avoid errors rebuilding the Gtk icon cache, at least on i686-linux. + "--without-galleries" "--enable-build-opensymbol"))) (native-inputs (list bison @@ -1251,6 +1301,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") clucene cups dbus-glib + dragonbox-for-libreoffice firebird fontconfig fontforge @@ -1271,6 +1322,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") libcdr libcmis libcuckoo + libfixmath libjpeg-turbo libe-book libepubgen @@ -1287,7 +1339,9 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") libpagemaker libqxp libstaroffice + libtiff libvisio + libwebp libwpg libwps libxrandr diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 601162b465..2e1da21800 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -33,7 +33,7 @@ ;;; Copyright © 2018, 2019 Pierre Langlois <pierre.langlois@gmx.com> ;;; Copyright © 2018 Vasile Dumitrascu <va511e@yahoo.com> ;;; Copyright © 2019 Tim Gesthuizen <tim.gesthuizen@yahoo.de> -;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2019, 2020, 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Stefan Stefanović <stefanx2ovic@gmail.com> ;;; Copyright © 2019-2022 Brice Waegeneire <brice@waegenei.re> ;;; Copyright © 2019 Kei Kebreau <kkebreau@posteo.net> @@ -108,8 +108,9 @@ #:use-module (gnu packages docbook) #:use-module (gnu packages documentation) #:use-module (gnu packages elf) - #:use-module (gnu packages flex) #:use-module (gnu packages file) + #:use-module (gnu packages flex) + #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) @@ -119,6 +120,7 @@ #:use-module (gnu packages gnupg) #:use-module (gnu packages golang) #:use-module (gnu packages gperf) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-apps) @@ -355,7 +357,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The current "stable" kernels. That is, the most recently released major ;; versions that are still supported upstream. -(define-public linux-libre-6.0-version "6.0.9") +(define-public linux-libre-6.0-version "6.0.10") (define-public linux-libre-6.0-gnu-revision "gnu") (define deblob-scripts-6.0 (linux-libre-deblob-scripts @@ -365,7 +367,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "06iqxkg5hakzvmz6gcz878k1sr553zbng2j1b2whgfg7zmhxkb34"))) (define-public linux-libre-6.0-pristine-source (let ((version linux-libre-6.0-version) - (hash (base32 "1irip1yk62carcisxlacwcxsiqib4qswx6h5mfhv8f97x04a4531"))) + (hash (base32 "1l0xak4w7c16cg8lhracy8r18zzdl0x5s654w6ivyw6dhk6pzr9r"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-6.0))) @@ -373,7 +375,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." ;; The "longterm" kernels — the older releases with long-term upstream support. ;; Here are the support timelines: ;; <https://www.kernel.org/category/releases.html> -(define-public linux-libre-5.15-version "5.15.79") +(define-public linux-libre-5.15-version "5.15.80") (define-public linux-libre-5.15-gnu-revision "gnu") (define deblob-scripts-5.15 (linux-libre-deblob-scripts @@ -383,12 +385,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0h8a48dvgxyj3v08lp99kh5pfa93r4rks78cj0j1rwz1516xk8h3"))) (define-public linux-libre-5.15-pristine-source (let ((version linux-libre-5.15-version) - (hash (base32 "0m61k7k6lj24z9a266q08wzghggjik2wizcabdwd1vn0vcqr18yb"))) + (hash (base32 "0kgxznd3sfbmnygjvp9dzhzg5chxlaxk6kldxmh1y0njcrj1lciv"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.15))) -(define-public linux-libre-5.10-version "5.10.155") +(define-public linux-libre-5.10-version "5.10.156") (define-public linux-libre-5.10-gnu-revision "gnu1") (define deblob-scripts-5.10 (linux-libre-deblob-scripts @@ -398,42 +400,42 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "1m9l554w6a72mq0kf7ggm44z247m2yz6zhafwqxh96qpjpcaabpj"))) (define-public linux-libre-5.10-pristine-source (let ((version linux-libre-5.10-version) - (hash (base32 "1wyla96qsdf50n7qjj4hdf36bj56whv7gc9mgw9bvrsqdi92gc7i"))) + (hash (base32 "08srjps110zi4ivzh0z2jf78ddyfj2wivdliffb2f03jr9j9k7k7"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.10))) -(define-public linux-libre-5.4-version "5.4.224") +(define-public linux-libre-5.4-version "5.4.225") (define-public linux-libre-5.4-gnu-revision "gnu1") (define deblob-scripts-5.4 (linux-libre-deblob-scripts linux-libre-5.4-version linux-libre-5.4-gnu-revision (base32 "1nlgk8ajb5wl3aa96h9a0pb9j5a5wmrbpk63varn557x1d00r7wj") - (base32 "1vnjbdyssa7dwyjl9kg35alwvf7yh597cl74yr1wy2gk5bc9paw6"))) + (base32 "1bgblfkcnrabnr9hpdl07qgps57h6bq4v5pjrxs798vq43db66va"))) (define-public linux-libre-5.4-pristine-source (let ((version linux-libre-5.4-version) - (hash (base32 "0dixs4w7nmkjgxv9dxgjdy8v6r4parkpqyvdfyr0wqk0amdz4zcb"))) + (hash (base32 "1ak0qlxzfylgvkldh2whq4mzynh1rymhnnc1yif9a5s3f7v9dxar"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-5.4))) -(define-public linux-libre-4.19-version "4.19.265") +(define-public linux-libre-4.19-version "4.19.267") (define-public linux-libre-4.19-gnu-revision "gnu1") (define deblob-scripts-4.19 (linux-libre-deblob-scripts linux-libre-4.19-version linux-libre-4.19-gnu-revision (base32 "06pqv050bkii0hc2v7ymny5264w1bca8db0dp1pw9mfmjg865am5") - (base32 "00i91lx938nqlgy63hiricqd0fnbbf26vgya9c5lb7m1f4x324im"))) + (base32 "0g1yhzxm3ixfll6n630v7lddcyvf888sg114nimh0lkvzd180s99"))) (define-public linux-libre-4.19-pristine-source (let ((version linux-libre-4.19-version) - (hash (base32 "1l5cdpgng1gci1p1gdr2jzqw486h3w56gpyc7fbq74hlc6nnwh1p"))) + (hash (base32 "035yxx13jz5f5ig2r6ybzgivm8vjafgnvjws0jfzha4w6klf7r9l"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.19))) -(define-public linux-libre-4.14-version "4.14.299") +(define-public linux-libre-4.14-version "4.14.300") (define-public linux-libre-4.14-gnu-revision "gnu1") (define deblob-scripts-4.14 (linux-libre-deblob-scripts @@ -443,12 +445,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "00i91lx938nqlgy63hiricqd0fnbbf26vgya9c5lb7m1f4x324im"))) (define-public linux-libre-4.14-pristine-source (let ((version linux-libre-4.14-version) - (hash (base32 "0p5ic2mrb9vl3qkzvqxhia3kygjv8xa6s1kqkwgd6b4rmq1kc8r6"))) + (hash (base32 "047vmh09icm45g7mnmdvyj9cam7747bcpah1s7n9dm5i2j2f906y"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.14))) -(define-public linux-libre-4.9-version "4.9.333") +(define-public linux-libre-4.9-version "4.9.334") (define-public linux-libre-4.9-gnu-revision "gnu1") (define deblob-scripts-4.9 (linux-libre-deblob-scripts @@ -458,7 +460,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (base32 "0bib3641dbcqdkx3anna3caxnsg3nw9cnmhcklq0s93g3m57041h"))) (define-public linux-libre-4.9-pristine-source (let ((version linux-libre-4.9-version) - (hash (base32 "0ash877gkrrc063h6ncl9d4gzyhndanpxsdgf1a93abbfv281gs1"))) + (hash (base32 "0sjh492mfic6llgwb957nj7gd7c0dvqnk97ngq8d50sjsyjznyk9"))) (make-linux-libre-source version (%upstream-linux-source version hash) deblob-scripts-4.9))) @@ -494,17 +496,20 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS." (define-public linux-libre-6.0-source (source-with-patches linux-libre-6.0-pristine-source (list %boot-logo-patch - %linux-libre-arm-export-__sync_icache_dcache-patch))) + %linux-libre-arm-export-__sync_icache_dcache-patch + (search-patch "linux-libre-infodocs-target.patch")))) (define-public linux-libre-5.15-source (source-with-patches linux-libre-5.15-pristine-source (list %boot-logo-patch - %linux-libre-arm-export-__sync_icache_dcache-patch))) + %linux-libre-arm-export-__sync_icache_dcache-patch + (search-patch "linux-libre-infodocs-target.patch")))) (define-public linux-libre-5.10-source (source-with-patches linux-libre-5.10-pristine-source (list %boot-logo-patch - %linux-libre-arm-export-__sync_icache_dcache-patch))) + %linux-libre-arm-export-__sync_icache_dcache-patch + (search-patch "linux-libre-infodocs-target.patch")))) (define-public linux-libre-5.4-source (source-with-patches linux-libre-5.4-pristine-source @@ -759,6 +764,11 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." ;;; Kernel package utilities. ;;; +(define (doc-supported? version) + ;; Versions older than 5.10 have different enough build scripts that the + ;; infodocs patch doesn't apply. + (version>=? version "5.10")) + (define* (make-linux-libre version gnu-revision hash-string supported-systems #:key (extra-version #f) @@ -767,7 +777,13 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." (configuration-file #f) (defconfig "defconfig") (extra-options %default-extra-linux-options) - (patches (list %boot-logo-patch))) + (build-doc? (doc-supported? version)) + (patches + `(,%boot-logo-patch + ,@(if build-doc? + (list (search-patch + "linux-libre-infodocs-target.patch")) + '())))) (make-linux-libre* version gnu-revision (origin (method url-fetch) @@ -778,7 +794,8 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." #:extra-version extra-version #:configuration-file configuration-file #:defconfig defconfig - #:extra-options extra-options)) + #:extra-options extra-options + #:build-doc? build-doc?)) (define* (make-linux-libre* version gnu-revision source supported-systems #:key @@ -787,7 +804,10 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." ;; See kernel-config for an example. (configuration-file #f) (defconfig "defconfig") - (extra-options %default-extra-linux-options)) + (extra-options %default-extra-linux-options) + (build-doc? (doc-supported? version))) + (when (and build-doc? (not (doc-supported? version))) + (error "unsupported 'build-doc?' for kernels <5.10")) (package (name (if extra-version (string-append "linux-libre-" extra-version) @@ -796,11 +816,127 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." (source source) (supported-systems supported-systems) (build-system gnu-build-system) + (arguments + (list + #:modules '((guix build gnu-build-system) + (guix build utils) + (srfi srfi-1) + (srfi srfi-26) + (ice-9 ftw) + (ice-9 match)) + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-/bin/pwd + (lambda _ + (substitute* (find-files + "." "^Makefile(\\.include)?$") + (("/bin/pwd") "pwd")))) + #$@(if build-doc? + #~((add-before 'configure 'build-doc + (lambda _ + (substitute* "Documentation/Makefile" + ;; Remove problematic environment check script. + ((".*scripts/sphinx-pre-install.*") "")) + (invoke "make" "infodocs"))) + (add-after 'build-doc 'install-doc + (lambda _ + (with-directory-excursion "Documentation/output" + (invoke "make" "-C" "texinfo" "install-info" + (string-append "infodir=" #$output + "/share/info")))))) + #~()) + (replace 'configure + (lambda* (#:key inputs target #:allow-other-keys) + ;; Avoid introducing timestamps. + (setenv "KCONFIG_NOTIMESTAMP" "1") + (setenv "KBUILD_BUILD_TIMESTAMP" (getenv "SOURCE_DATE_EPOCH")) + + ;; Other variables useful for reproducibility. + (setenv "KBUILD_BUILD_USER" "guix") + (setenv "KBUILD_BUILD_HOST" "guix") + + ;; Set ARCH and CROSS_COMPILE. + (let ((arch #$(platform-linux-architecture + (lookup-platform-by-target-or-system + (or (%current-target-system) + (%current-system)))))) + (setenv "ARCH" arch) + (format #t "`ARCH' set to `~a'~%" (getenv "ARCH")) + + (when target + (setenv "CROSS_COMPILE" (string-append target "-")) + (format #t "`CROSS_COMPILE' set to `~a'~%" + (getenv "CROSS_COMPILE")))) + + (setenv "EXTRAVERSION" + #$(and extra-version + (string-append "-" extra-version))) + + (let ((config (assoc-ref inputs "kconfig"))) + + ;; Use a custom kernel configuration file or a default + ;; configuration file. + (if config + (begin + (copy-file config ".config") + (chmod ".config" #o666)) + (invoke "make" #$defconfig)) + + ;; Appending works even when the option wasn't in the + ;; file. The last one prevails if duplicated. + (let ((port (open-file ".config" "a")) + (extra-configuration #$(config->string extra-options))) + (display extra-configuration port) + (close-port port)) + + (invoke "make" "oldconfig")))) + (replace 'install + (lambda* (#:key inputs native-inputs #:allow-other-keys) + (let ((moddir (string-append #$output "/lib/modules")) + (dtbdir (string-append #$output "/lib/dtbs"))) + ;; Install kernel image, kernel configuration and link map. + (for-each (lambda (file) (install-file file #$output)) + (find-files "." "^(\\.config|bzImage|zImage|Image\ +|vmlinuz|System\\.map|Module\\.symvers)$")) + ;; Install device tree files + (unless (null? (find-files "." "\\.dtb$")) + (mkdir-p dtbdir) + (invoke "make" (string-append "INSTALL_DTBS_PATH=" dtbdir) + "dtbs_install")) + ;; Install kernel modules + (mkdir-p moddir) + (invoke "make" + ;; Disable depmod because the Guix system's + ;; module directory is an union of potentially + ;; multiple packages. It is not possible to use + ;; depmod to usefully calculate a dependency + ;; graph while building only one of them. + "DEPMOD=true" + (string-append "MODULE_DIR=" moddir) + (string-append "INSTALL_PATH=" #$output) + (string-append "INSTALL_MOD_PATH=" #$output) + "INSTALL_MOD_STRIP=1" + "modules_install") + (let* ((versions (filter (lambda (name) + (not (string-prefix? "." name))) + (scandir moddir))) + (version (match versions + ((x) x)))) + ;; There are symlinks to the build and source directory. + ;; Both will point to target /tmp/guix-build* and thus + ;; not be useful in a profile. Delete the symlinks. + (false-if-file-not-found + (delete-file + (string-append moddir "/" version "/build"))) + (false-if-file-not-found + (delete-file + (string-append moddir "/" version "/source")))))))))) (native-inputs `(("perl" ,perl) ("bc" ,bc) ("openssl" ,openssl) - ("elfutils" ,elfutils) ; Needed to enable CONFIG_STACK_VALIDATION + ("elfutils" ,elfutils) ;needed to enable CONFIG_STACK_VALIDATION ("flex" ,flex) ("bison" ,bison) @@ -809,6 +945,18 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." ("mpfr" ,mpfr) ("mpc" ,mpc) + ;; For generating the documentation. + ,@(if build-doc? + ;; TODO: remove fontconfig after the 5.10 kernel is dropped. + ;; Also replace python-wrapper by python at that time. + `(("fontconfig" ,fontconfig) + ("graphviz" ,graphviz) + ("python" ,python-wrapper) + ("python-sphinx" ,python-sphinx) + ("texinfo" ,texinfo) + ("which" ,which)) + '()) + ,@(match (let ((arch (platform-linux-architecture (lookup-platform-by-target-or-system (or (%current-target-system) @@ -817,115 +965,14 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." (configuration-file arch #:variant (version-major+minor version)))) - (#f ;no config for this platform + (#f ;no config for this platform '()) ((? string? config) `(("kconfig" ,config)))))) - (arguments - (list #:modules '((guix build gnu-build-system) - (guix build utils) - (srfi srfi-1) - (srfi srfi-26) - (ice-9 ftw) - (ice-9 match)) - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'patch-/bin/pwd - (lambda _ - (substitute* (find-files "." "^Makefile(\\.include)?$") - (("/bin/pwd") "pwd")))) - (replace 'configure - (lambda* (#:key inputs target #:allow-other-keys) - ;; Avoid introducing timestamps. - (setenv "KCONFIG_NOTIMESTAMP" "1") - (setenv "KBUILD_BUILD_TIMESTAMP" - (getenv "SOURCE_DATE_EPOCH")) - - ;; Other variables useful for reproducibility. - (setenv "KBUILD_BUILD_USER" "guix") - (setenv "KBUILD_BUILD_HOST" "guix") - - ;; Set ARCH and CROSS_COMPILE. - (let ((arch #$(platform-linux-architecture - (lookup-platform-by-target-or-system - (or (%current-target-system) - (%current-system)))))) - (setenv "ARCH" arch) - (format #t "`ARCH' set to `~a'~%" (getenv "ARCH")) - - (when target - (setenv "CROSS_COMPILE" (string-append target "-")) - (format #t "`CROSS_COMPILE' set to `~a'~%" - (getenv "CROSS_COMPILE")))) - - (setenv "EXTRAVERSION" - #$(and extra-version - (string-append "-" extra-version))) - - (let ((config (assoc-ref inputs "kconfig"))) - - ;; Use a custom kernel configuration file or a default - ;; configuration file. - (if config - (begin - (copy-file config ".config") - (chmod ".config" #o666)) - (invoke "make" #$defconfig)) - - ;; Appending works even when the option wasn't in the - ;; file. The last one prevails if duplicated. - (let ((port (open-file ".config" "a")) - (extra-configuration #$(config->string extra-options))) - (display extra-configuration port) - (close-port port)) - - (invoke "make" "oldconfig")))) - (replace 'install - (lambda* (#:key inputs native-inputs #:allow-other-keys) - (let ((moddir (string-append #$output "/lib/modules")) - (dtbdir (string-append #$output "/lib/dtbs"))) - ;; Install kernel image, kernel configuration and link map. - (for-each (lambda (file) (install-file file #$output)) - (find-files "." "^(\\.config|bzImage|zImage|Image|vmlinuz|System\\.map|Module\\.symvers)$")) - ;; Install device tree files - (unless (null? (find-files "." "\\.dtb$")) - (mkdir-p dtbdir) - (invoke "make" (string-append "INSTALL_DTBS_PATH=" dtbdir) - "dtbs_install")) - ;; Install kernel modules - (mkdir-p moddir) - (invoke "make" - ;; Disable depmod because the Guix system's - ;; module directory is an union of potentially - ;; multiple packages. It is not possible to use - ;; depmod to usefully calculate a dependency - ;; graph while building only one of them. - "DEPMOD=true" - (string-append "MODULE_DIR=" moddir) - (string-append "INSTALL_PATH=" #$output) - (string-append "INSTALL_MOD_PATH=" #$output) - "INSTALL_MOD_STRIP=1" - "modules_install") - (let* ((versions (filter (lambda (name) - (not (string-prefix? "." name))) - (scandir moddir))) - (version (match versions - ((x) x)))) - ;; There are symlinks to the build and source directory. - ;; Both will point to target /tmp/guix-build* and thus - ;; not be useful in a profile. Delete the symlinks. - (false-if-file-not-found - (delete-file - (string-append moddir "/" version "/build"))) - (false-if-file-not-found - (delete-file - (string-append moddir "/" version "/source")))))))) - #:tests? #f)) (home-page "https://www.gnu.org/software/linux-libre/") (synopsis "100% free redistribution of a cleaned Linux kernel") - (description - "GNU Linux-Libre is a free (as in freedom) variant of the Linux kernel. -It has been modified to remove all non-free binary blobs.") + (description "GNU Linux-Libre is a free (as in freedom) variant of the +Linux kernel. It has been modified to remove all non-free binary blobs.") (license license:gpl2) (properties '((max-silent-time . 3600))))) ;don't timeout on blob scan. @@ -5555,7 +5602,7 @@ and copy/paste text in the console and in xterm.") (define-public btrfs-progs (package (name "btrfs-progs") - (version "5.18.1") + (version "6.0.2") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/linux/kernel/" @@ -5563,7 +5610,7 @@ and copy/paste text in the console and in xterm.") "btrfs-progs-v" version ".tar.xz")) (sha256 (base32 - "0mbj3j2fpjds9i9gm8kk8a20yjacc562ibd1v9a96bpmrxfag63f")))) + "063hmqwqlmp0llgqnfqgcj7slrv762kmbk6srhrgqifr94q8crb6")))) (build-system gnu-build-system) (outputs '("out" "static")) ; static versions of the binaries in "out" @@ -8456,7 +8503,7 @@ compatible with Python's ConfigParser style of .INI files, including RFC (define-public xfsprogs (package (name "xfsprogs") - (version "5.14.2") + (version "6.0.0") (source (origin (method url-fetch) (uri (string-append @@ -8464,7 +8511,7 @@ compatible with Python's ConfigParser style of .INI files, including RFC "xfsprogs-" version ".tar.gz")) (sha256 (base32 - "0368dacdjq55ip38yizs9spdyl7b0b1c0vz3gr1gvcb9rw3a6dnp")))) + "14hc61nfc73nqwhyasc4haj5g7046im1dwz61bx338f86mjj5n5y")))) (build-system gnu-build-system) (outputs (list "out" "python")) (arguments @@ -8503,6 +8550,20 @@ file systems.") ;; licensed under lgpl2.1. the other stuff is licensed under gpl2. (license (list license:gpl2 license:lgpl2.1)))) +(define-public xfsprogs-5.9 + (package + (inherit xfsprogs) + (name "xfsprogs") + (version "5.9.0") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://kernel.org/linux/utils/fs/xfs/xfsprogs/" + "xfsprogs-" version ".tar.gz")) + (sha256 + (base32 + "13xkn9jpmwp4fm9r68vhgznkmxhnv83n2b39mhy2qdaph90w2a1l")))))) + (define-public xfsprogs/static (package (inherit xfsprogs) diff --git a/gnu/packages/lisp-check.scm b/gnu/packages/lisp-check.scm index 7002cd9d92..038ca1f18b 100644 --- a/gnu/packages/lisp-check.scm +++ b/gnu/packages/lisp-check.scm @@ -94,6 +94,90 @@ consists of: @code{test}, @code{is}, @code{signals}, @code{finishes}, (define-public ecl-2am (sbcl-package->ecl-package sbcl-2am)) +(define-public sbcl-assertion-error + (let ((commit "8eab692a990d4caa193a46bae99af3e13e717b86") + (revision "1")) + (package + (name "sbcl-assertion-error") + (version (git-version "0.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/noloop/assertion-error") + (commit commit))) + (file-name (git-file-name "assertion-error" version)) + (sha256 + (base32 "0ix23kkakmf4nwx852zsssb831jvajr3qyppqfyks7y1ls617svn")))) + (build-system asdf-build-system/sbcl) + (inputs (list sbcl-dissect)) + (home-page "https://github.com/noloop/assertion-error") + (synopsis "Error pattern for assertion libraries in Common Lisp") + (description "This package provides a Common Lisp assertion system with +minimal dependencies on DISSECT.") + (license license:gpl3)))) + +(define-public ecl-assertion-error + (sbcl-package->ecl-package sbcl-assertion-error)) + +(define-public cl-assertion-error + (sbcl-package->cl-source-package sbcl-assertion-error)) + +(define-public sbcl-assert-p + (package + (name "sbcl-assert-p") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/noloop/assert-p") + (commit (string-append "v" version)))) + (file-name (git-file-name "assert-p" version)) + (sha256 + (base32 "1x24rkqkqiw8zd26swi9rmhfplkmr5scz3bhjwccah9d2s36b1xs")))) + (build-system asdf-build-system/sbcl) + (inputs (list sbcl-assertion-error sbcl-simplet)) + (home-page "https://github.com/noloop/assert-p") + (synopsis "Common Lisp assertion library") + (description "This package provides a Common Lisp collection of assertions.") + (license license:gpl3))) + +(define-public ecl-assert-p + (sbcl-package->ecl-package sbcl-assert-p)) + +(define-public cl-assert-p + (sbcl-package->cl-source-package sbcl-assert-p)) + +(define-public sbcl-cacau + (package + (name "sbcl-cacau") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/noloop/cacau") + (commit (string-append "v" version)))) + (file-name (git-file-name "cacau" version)) + (sha256 + (base32 "0m8v1xw68cr5ldv045rxgvnhigr4iahh7v6v32z6xlq2sj6r55x0")))) + (build-system asdf-build-system/sbcl) + (native-inputs (list sbcl-assert-p)) + (inputs (list sbcl-assertion-error sbcl-eventbus)) + (home-page "https://github.com/noloop/cacau") + (synopsis "Comon Lisp test runner") + (description + "This package provides a Common Lisp testing framework system CACAU which was +built to be independent of assertions systems.") + (license license:gpl3))) + +(define-public ecl-cacau + (sbcl-package->ecl-package sbcl-cacau)) + +(define-public cl-cacau + (sbcl-package->cl-source-package sbcl-cacau)) + (define-public sbcl-check-it (let ((commit "b79c9103665be3976915b56b570038f03486e62f")) (package @@ -634,11 +718,11 @@ by Chris Riesbeck.") (sbcl-package->cl-source-package sbcl-nst)) (define-public sbcl-parachute - (let ((commit "86563473dc23fb1277d35a3ad2c911a6c8e5b0da") - (revision "1")) + (let ((commit "8bc3e1b5a1808341967aeb89516f9fab23cd1d9e") + (revision "0")) (package (name "sbcl-parachute") - (version (git-version "1.1.1" revision commit)) + (version (git-version "1.5.0" revision commit)) (source (origin (method git-fetch) @@ -646,13 +730,14 @@ by Chris Riesbeck.") (git-reference (url "https://github.com/Shinmera/parachute") (commit commit))) - (file-name (git-file-name name version)) + (file-name (git-file-name "cl-parachute" version)) (sha256 - (base32 - "026crl465xqh3fnskfd4c1sxa9c33dfy702cf3l5apbjyj1dg20n")))) + (base32 "0cppp1sp9xqkgxgkwidhqzlsj03ywnar7z9mzwcliww8y0kv5555")))) (build-system asdf-build-system/sbcl) (inputs - (list sbcl-documentation-utils sbcl-form-fiddle)) + (list sbcl-documentation-utils + sbcl-form-fiddle + sbcl-trivial-custom-debugger)) (synopsis "Extensible and cross-compatible testing framework for Common Lisp") (description "Parachute is a simple-to-use and extensible testing framework. @@ -840,6 +925,32 @@ take.") (define-public ecl-should-test (sbcl-package->ecl-package sbcl-should-test)) +(define-public sbcl-simplet + (package + (name "sbcl-simplet") + (version "1.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/noloop/simplet") + (commit (string-append "v" version)))) + (file-name (git-file-name "simplet" version)) + (sha256 + (base32 "1iwp3a43mns885k2arr7gbmyv5rsrjfvgarxickj7r2bfgwp1cnn")))) + (build-system asdf-build-system/sbcl) + (home-page "https://github.com/noloop/simplet") + (synopsis "Simple test runner in Common Lisp") + (description "This package provides a Common Lisp test runner system +SIMPLET.") + (license license:gpl3))) + +(define-public ecl-simplet + (sbcl-package->ecl-package sbcl-simplet)) + +(define-public cl-simplet + (sbcl-package->cl-source-package sbcl-simplet)) + (define-public sbcl-stefil (let ((commit "0398548ec95dceb50fc2c2c03e5fb0ce49b86c7a") (revision "0")) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 27312cb369..e3ddc26eac 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -490,6 +490,39 @@ interface to the Linux inotify API.") (define-public ecl-cl-inotify (sbcl-package->ecl-package sbcl-cl-inotify)) +(define-public sbcl-file-notify + (let ((commit "f12dc2f2aae5fee13355cd93a8cae0c4c412b76d") + (revision "0")) + (package + (name "sbcl-file-notify") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/file-notify") + (commit commit))) + (file-name (git-file-name "cl-file-notify" version)) + (sha256 + (base32 "0788d98rqm1krl8nbfh8qshvyf6g336i9bqrdhkx06cfvbh0wcny")))) + (build-system asdf-build-system/sbcl) + (inputs + (list sbcl-cffi + sbcl-documentation-utils + sbcl-trivial-features)) + (home-page "https://github.com/Shinmera/file-notify") + (synopsis "Get notifications for file accesses and changes") + (description + "File-Notify is a Common Lisp library for getting notifications for file +accesses and changes.") + (license license:zlib)))) + +(define-public cl-file-notify + (sbcl-package->cl-source-package sbcl-file-notify)) + +(define-public ecl-file-notify + (sbcl-package->ecl-package sbcl-file-notify)) + (define-public sbcl-bodge-queue (let ((commit "948c9a501dcd412689952d09eb7453ec2722336a") (revision "0")) @@ -708,6 +741,36 @@ or cl-launch for portable processing of command-line arguments.") (define-public cl-command-line-arguments (sbcl-package->cl-source-package sbcl-command-line-arguments)) +(define-public sbcl-adopt + (package + (name "sbcl-adopt") + (version "1.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/sjl/adopt") + (commit (string-append "v" version)))) + (file-name (git-file-name "cl-adopt" version)) + (sha256 + (base32 "16kzkai96qk7vmclp8wxc9aghhnisw8gg9s7hra68300bgj86wzr")))) + (build-system asdf-build-system/sbcl) + (native-inputs (list sbcl-1am)) + (inputs (list sbcl-bobbin sbcl-split-sequence)) + (home-page "https://hg.stevelosh.com/adopt") + (synopsis "Common Lisp option parsing library") + (description + "@acronym{ADOPT, A Damn OPTion} is a simple UNIX-style option parser in +Common Lisp, heavily influenced by Python's @code{optparse} and +@code{argparse}.") + (license license:expat))) + +(define-public ecl-adopt + (sbcl-package->ecl-package sbcl-adopt)) + +(define-public cl-adopt + (sbcl-package->cl-source-package sbcl-adopt)) + (define-public sbcl-cl-irc (let ((commit "963823537c7bfcda2edd4c44d172192da6722175") (revision "0")) @@ -1049,6 +1112,59 @@ compatible with ANSI-compliant Common Lisp implementations.") (define-public ecl-cl-ppcre (sbcl-package->ecl-package sbcl-cl-ppcre)) +(define-public sbcl-one-more-re-nightmare + (let ((commit "09c33feed35797512bf123ccca053cf8ba42bfbd") + (revision "0")) + (package + (name "sbcl-one-more-re-nightmare") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/telekons/one-more-re-nightmare") + (commit commit))) + (file-name (git-file-name "cl-one-more-re-nightmare" version)) + (sha256 + (base32 "0vc0lxvn3anjb63hr26r1l18aw5nbj80w9ja3a32fip6nbwfsrfv")))) + (build-system asdf-build-system/sbcl) + (arguments + '(#:asd-test-systems '("one-more-re-nightmare-tests") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "Tests/one-more-re-nightmare-tests.asd" + ((":depends-on") + (string-append + ":perform (test-op (o c) (symbol-call :one-more-re-nightmare-tests '#:run-tests))" + "\n :depends-on")))))))) + (native-inputs + (list sbcl-lparallel sbcl-parachute)) + (inputs + (list sbcl-alexandria + sbcl-babel + sbcl-bordeaux-threads + sbcl-dynamic-mixins + sbcl-esrap + sbcl-stealth-mixin + sbcl-trivia + sbcl-trivial-indent)) + (home-page "https://github.com/telekons/one-more-re-nightmare") + (synopsis "Regular expression compiler in Common Lisp") + (description "@code{one-more-re-nightmare} is a regular expression engine +that uses the technique presented in Regular-expression derivatives +re-examined (Owens, Reppy and Turon, 2009; +@url{doi:10.1017/S0956796808007090}) to interpret and compile regular +expressions.") + (license license:bsd-2)))) + +(define-public cl-one-more-re-nightmare + (sbcl-package->cl-source-package sbcl-one-more-re-nightmare)) + +(define-public ecl-one-more-re-nightmare + (sbcl-package->ecl-package sbcl-one-more-re-nightmare)) + (define-public sbcl-parse (let ((commit "2351ee78acac065fcf10b8713d3f404e2e910786") (revision "1")) @@ -2400,7 +2516,7 @@ clause if no operation becomes available within a set amount of time. Calispel is a message-passing library, and as such leaves the role of threading abstractions and utilities left to be filled by complementary libraries such as Bordeaux-Threads and Eager Future.") - (home-page "https://www.thoughtcrime.us/software/jpl-queues/") + (home-page "https://www.thoughtcrime.us/software/calispel/") (license license:isc)))) (define-public cl-calispel @@ -2971,6 +3087,89 @@ pretty, documentation is code.") (define-public ecl-mgl-pax (sbcl-package->ecl-package sbcl-mgl-pax)) +(define-public sbcl-40ants-doc + (let ((commit "7725ff67a380e9ebfc6155e14d91e650f256711b") + (revision "0")) + (package + (name "sbcl-40ants-doc") + (version (git-version "0.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/40ants/doc") + (commit commit))) + (sha256 + (base32 "1v6gnhrk02vsixmprzk4wvvj7vh11vp5waxyih0qz2ih8d38r5pg")) + (file-name (git-file-name "cl-40ants-doc" version)))) + (build-system asdf-build-system/sbcl) + (arguments + ;; TODO: Add remaining dependencies of 40ants-doc-full and + ;; 40ants-doc-test missing from Guix. + '(#:asd-systems '("40ants-doc" + ;;"40ants-doc-full" + ) + #:tests? #f)) + ;;(native-inputs + ;; (list sbcl-rove)) + (inputs + (list sbcl-named-readtables + sbcl-pythonic-string-reader + ;; For 40ants-doc-full: + ;;sbcl-3bmd + ;;sbcl-alexandria + ;;sbcl-babel + ;;sbcl-cl-cookie + ;;sbcl-cl-fad + ;;sbcl-cl-ppcre + ;;sbcl-common-doc ; Missing from Guix + ;;sbcl-common-html ; Missing from Guix + ;;sbcl-commondoc-markdown ; Missing from Guix + ;;sbcl-dexador + ;;sbcl-docs-builder ; Missing from Guix + ;;sbcl-fare-utils + ;;sbcl-jonathan + ;;sbcl-lass + ;;sbcl-local-time + ;;sbcl-log4cl + ;;sbcl-slime-swank + ;;sbcl-slynk + ;;sbcl-spinneret + ;;sbcl-stem ; Missing from Guix; also, license is unconfirmed + ;;sbcl-str + ;;sbcl-tmpdir ; Missing from Guix + ;;sbcl-trivial-extract ; Missing from Guix + ;;sbcl-xml-emitter + )) + (home-page "https://40ants.com/doc/") + (synopsis "Exploratory programming environment and documentation generator") + (description + "@code{40ants-doc} provides a rudimentary explorable programming +environment. The narrative primarily lives in so-called sections that mix +Markdown docstrings with references to functions, variables, etc., all of +which should probably have their own docstrings. + +The primary focus is on making code easily explorable by using SLIME's +@kbd{M-.} (@code{slime-edit-definition}). Generating documentation in +Markdown or HTML format from sections and all the referenced items is also +implemented. + +With the simplistic tools provided, one may obtain results similar to literate +programming, but documentation is generated from code, not the other way +around, and there is no support for chunking. Code comes first, code must +look pretty, documentation is code. + +@code{40ants-doc} is a fork of MGL-PAX with fewer dependencies (only +@code{named-readtables} and @code{pythonic-string-reader}) for the core +system, and additional features in the full system.") + (license license:expat)))) + +(define-public cl-40ants-doc + (sbcl-package->cl-source-package sbcl-40ants-doc)) + +(define-public ecl-40ants-doc + (sbcl-package->ecl-package sbcl-40ants-doc)) + (define-public sbcl-mssql (let ((commit "045602a19a32254108f2b75871049293f49731eb") (revision "1")) @@ -7600,8 +7799,8 @@ extension-points via the concept of hooks.") (define-public sbcl-s-sysdeps ;; No release since 2013. - (let ((commit "9aa23bbdceb24bcdbe0e7c39fa1901858f823106") - (revision "2")) + (let ((commit "7f8de283b7fbd8b038fdf08493063a736db36ce7") + (revision "3")) (package (name "sbcl-s-sysdeps") (build-system asdf-build-system/sbcl) @@ -7616,7 +7815,7 @@ extension-points via the concept of hooks.") (file-name (git-file-name name version)) (sha256 (base32 - "1fh8r7kf8s3hvqdg6b71b8p7w3v2kkga9bw8j3qqdxhzr6anpm0b")))) + "0rp81iq0rgl48qdwbmfy89glga81hmry2lp8adjbr5h5ybr92b4n")))) (inputs (list sbcl-bordeaux-threads sbcl-usocket)) (synopsis "Common Lisp abstraction layer over platform dependent functionality") @@ -7641,8 +7840,8 @@ number of other projects. (sbcl-package->ecl-package sbcl-s-sysdeps)) (define-public sbcl-cl-prevalence - (let ((commit "5a76be036092ed6c18cb695a9e03bce87e21b840") - (revision "4")) + (let ((commit "e6b27640ce89ae5f8af38beb740e319bb6cd2368") + (revision "6")) (package (name "sbcl-cl-prevalence") (build-system asdf-build-system/sbcl) @@ -7657,11 +7856,11 @@ number of other projects. (file-name (git-file-name name version)) (sha256 (base32 - "050h6hwv8f16b5v6fzba8zmih92hgaaq27i2x9wv1iib41gbia3r")))) + "1lb957ivshgp56phqhvhsmnc4r55x5shvi3mpsan2xsm4hvqspp0")))) (inputs - (list sbcl-s-sysdeps sbcl-s-xml)) + (list sbcl-moptilities sbcl-s-sysdeps sbcl-s-xml)) (native-inputs - (list sbcl-fiveam)) + (list sbcl-fiveam sbcl-find-port)) (synopsis "Implementation of object prevalence for Common Lisp") (description "This Common Lisp library implements object prevalence (see @url{https://en.wikipedia.org/wiki/System_prevalence}). It allows @@ -8820,8 +9019,8 @@ macro. This library provides a set of simple utilities to help with that.") (sbcl-package->ecl-package sbcl-form-fiddle)) (define-public sbcl-array-utils - (let ((commit "f90eb9070d0b2205af51126a35033574725e5c56") - (revision "0")) + (let ((commit "40cea8fc895add87d1dba9232da817750222b528") + (revision "1")) (package (name "sbcl-array-utils") (version (git-version "1.1.1" revision commit)) @@ -8832,10 +9031,9 @@ macro. This library provides a set of simple utilities to help with that.") (git-reference (url "https://github.com/Shinmera/array-utils") (commit commit))) - (file-name (git-file-name name version)) + (file-name (git-file-name "cl-array-utils" version)) (sha256 - (base32 - "0zhwfbpr53vs1ii4sx75dz2k9yhh1xpwdqqpg8nmfndxkmhpbi3x")))) + (base32 "0d7nddak8h2aa82z11vdbd97srk5bdgq41pzmibsz3ymspnndicd")))) (build-system asdf-build-system/sbcl) (native-inputs (list sbcl-parachute)) @@ -8889,8 +9087,8 @@ LASS files.") (sbcl-package->ecl-package sbcl-lass)) (define-public sbcl-plump - (let ((commit "3584275f0be9d06c0c51b5c08f89005deafc4ada") - (revision "2")) + (let ((commit "0c3e0b57b43b6e0c5794b6a902f1cf5bee2a2927") + (revision "3")) (package (name "sbcl-plump") (version (git-version "2.0.0" revision commit)) @@ -8901,10 +9099,9 @@ LASS files.") (git-reference (url "https://github.com/Shinmera/plump") (commit commit))) - (file-name (git-file-name name version)) + (file-name (git-file-name "cl-plump" version)) (sha256 - (base32 - "1w4wz7f6dc2ckdq9wq9r5014bg2nxjifj9yz1zzn41r8h1h5xfcd")))) + (base32 "1fyb66pqvr1iy31ah9638ihs8cax17zkxk0zq14jy7x5l9rq1qlf")))) (build-system asdf-build-system/sbcl) (inputs (list sbcl-array-utils sbcl-documentation-utils)) @@ -9362,6 +9559,103 @@ archives such as those generated by the tar and cpio programs on Unix.") (define-public ecl-archive (sbcl-package->ecl-package sbcl-archive)) +(define-public sbcl-tar-file + (let ((commit "0c10bc82f14702c97a26dc25ce075b5d3a2347d1") + (revision "0")) + (package + (name "sbcl-tar-file") + (version (git-version "0.2.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.common-lisp.net/cl-tar/cl-tar-file") + (commit commit))) + (file-name (git-file-name "cl-tar-file" version)) + (sha256 + (base32 "0i8j05fkgdqy4c4pqj0c68sh4s3klpx9kc5wp73qwzrl3xqd2svy")))) + (build-system asdf-build-system/sbcl) + (native-inputs + (list sbcl-parachute)) + (inputs + (list sbcl-40ants-doc + sbcl-alexandria + sbcl-babel + sbcl-chipz + sbcl-flexi-streams + sbcl-salza2 + sbcl-trivial-gray-streams)) + (home-page "https://gitlab.common-lisp.net/cl-tar/cl-tar-file") + (synopsis "Read and write physical entries to and from tar files") + (description + "@code{cl-tar-file} is a Common Lisp library that allows reading from +and writing to various tar archive formats. Currently supported are the POSIX +ustar, PAX (ustar with a few new entry types), GNU, and v7 (very old) formats. + +This library is rather low level and is focused exclusively on reading and +writing physical tar file entries using streams. Therefore, it contains no +functionality for automatically building archives from a set of files on the +filesystem or writing the contents of a file to the filesystem. Additionally, +there are no smarts that read multiple physical entries and combine them into +a single logical entry (e.g., with PAX extended headers or GNU long link/path +name support). For a higher-level library that reads and writes logical +entries, and also includes filesystem integration, see @code{cl-tar}.") + (license license:bsd-3)))) + +(define-public cl-tar-file + (sbcl-package->cl-source-package sbcl-tar-file)) + +(define-public ecl-tar-file + (sbcl-package->ecl-package sbcl-tar-file)) + +(define-public sbcl-tar + (let ((commit "7c6e07a10c93d9e311f087b5f6328cddd481669a") + (revision "0")) + (package + (name "sbcl-tar") + (version (git-version "0.2.3" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.common-lisp.net/cl-tar/cl-tar") + (commit commit))) + (file-name (git-file-name "cl-tar" version)) + (sha256 + (base32 "0wp23cs3i6a89dibifiz6559la5nk58d1n17xvbxq4nrl8cqsllf")))) + (build-system asdf-build-system/sbcl) + ;; TODO: Build the tar program with 'build-program' when the + ;; 'asdf-release-ops' library is added to Guix. + (arguments + '(#:asd-systems '("tar" + "tar/common-extract" + "tar/create" + "tar/docs" + "tar/extract" + "tar/simple-extract"))) + (native-inputs + (list sbcl-parachute)) + (inputs + (list sbcl-40ants-doc + sbcl-alexandria + sbcl-babel + sbcl-local-time + sbcl-osicat + sbcl-split-sequence + sbcl-tar-file)) + (home-page "https://gitlab.common-lisp.net/cl-tar/cl-tar") + (synopsis "High-level interface for tar files") + (description + "@code{cl-tar} is a Common Lisp library providing a high-level interface +for interacting with tar archives.") + (license license:expat)))) + +(define-public cl-tar + (sbcl-package->cl-source-package sbcl-tar)) + +(define-public ecl-tar + (sbcl-package->ecl-package sbcl-tar)) + (define-public sbcl-misc-extensions (let ((commit "101c05112bf2f1e1bbf527396822d2f50ca6327a") (revision "1")) @@ -12800,6 +13094,44 @@ than a few Kb.") (define-public ecl-mmap (sbcl-package->ecl-package sbcl-mmap)) +(define-public sbcl-marray + (let ((commit "0352f316b6830f0b119088ba9be836e4726bd7d8") + (revision "0")) + (package + (name "sbcl-marray") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/death/marray") + (commit commit))) + (file-name (git-file-name "cl-marray" version)) + (sha256 + (base32 "0l4kvzpiw14vqhlsaflp3c7y51vznjjgbdi0q3axqk1wxvzy1zlx")))) + (build-system asdf-build-system/sbcl) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-dependencies + (lambda _ + (substitute* "marray.asd" + ((":components") + ":depends-on (#+sbcl \"sb-posix\")\n :components"))))))) + (home-page "https://github.com/death/marray") + (synopsis "Memory-mapped files as Common Lisp arrays") + (description + "MARRAY is a library which provides access to memory-mapped files +through Common Lisp arrays.") + (license license:expat)))) + +(define-public cl-marray + (sbcl-package->cl-source-package sbcl-marray)) + +;; ECL support not implemented yet. +;; (define-public ecl-marray +;; (sbcl-package->ecl-package sbcl-marray)) + (define-public sbcl-3bz (let ((commit "569614c40408f3aefc77ba233e0e4bd66d3850ad") (revision "1")) @@ -13971,6 +14303,39 @@ directly.") (define-public ecl-custom-hash-table (sbcl-package->ecl-package sbcl-custom-hash-table)) +(define-public sbcl-concurrent-hash-tables + (let ((commit "1b9f0b5da54fece4f42296e1bdacfcec0c370a5a") + (revision "0")) + (package + (name "sbcl-concurrent-hash-tables") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/no-defun-allowed/concurrent-hash-tables") + (commit commit))) + (file-name (git-file-name "cl-concurrent-hash-tables" version)) + (sha256 + (base32 "03g24ycr1ngzg8bv10iwp1bmnldz5bxbfdqrzhfxhicpibh49r96")))) + (build-system asdf-build-system/sbcl) + (inputs + (list sbcl-atomics sbcl-bordeaux-threads)) + (home-page "https://github.com/no-defun-allowed/concurrent-hash-tables") + (synopsis "Portability library for concurrent hash tables in Common Lisp") + (description "@code{concurrent-hash-tables} is a Common Lisp portability +library wrapping some implementations of concurrent hash tables which do not +have to be entirely locked in their operation, including +@code{42nd-at-threadmill}, @code{luckless}, and a fallback, segmented hash +table.") + (license license:bsd-2)))) + +(define-public cl-concurrent-hash-tables + (sbcl-package->cl-source-package sbcl-concurrent-hash-tables)) + +(define-public ecl-concurrent-hash-tables + (sbcl-package->ecl-package sbcl-concurrent-hash-tables)) + (define-public sbcl-collectors (let ((commit "13acef25d8422d1d82e067b1861e513587c166ee")) (package @@ -14272,6 +14637,34 @@ with a complex event filtering system.") (define-public ecl-deeds (sbcl-package->ecl-package sbcl-deeds)) +(define-public sbcl-eventbus + (let ((commit "92c1fa3846ba0e3cc9e6d7605d765379c8658d84") + (revision "1")) + (package + (name "sbcl-eventbus") + (version (git-version "0.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/noloop/eventbus") + (commit commit))) + (file-name (git-file-name "eventbus" version)) + (sha256 + (base32 "0slqx3zq6sbz3rg4g79j8y25sx4405y6ff3x6l5v8v4v42m1s0p2")))) + (build-system asdf-build-system/sbcl) + (native-inputs (list sbcl-simplet)) + (home-page "https://github.com/noloop/eventbus") + (synopsis "Event bus implementation in Common Lisp") + (description "This package provides a Common Lisp system implementing event bus.") + (license license:gpl3)))) + +(define-public ecl-eventbus + (sbcl-package->ecl-package sbcl-eventbus)) + +(define-public cl-eventbus + (sbcl-package->cl-source-package sbcl-eventbus)) + (define-public sbcl-make-hash ;; no tagged branch (let ((revision "1") @@ -15014,6 +15407,80 @@ even by adding additional statistical @code{compute}ations.") (define-public ecl-trivial-benchmark (sbcl-package->ecl-package sbcl-trivial-benchmark)) +(define-public sbcl-the-cost-of-nothing + (let ((commit "f364029fbbf37ae5786f2f9ddf6185dd204a7185") + (revision "0")) + (package + (name "sbcl-the-cost-of-nothing") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/marcoheisig/the-cost-of-nothing") + (commit commit))) + (file-name (git-file-name "cl-the-cost-of-nothing" version)) + (sha256 + (base32 "1ccrglyr1wnnfp218w1qj7yfl4yzlxkki3hqaifi5axgbi5dmmh8")))) + (build-system asdf-build-system/sbcl) + (arguments + ;; The test operation benchmarks the Common Lisp implementation; it + ;; doesn't test the package. + (list #:tests? #f)) + (inputs + (list sbcl-alexandria + sbcl-closer-mop + sbcl-local-time + sbcl-trivial-garbage)) + (home-page "https://github.com/marcoheisig/the-cost-of-nothing") + (synopsis "Measure the run time of Common Lisp code") + (description + "THE-COST-OF-NOTHING is a library for measuring the run time of Common +Lisp code. It provides macros and functions for accurate benchmarking and +lightweight monitoring. Furthermore, it provides predefined benchmarks to +determine the cost of certain actions on a given platform and implementation.") + (license license:expat)))) + +(define-public cl-the-cost-of-nothing + (sbcl-package->cl-source-package sbcl-the-cost-of-nothing)) + +(define-public ecl-the-cost-of-nothing + (sbcl-package->ecl-package sbcl-the-cost-of-nothing)) + +(define-public sbcl-atomichron + (let ((commit "5b3578bbad8c37ab559e56924d98c373efe11de5") + (revision "0")) + (package + (name "sbcl-atomichron") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/no-defun-allowed/atomichron") + (commit commit))) + (file-name (git-file-name "cl-atomichron" version)) + (sha256 + (base32 "1fmmhb3pbv7j4d1cc02zv24bpd0kd2agfjjcj46w3gmv1bb0hva1")))) + (build-system asdf-build-system/sbcl) + (inputs + (list sbcl-atomics sbcl-bordeaux-threads)) + (home-page "https://github.com/no-defun-allowed/atomichron") + (synopsis "Atomic metering library for Common Lisp") + (description + "@code{atomichron} is a Common Lisp library which implements a time +meter which tracks how many times a form is evaluated, and how long evaluation +takes. It uses atomic instructions so that meters will present correct +results in the presence of multiple threads, while trying to minimize +synchronization latency.") + (license license:bsd-2)))) + +(define-public cl-atomichron + (sbcl-package->cl-source-package sbcl-atomichron)) + +(define-public ecl-atomichron + (sbcl-package->ecl-package sbcl-atomichron)) + (define-public sbcl-glyphs (let ((commit "1ff5714e8c1dca327bc604dfe3e3d1f4b7755373")) (package @@ -16499,6 +16966,35 @@ return the CPU count of the current system.") (define-public cl-cpus (sbcl-package->cl-source-package sbcl-cl-cpus)) +(define-public sbcl-system-load + (let ((commit "3ff1a40be55866cc5316ac7a530d872b12510294") + (revision "0")) + (package + (name "sbcl-system-load") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/system-load") + (commit commit))) + (file-name (git-file-name "cl-system-load" version)) + (sha256 + (base32 "08d8kr8j5l2m8p69f47iklxhna394vx9mrys0sgplf5f2bqb7xcv")))) + (build-system asdf-build-system/sbcl) + (home-page "https://github.com/Shinmera/system-load") + (synopsis "Access system's CPU and memory usage from Common Lisp") + (description + "System-Load is a Common Lisp library for accessing the system's CPU and +memory usage.") + (license license:zlib)))) + +(define-public cl-system-load + (sbcl-package->cl-source-package sbcl-system-load)) + +(define-public ecl-system-load + (sbcl-package->ecl-package sbcl-system-load)) + (define-public sbcl-fof (let ((commit "522879e7da110ecf2e841998b197b34062c54b29") (revision "1")) @@ -17628,6 +18124,35 @@ long-running threads. In principle, it is like an in-Lisp process supervisor.") (define-public ecl-moira (sbcl-package->ecl-package sbcl-moira)) +(define-public sbcl-with-user-abort + (let ((commit "60693b4a1354faf17107ad6003b0b870cca37081") + (revision "0")) + (package + (name "sbcl-with-user-abort") + (version (git-version "0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/compufox/with-user-abort") + (commit commit))) + (file-name (git-file-name "cl-with-user-abort" version)) + (sha256 + (base32 "0k1xxfvncdw4fx8nncis1ma128bqq05zky1mrzak5rjbivzjm8j1")))) + (build-system asdf-build-system/sbcl) + (home-page "https://github.com/compufox/with-user-abort") + (synopsis "Portability library for catching SIGINT from Common Lisp") + (description + "@code{with-user-abort} is a Common Lisp portability library providing a +like-named macro that catches the SIGINT signal.") + (license license:bsd-3)))) + +(define-public cl-with-user-abort + (sbcl-package->cl-source-package sbcl-with-user-abort)) + +(define-public ecl-with-user-abort + (sbcl-package->ecl-package sbcl-with-user-abort)) + (define-public sbcl-cl-package-locks (let ((commit "96a358ede7cef416d61d2f699e724fe1d9de602c") (revision "1")) @@ -23666,6 +24191,38 @@ objects to be mixed and updated without manually defining many permutations.") (define-public ecl-dynamic-mixins (sbcl-package->ecl-package sbcl-dynamic-mixins)) +(define-public sbcl-stealth-mixin + (let ((commit "2f853fcead554221d4be3b10522b502ea729e944") + (revision "0")) + (package + (name "sbcl-stealth-mixin") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/robert-strandh/Stealth-mixin") + (commit commit))) + (file-name (git-file-name "cl-stealth-mixin" version)) + (sha256 + (base32 "0ar9cdmbmdnqz1ywpw34n47hlh0vqmb6pl76f5vbfgip3c81xwyi")))) + (build-system asdf-build-system/sbcl) + (inputs + (list sbcl-closer-mop)) + (home-page "https://github.com/robert-strandh/Stealth-mixin") + (synopsis "Create stealth mixin classes") + (description + "Stealth-mixin is a Common Lisp library for creating stealth mixin +classes. These are classes that are dynamically mixed into other classes +without the latter being aware of it.") + (license license:bsd-2)))) + +(define-public cl-stealth-mixin + (sbcl-package->cl-source-package sbcl-stealth-mixin)) + +(define-public ecl-stealth-mixin + (sbcl-package->ecl-package sbcl-stealth-mixin)) + (define-public sbcl-sealable-metaobjects (let ((commit "e09ec97252e0844528f61abdc0c7ee256875f8ee")) (package @@ -24457,8 +25014,12 @@ between Lisp objects and some binary (i.e. octet-based) representation.") (sha256 (base32 "1iri5wsp9sc1f5q934cj87zd79r5dc8fda0gl7x1pz95v0wx28yk")))) (build-system asdf-build-system/sbcl) - (native-inputs - (list sbcl-parachute)) + (arguments + '(;; FIXME: Tests disabled because of a circular dependency between + ;; trivial-custom-debugger and parachute. + #:tests? #f)) + ;;(native-inputs + ;; (list sbcl-parachute)) (home-page "https://github.com/phoe/trivial-custom-debugger/") (synopsis "Allow arbitrary functions as the standard Lisp debugger") (description diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index f854493281..9ffdf8761b 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -563,11 +563,11 @@ output), and Binutils.") (define %llvm-monorepo-hashes '(("14.0.6" . "14f8nlvnmdkp9a9a79wv67jbmafvabczhah8rwnqrgd5g3hfxxxx") - ("15.0.4" . "0j5kx4s970qzcjr83kk6776zzjqfshl61x9fagqz8kjxcjbpg8cj"))) + ("15.0.5" . "1z2szqlanksdmj91590wnxqav5z437mpasg00ghb610xkam2v34m"))) (define %llvm-patches '(("14.0.6" . ("clang-14.0-libc-search-path.patch")) - ("15.0.4" . ("clang-15.0-libc-search-path.patch")))) + ("15.0.5" . ("clang-15.0-libc-search-path.patch")))) (define (llvm-monorepo version) (origin @@ -583,7 +583,7 @@ output), and Binutils.") (define-public llvm-15 (package (name "llvm") - (version "15.0.4") + (version "15.0.5") (source (llvm-monorepo version)) (build-system cmake-build-system) (outputs '("out" "opt-viewer")) @@ -740,7 +740,7 @@ of programming tools as well as libraries with equivalent functionality.") (package-version llvm-15))) (sha256 (base32 - "03adxlh84if9p53m6izjsql500rjza9rng8akab2pdqibgrg73rh"))))) + "0sa6si9v7ddsa9vmg6s3918xx969rvck2v1a0g7hb0fp9jk9j4r1"))))) (define-public clang-14 (clang-from-llvm @@ -1522,7 +1522,7 @@ Library.") (define-public lld-15 (package (name "lld") - (version "15.0.4") + (version (package-version llvm-15)) (source (llvm-monorepo version)) (build-system cmake-build-system) (inputs @@ -1634,7 +1634,7 @@ misuse of libraries outside of the store."))) (define-public lldb (package (name "lldb") - (version "14.0.6") + (version (package-version llvm-15)) (source (llvm-monorepo version)) (build-system cmake-build-system) (arguments @@ -1648,8 +1648,8 @@ misuse of libraries outside of the store."))) (native-inputs (list pkg-config swig)) (inputs - (list clang-14 - llvm-14 + (list clang-15 + llvm-15 ;; Optional (but recommended) inputs. ncurses libedit @@ -1668,7 +1668,7 @@ which highly leverage existing libraries in the larger LLVM project.") (define-public libcxx (package (name "libcxx") - (version "14.0.6") + (version (package-version llvm-15)) (source (llvm-monorepo version)) (build-system cmake-build-system) (arguments diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 606b483d3e..dde87382e8 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -100,7 +100,7 @@ to statistics about the system on which it's run.") (define-public lxqt-build-tools (package (name "lxqt-build-tools") - (version "0.11.0") + (version "0.12.0") (source (origin (method url-fetch) @@ -108,7 +108,7 @@ to statistics about the system on which it's run.") "/download/" version "/lxqt-build-tools-" version ".tar.xz")) (sha256 - (base32 "1ff1pkrlxd8h0j8v49p6wrfhnqrz8s5b53hi835m41cvkzjljpfx")))) + (base32 "0c4mm167hk0yihryi46d80ghxx2lwzkpivs4yj5wsfvdpbv5q1qh")))) (build-system cmake-build-system) (arguments (list @@ -148,7 +148,7 @@ itself as well as other components maintained by the LXQt project.") (define-public libqtxdg (package (name "libqtxdg") - (version "3.9.1") + (version "3.10.0") (source (origin (method url-fetch) @@ -156,7 +156,7 @@ itself as well as other components maintained by the LXQt project.") "https://github.com/lxqt/libqtxdg/releases/download/" version "/libqtxdg-" version ".tar.xz")) (sha256 - (base32 "1kh4hv59bkjifq20ksh1mizf9mp7x30v6fpwccr45mi7hasqvvfi")))) + (base32 "18mz3mxcnz6awkkgxnfg5p43d4lv92vamxk1d0xzdxrp9symfd9v")))) (build-system cmake-build-system) (arguments '(#:configure-flags @@ -183,7 +183,7 @@ in Qt.") (define-public qtxdg-tools (package (name "qtxdg-tools") - (version "3.9.1") + (version "3.10.0") (source (origin (method url-fetch) @@ -191,7 +191,7 @@ in Qt.") "https://github.com/lxqt/qtxdg-tools/releases/download/" version "/qtxdg-tools-" version ".tar.xz")) (sha256 - (base32 "0qn35v4dv71g0a4cqkbikppwmihxmfa560q9kw5pwk2y0xiwpncr")))) + (base32 "0iyn0s2mck948vzlmq6hk4p93i9z59h50z6m2kdhzv9ck2axvlik")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no tests (propagated-inputs (list libqtxdg)) @@ -206,7 +206,7 @@ applications.") (define-public liblxqt (package (name "liblxqt") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) @@ -214,7 +214,7 @@ applications.") "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1fickg1q54pcb8bv3x0ydg4xx02cqykibnjcq09as2kws6xbhk9n")))) + (base32 "057cdxmz6kh3p1vpbwah4i99hdknh22w2w8wqfiws2d4n6wwiavz")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; no tests @@ -270,14 +270,14 @@ and memory usage or network traffic.") (define-public lxqt-about (package (name "lxqt-about") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "03bqhbpdnfpan3l4snzzz6j0054m4r9zcgygcg21znslwicbqnw3")))) + (base32 "0xah1qhzr5q20dj637c91bjrv9gy0z65d3jv6pjsp1kz5cwa8gsr")))) (build-system cmake-build-system) (inputs (list kwindowsystem @@ -305,14 +305,14 @@ LXQt and the system it's running on.") (define-public lxqt-admin (package (name "lxqt-admin") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1zah3xdnif9miaq52mmfbbzvqjhca7w7h81ngrn25j9pvd2bflm8")))) + (base32 "1bjmarrra43gcnzi8i0g0lcam12hhgr2yi8dji6klmrcp4k67y89")))) (build-system cmake-build-system) (inputs (list kwindowsystem @@ -343,14 +343,14 @@ the operating system LXQt is running on.") (define-public lxqt-config (package (name "lxqt-config") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0f0x82qma86kjdvn08qlg0ydxh9fnqikijfhnicynxdqfnp50ia5")))) + (base32 "0h0n5an1pp3k50g4p2dxymy0lsnsh7m46gb22ndam69hdkflw71y")))) (build-system cmake-build-system) (inputs (list eudev @@ -393,7 +393,7 @@ configuration of both LXQt and the underlying operating system.") (define-public lxqt-globalkeys (package (name "lxqt-globalkeys") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) @@ -401,7 +401,7 @@ configuration of both LXQt and the underlying operating system.") "releases/download/" version "/" "lxqt-globalkeys-" version ".tar.xz")) (sha256 - (base32 "0bbw85aa59w0qnvkdggm3hbacps6yfcvcrs32d34mvvhc7d6g04l")))) + (base32 "1s49b8kly027f3amxcf2bx8id3jmmrl8365x7676bd8x2g5v3va2")))) (build-system cmake-build-system) (inputs (list kwindowsystem @@ -423,14 +423,14 @@ as a whole and are not limited to distinct applications.") (define-public lxqt-notificationd (package (name "lxqt-notificationd") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0bz3qdvv591zvpkxqzqqmh1yq5icc3iinmjr13qzws3ajlj19z44")))) + (base32 "1qlvk12ldqwxskxy283h6yqhn8rp29vynqs1lhwn8byli792nb7y")))) (build-system cmake-build-system) (inputs (list kwindowsystem @@ -451,14 +451,14 @@ according to the Desktop Notifications Specification.") (define-public lxqt-openssh-askpass (package (name "lxqt-openssh-askpass") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1hxix513z2sanmygfzq1fgx30kaxw5rjmmklbyyzl8bv1xzjcwk7")))) + (base32 "0w662issh8cagmza881wdrxbngn33w8shp0jvzna1f8pf9g9f7bj")))) (build-system cmake-build-system) (inputs (list kwindowsystem @@ -479,14 +479,14 @@ of other programs.") (define-public lxqt-panel (package (name "lxqt-panel") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "11dg18ac6kj8qkkrg940bzpykjih6nnw8y3hfww3wiyg6dka9gd7")))) + (base32 "1m0mm07ydmdlyyi6s4q1cwpxp609kcyc3gcmwbmyf0smadan3yd8")))) (build-system cmake-build-system) (inputs (list alsa-lib @@ -538,14 +538,14 @@ of other programs.") (define-public lxqt-policykit (package (name "lxqt-policykit") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "150ggcfprascnwgsz721vnmay9cbar9annlhp6h2yzkl69iyc49r")))) + (base32 "01wyqhrapim0pzkghr54g0z8drhlmcszwpb6p8qfqds90k1vq6gc")))) (build-system cmake-build-system) (inputs (list kwindowsystem @@ -568,14 +568,14 @@ LXQt.") (define-public lxqt-powermanagement (package (name "lxqt-powermanagement") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0zy6abbf3iwrxsr18gbxidb4m5spsigpa2778xg7y9r7fwgmqqkk")))) + (base32 "1b0m3nllfx5fcwpkp73ac7fbw0jn86h90k5y3r674csm46zs3c05")))) (build-system cmake-build-system) (inputs (list kidletime @@ -600,14 +600,14 @@ when laptop batteries are low on power.") (define-public lxqt-qtplugin (package (name "lxqt-qtplugin") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1zw79lnm35gj3dyd4vlnk08n1lnr8391n36nbn81d0fgmvs21yx4")))) + (base32 "06cdx4fffggk2wjfpi8zlbkiapmbqq2qsz25cngg4kqznq0kayb3")))) (build-system cmake-build-system) (inputs (list libdbusmenu-qt @@ -637,14 +637,14 @@ Qt with LXQt.") (define-public lxqt-runner (package (name "lxqt-runner") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1wfng8g28mq97ibrgpfbj353i15vdimmjp83pfqrmkddx0yvzcdv")))) + (base32 "0kighmlm9hqmw8h41fbmwqyy8qs06q2bbja6snw8j1a2yvz636qz")))) (build-system cmake-build-system) (inputs (list kwindowsystem @@ -668,14 +668,14 @@ allows for launching applications or shutting down the system.") (define-public lxqt-session (package (name "lxqt-session") - (version "1.1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0j8q5jfpb2l0vvji3xs8y0jcr792z6sxzj111qqvmdrbpxrkwxnw")))) + (base32 "0rjw3rw6kpaa3csrga005qg5bxmdxfgrnn1qngs2nrny35v97ckl")))) (build-system cmake-build-system) (inputs (list eudev @@ -726,14 +726,14 @@ for the LXQt desktop environment.") (define-public lxqt-sudo (package (name "lxqt-sudo") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "064w40v43m91y9aywxxf2pj5rpcl4gbsgj7dv97pg4vhj9s790b8")))) + (base32 "0lx889bpadgizgca37rwll5hlxnbpqpzxnpscyc35n72vyix8m7k")))) (build-system cmake-build-system) (inputs (list kwindowsystem @@ -756,14 +756,14 @@ permissions of other users including root.") (define-public lxqt-themes (package (name "lxqt-themes") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "18zrp2j0xpsrzy6m2dw8k55zczcc9jzavncasrp5j1dxscnzwrcr")))) + (base32 "1w566l7xcqscnx5k4f59c2cp4hb4bf2lvqgd9lvdv7dd43qb848z")))) (build-system cmake-build-system) (native-inputs (list lxqt-build-tools)) @@ -782,14 +782,14 @@ for LXQt.") (define-public libfm-qt (package (name "libfm-qt") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0m2fq1wh553yqi64a5nrdvm57fk3jnc3kxgaf0ja7h95jw6czvm5")))) + (base32 "0b423s6bkwijjrh14wca49ypz79sxci9lalxc5s29vwbhync09x0")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no tests @@ -813,14 +813,14 @@ components to build desktop file managers which belongs to LXDE.") (define-public pcmanfm-qt (package (name "pcmanfm-qt") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0pwl2j5kbs86vmq86phavq89bl2i82ic839bjk0v8kmxm9q2mrh9")))) + (base32 "1k44a659mval4513p4yv63hqrbg9jqc8vrinl4mx5aja33pww5yg")))) (build-system cmake-build-system) (arguments (list @@ -873,14 +873,14 @@ manager Compton.") (define-public lximage-qt (package (name "lximage-qt") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0nal8n7nmkafapdbcs9c8rk313md2fak4xjl9m56n10dxcjpi2wb")))) + (base32 "0qz40vlps82nzz62w7d9ar43gmzvlk9wqzm8lwga90vip8gb2zkm")))) (build-system cmake-build-system) (inputs (list libexif libfm-qt qtbase-5 qtsvg-5 qtx11extras)) @@ -930,14 +930,14 @@ window manager OpenBox.") (define-public pavucontrol-qt (package (name "pavucontrol-qt") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "0y3ql25cmg1cmzjvadf7zcb58hh69gcslvr944sxxhaqp4daz10v")))) + (base32 "19r3wgs18mc0m4l8znwhycf137xcd53119ribwb069g4j6hiyvz3")))) (build-system cmake-build-system) (inputs (list glib pcre pulseaudio qtbase-5 qtx11extras)) @@ -954,14 +954,14 @@ window manager OpenBox.") (define-public qps (package (name "qps") - (version "2.5.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "16ybq07xpkl22mszakc1175xlqcayyj21i2h6wlxb8bmb7csg30n")))) + (base32 "1i8d11yfcx556cm3jb3j49dmnhizx2zrb7g09xfqdwnqbak3ak9r")))) (build-system cmake-build-system) (inputs (list kwindowsystem @@ -983,14 +983,14 @@ processes currently in existence, much like code{top} or code{ps}.") (define-public qtermwidget (package (name "qtermwidget") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1m64c1m8dkb06fgfk09da2anjspphph6qdk41rqhds2qymh090v4")))) + (base32 "13781ljapvk8dy0xd31grx43fqvn62msyb8rlnsa2fv893zl7fj4")))) (build-system cmake-build-system) (inputs (list qtbase-5 utf8proc)) @@ -1006,14 +1006,14 @@ processes currently in existence, much like code{top} or code{ps}.") (define-public qterminal (package (name "qterminal") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1b9568y5xyxymk8r7pkz878ba24dyaxql2sfiy6blr8szf308c5l")))) + (base32 "0px42vvmxf3lgd5wwxl260nm18a46943iiqhhmjb0l4xi5s0lhfr")))) (build-system cmake-build-system) (inputs (list qtbase-5 qtx11extras qtermwidget)) @@ -1030,14 +1030,14 @@ QTermWidget.") (define-public screengrab (package (name "screengrab") - (version "2.4.0") + (version "2.5.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/screengrab/releases/download/" version "/screengrab-" version ".tar.xz")) (sha256 - (base32 "14kh287d70v1lpd5w8pji88nmw3jd44q4h927vnszrkv6bwplzx7")))) + (base32 "0jqzpx44x2hbl5yvlx7md9zg2qrnchh54lbbmk8nmgrsa2wps9rv")))) (build-system cmake-build-system) (inputs (list kwindowsystem libqtxdg qtbase-5 qtsvg-5 qtx11extras)) @@ -1055,14 +1055,14 @@ easily publishing them on internet image hosting services.") (define-public lxqt-archiver (package (name "lxqt-archiver") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/lxqt/" name "/releases/download/" version "/" name "-" version ".tar.xz")) (sha256 - (base32 "1cxxr7rpflh2ki272pac927gzcw2w1lp3qz8vplflf148laigwc0")))) + (base32 "0vd4klwmg4rr0z4zilv6djd3mfin73hdf6jpw3fsrn24yncg7kgq")))) (build-system cmake-build-system) (inputs (list glib json-glib libfm-qt qtbase-5 qtx11extras)) @@ -1128,7 +1128,7 @@ desktop.") (define-public lxqt (package (name "lxqt") - (version "17.0") + (version (package-version liblxqt)) (source #f) (build-system trivial-build-system) (arguments '(#:builder (begin (mkdir %output) #t))) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 61b0400715..fbc06f96b6 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -3224,18 +3224,14 @@ Python.") (define-public python-hmmlearn (package (name "python-hmmlearn") - (version "0.2.6") + (version "0.2.7") (source (origin (method url-fetch) (uri (pypi-uri "hmmlearn" version)) (sha256 (base32 - "1my0j3rzp17438idr32ssh0j969a98yjblx5igx5kgiiigr9qa1a")) - (snippet - #~(begin - (use-modules ((guix build utils))) - (delete-file "lib/hmmlearn/_hmmc.c"))))) + "1qgnf1kdxicygy8nvpv866iqvwq0rc6xkd3s6slmvxvsy8h2fjvb")))) (build-system python-build-system) (arguments `(#:phases @@ -3247,7 +3243,11 @@ Python.") (with-directory-excursion (string-append (assoc-ref outputs "out") "/lib") (invoke "python" "-m" "pytest")))))))) (propagated-inputs - (list python-cython python-numpy python-scikit-learn python-scipy + (list pybind11 + python-cython + python-numpy + python-scikit-learn + python-scipy python-setuptools-scm)) (native-inputs (list python-pytest)) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 414308d9fe..cef5fe2916 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -50,6 +50,7 @@ ;;; Copyright © 2022 Guillaume Le Vaillant <glv@posteo.net> ;;; Copyright © 2022 muradm <mail@muradm.net> ;;; Copyright © 2022 jgart <jgart@dismail.de> +;;; Copyright © 2022 ( <paren@disroot.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -151,6 +152,7 @@ #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages ruby) + #:use-module (gnu packages rust-apps) #:use-module (gnu packages search) #:use-module (gnu packages serialization) #:use-module (gnu packages samba) @@ -4557,7 +4559,7 @@ databases, and other tools to process Outlook email archives.") (build-system gnu-build-system) (arguments `(#:tests? #f ;no tests - #:make-flags `((string-append "CC=" ,(cc-for-target))) + #:make-flags (list (string-append "CC=" ,(cc-for-target))) #:phases (modify-phases %standard-phases (delete 'configure) ;no configure script @@ -4754,3 +4756,120 @@ addresses.") mailserver on their machine. It enables these users to send their mail over a remote SMTP server.") (license license:gpl2+))) + +(define-public aerc + (package + (name "aerc") + (version "0.13.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.sr.ht/~rjarry/aerc") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "18rykklc0ppl53sm9lzhrw6kv4rcc7x45nv7qii7m4qads2pyjm5")))) + (build-system go-build-system) + (arguments + (list #:import-path "git.sr.ht/~rjarry/aerc" + ;; Installing the source is only necessary for Go libraries. + #:install-source? #f + #:build-flags + #~(list "-tags=notmuch" "-ldflags" + (string-append "-X main.Version=" #$version + " -X git.sr.ht/~rjarry/aerc/config.shareDir=" + #$output "/share/aerc")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda* (#:key import-path inputs #:allow-other-keys) + (with-directory-excursion + (string-append "src/" import-path) + (substitute* (list "config/config.go" + "lib/templates/template.go" + "widgets/compose.go" + "widgets/msgviewer.go" + "worker/maildir/worker.go" + "worker/notmuch/worker.go") + (("\"sh\"") + (string-append + "\"" (search-input-file inputs "bin/sh") + "\""))) + (substitute* "commands/z.go" + (("\"zoxide\"") + (string-append + "\"" (search-input-file inputs "bin/zoxide") + "\""))) + (substitute* (list "lib/crypto/gpg/gpg.go" + "lib/crypto/gpg/gpg_test.go" + "lib/crypto/gpg/gpgbin/keys.go" + "lib/crypto/gpg/gpgbin/gpgbin.go") + (("\"gpg\"") + (string-append + "\"" (search-input-file inputs "bin/gpg") + "\"")) + (("strings\\.Contains\\(stderr\\.String\\(\\), .*\\)") + "strings.Contains(stderr.String(), \"gpg\")"))))) + (add-after 'build 'doc + (lambda* (#:key import-path build-flags #:allow-other-keys) + (invoke "make" "doc" "-C" + (string-append "src/" import-path)))) + (replace 'install + (lambda* (#:key import-path build-flags #:allow-other-keys) + (invoke "make" "install" "-C" + (string-append "src/" import-path) + (string-append "PREFIX=" #$output))))))) + (inputs (list gnupg + go-github-com-zenhack-go-notmuch + go-golang-org-x-oauth2 + go-github-com-xo-terminfo + go-github-com-stretchr-testify + go-github-com-riywo-loginshell + go-github-com-pkg-errors + go-github-com-mitchellh-go-homedir + go-github-com-miolini-datacounter + go-github-com-mattn-go-runewidth + go-github-com-mattn-go-isatty + go-github-com-lithammer-fuzzysearch + go-github-com-kyoh86-xdg + go-github-com-imdario-mergo + go-github-com-google-shlex + go-github-com-go-ini-ini + go-github-com-gdamore-tcell-v2 + go-github-com-gatherstars-com-jwz + go-github-com-fsnotify-fsnotify + go-github-com-emersion-go-smtp + go-github-com-emersion-go-sasl + go-github-com-emersion-go-pgpmail + go-github-com-emersion-go-message + go-github-com-emersion-go-maildir + go-github-com-emersion-go-imap-sortthread + go-github-com-emersion-go-imap + go-github-com-emersion-go-msgauth + go-github-com-emersion-go-mbox + go-github-com-ddevault-go-libvterm + go-github-com-danwakefield-fnmatch + go-github-com-creack-pty + go-github-com-arran4-golang-ical + go-github-com-protonmail-go-crypto + go-github-com-syndtr-goleveldb-leveldb + go-git-sr-ht-sircmpwn-getopt + go-git-sr-ht-rockorager-tcell-term + zoxide)) + (native-inputs (list scdoc)) + (home-page "https://git.sr.ht/~rjarry/aerc") + (synopsis "Email client for the terminal") + (description "@code{aerc} is a textual email client for terminals. It +features: +@enumerate +@item First-class support for using patches and @code{git send-email} +@item Vi-like keybindings and command system +@item A built-in console +@item Support for multiple accounts +@end enumerate") + ;; The license given is MIT/Expat; however, linking against notmuch + ;; effectively makes it GPL-3.0-or-later. See this thread discussing it: + ;; <https://lists.sr.ht/~rjarry/aerc-devel/%3Cb5cb213a7d0c699a886971658c2476 + ;; 1073eb2391%40disroot.org%3E> + (license license:gpl3+))) diff --git a/gnu/packages/mate.scm b/gnu/packages/mate.scm index 03dfabc135..ce62366985 100644 --- a/gnu/packages/mate.scm +++ b/gnu/packages/mate.scm @@ -1490,48 +1490,51 @@ used to bring up authentication dialogs.") (native-inputs (list desktop-file-utils)) (inputs ;; TODO: Add more packages - `(("at-spi2-core" ,at-spi2-core) - ("atril" ,atril) - ("caja" ,caja) - ("dbus" ,dbus) - ("dconf" ,dconf) - ("engrampa" ,engrampa) - ("eom" ,eom) - ("font-abattis-cantarell" ,font-abattis-cantarell) - ("glib-networking" ,glib-networking) - ("gnome-keyring" ,gnome-keyring) - ("gvfs" ,gvfs) - ("hicolor-icon-theme" ,hicolor-icon-theme) - ("libmatekbd" ,libmatekbd) - ("libmateweather" ,libmateweather) - ("libmatemixer" ,libmatemixer) - ("marco" ,marco) - ("mate-session-manager" ,mate-session-manager) - ("mate-settings-daemon" ,mate-settings-daemon) - ("mate-desktop" ,mate-desktop) - ("mate-terminal" ,mate-terminal) - ("mate-themes" ,mate-themes) - ("mate-icon-theme" ,mate-icon-theme) - ("mate-power-manager" ,mate-power-manager) - ("mate-menu" ,mate-menus) - ("mate-panel" ,mate-panel) - ("mate-control-center" ,mate-control-center) - ("mate-media" ,mate-media) - ("mate-applets" ,mate-applets) - ("mate-user-guide" ,mate-user-guide) - ("mate-calc" ,mate-calc) - ("mate-backgrounds" ,mate-backgrounds) - ("mate-netbook" ,mate-netbook) - ("mate-utils" ,mate-utils) - ("mate-polkit" ,mate-polkit) - ("mate-system-monitor" ,mate-system-monitor) - ("mate-utils" ,mate-utils) - ("pluma" ,pluma) - ("pinentry-gnome3" ,pinentry-gnome3) - ("pulseaudio" ,pulseaudio) - ("shared-mime-info" ,shared-mime-info) - ("yelp" ,yelp) - ("zenity" ,zenity))) + (append (if (or (%current-target-system) + (supported-package? gnome-keyring)) + (list gnome-keyring) + '()) + (list at-spi2-core + atril + caja + dbus + dconf + engrampa + eom + font-abattis-cantarell + glib-networking + gvfs + hicolor-icon-theme + libmatekbd + libmateweather + libmatemixer + marco + mate-session-manager + mate-settings-daemon + mate-desktop + mate-terminal + mate-themes + mate-icon-theme + mate-power-manager + mate-menus + mate-panel + mate-control-center + mate-media + mate-applets + mate-user-guide + mate-calc + mate-backgrounds + mate-netbook + mate-utils + mate-polkit + mate-system-monitor + mate-utils + pluma + pinentry-gnome3 + pulseaudio + shared-mime-info + yelp + zenity))) (propagated-inputs ;; Default font that applications such as IceCat require. (list font-dejavu)) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 975d764a2a..c0bc07977b 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -55,6 +55,8 @@ ;;; Copyright © 2022 Philip McGrath <philip@philipmcgrath.com> ;;; Copyright © 2022 Marek Felšöci <marek@felsoci.sk> ;;; Copyright © 2022 vicvbcun <guix@ikherbers.com> +;;; Copyright © 2022 Liliana Marie Prikler <liliana.prikler@gmail.com> +;;; Copyright © 2022 Maximilian Heisinger <mail@maxheisinger.at> ;;; ;;; This file is part of GNU Guix. ;;; @@ -158,6 +160,7 @@ #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages sphinx) + #:use-module (gnu packages sqlite) #:use-module (gnu packages swig) #:use-module (gnu packages tcl) #:use-module (gnu packages texinfo) @@ -894,20 +897,6 @@ large scale eigenvalue problems.") (license (license:non-copyleft "file://COPYING" "See COPYING in the distribution.")))) -(define-public arpack-ng-3.3.0 - (package - (inherit arpack-ng) - (version "3.3.0") - (source - (origin - (method git-fetch) - (uri (git-reference (url (package-home-page arpack-ng)) - (commit version))) - (file-name (git-file-name (package-name arpack-ng) version)) - (sha256 - (base32 - "00h6bjvxjq7bv0b8pwnc0gw33ns6brlqv00xx2rh3w9b5n205918")))))) - (define-public arpack-ng-openmpi (package (inherit arpack-ng) (name "arpack-ng-openmpi") @@ -2426,6 +2415,43 @@ and quadratic objectives using the Simplex algorithm.") systems and applications. It provides a modular and extensible solver.") (license license:expat))) +(define-public libfixmath + (let ((commit "1416c9979635c69f344d3c1de84b3246001a6540") + (revision "1")) + (package + (name "libfixmath") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PetteriAimonen/libfixmath") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1vnpycw30rq3xwqyvj20l7pnw74dc4f27304i0918igsrdsjw501")))) + (build-system cmake-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'install + (lambda _ + (let ((includes (string-append #$output "/include/libfixmath")) + (lib (string-append #$output "/lib"))) + (mkdir-p includes) + (for-each (lambda (file) + (install-file file includes)) + (find-files "../source" "\\.h(pp)?$")) + (for-each (lambda (file) + (install-file file lib)) + (find-files "." "\\.a$")))))))) + (home-page "https://code.google.com/archive/p/libfixmath/") + (synopsis "Cross platform fixed point maths library") + (description "This library implements the @file{math.h} functions in +fixed point (16.16) format.") + (license license:expat)))) + (define-public libflame (package (name "libflame") @@ -2556,7 +2582,7 @@ between aspif and smodels format or to a human-readable text format.") (define-public clasp (package (name "clasp") - (version "3.3.6") + (version "3.3.9") (source (origin (method git-fetch) (uri (git-reference @@ -2565,7 +2591,7 @@ between aspif and smodels format or to a human-readable text format.") (file-name (git-file-name name version)) (sha256 (base32 - "0rahqiq530jckvx717858h1q5p8znp1kb6sjm95p8blkr4n3pvmj")))) + "163ps9zq7xppqy9hj5qnw6z5lcjnm4xf5fwjsavpia5ynm3hngcw")))) (build-system cmake-build-system) (arguments `(#:configure-flags '("-DCLASP_BUILD_TESTS=on" @@ -2761,7 +2787,7 @@ can solve two kinds of problems: (define-public octave-cli (package (name "octave-cli") - (version "7.1.0") + (version "7.2.0") (source (origin (method url-fetch) @@ -2769,7 +2795,7 @@ can solve two kinds of problems: version ".tar.xz")) (sha256 (base32 - "0wv26nsfi6cq80np6p4av4wfrvbaflca6szajf6c60mbpdg63m1z")))) + "0w81ncl9d4x1ay3ylsag87k20c0byiyjcmfd9kb7b7ylr71pivsa")))) (build-system gnu-build-system) (inputs `(("alsa-lib" ,alsa-lib) @@ -2937,7 +2963,7 @@ Open CASCADE library.") (define-public opencascade-occt (package (name "opencascade-occt") - (version "7.6.0") + (version "7.6.2") (source (origin (method git-fetch) @@ -2949,7 +2975,7 @@ Open CASCADE library.") version))))) (file-name (git-file-name name version)) (sha256 - (base32 "1rcwm9fkx0j4wrsyikb6g7qd611kpry7dand5dzdjvs5vzd13zvd")) + (base32 "07z5d83vm9f50an7vhimzl7gbmri1dn6p2g999l5fgyaj5sg5f02")) (modules '((guix build utils))) (snippet '(begin @@ -4874,7 +4900,7 @@ Fresnel integrals, and similar related functions as well.") (define-public suitesparse (package (name "suitesparse") - (version "5.12.0") + (version "5.13.0") (source (origin (method git-fetch) @@ -4884,7 +4910,7 @@ Fresnel integrals, and similar related functions as well.") (file-name (git-file-name name version)) (sha256 (base32 - "0zpl51pfpv7ap7z97jlryba2la1qdmzm11bhzkn55wlb03xzi6k6")) + "1zwri246yr39p9ymjp18dzv36ch0dn107sf0jghj7capigasfxq2")) (patches (search-patches "suitesparse-mongoose-cmake.patch")) (modules '((guix build utils))) (snippet @@ -6825,7 +6851,7 @@ assemble global function spaces on finite-element grids.") "doc/dune-grid/grids/gridfactory/testgrids")) #t)) (add-after 'build 'build-tests - (lambda* (#:key make-flags parallel-build? #:allow-other-keys) + (lambda* (#:key inputs make-flags parallel-build? #:allow-other-keys) (setenv "CPLUS_INCLUDE_PATH" (string-append (assoc-ref inputs "dune-grid") "/share")) (apply invoke "make" "build_tests" @@ -7376,6 +7402,221 @@ back to C with improved data structures, better scheduling of inprocessing and optimized algorithms and implementation.") (license license:expat))) +(define-public aiger + (package + (name "aiger") + (version "1.9.9") + (source (origin + (method url-fetch) + (uri (string-append "http://fmv.jku.at/aiger/aiger-" + version ".tar.gz")) + (sha256 + (base32 + "1ish0dw0nf9gyghxsdhpy1jjiy5wp54c993swp85xp7m6vdx6l0y")))) + (outputs (list "out" "static")) + (build-system gnu-build-system) + (arguments + (list #:tests? #f ; no check target + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "aiger.c" + (("\"(gzip|gunzip)" all cmd) + (string-append + "\"" + (search-input-file inputs (string-append "bin/" cmd))))))) + (add-after 'unpack 'patch-build-files + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "makefile.in" + (("test -d .*") "true") + (("/usr/local") (assoc-ref outputs "out"))))) + (replace 'configure + (lambda* (#:key configure-flags #:allow-other-keys) + (apply invoke "./configure.sh" configure-flags))) + (add-after 'install 'install-static + (lambda* (#:key outputs #:allow-other-keys) + (apply invoke #$(ar-for-target) "rcs" "libaiger.a" + (find-files "." "\\.o$")) + (let* ((static (assoc-ref outputs "static")) + (lib (string-append static "/lib")) + (incl (string-append static "/include/aiger"))) + (mkdir-p lib) + (mkdir-p incl) + (install-file "libaiger.a" lib) + (for-each (lambda (f) (install-file f incl)) + (find-files "." "\\.h$")))))))) + (inputs (list gzip)) + (home-page "http://fmv.jku.at/aiger") + (synopsis "Utilities for And-Inverter Graphs") + (description "AIGER is a format, library and set of utilities for +@acronym{AIG, And-Inverter Graphs}s. The focus is on conversion utilities and a +generic reader and writer API.") + (license (list license:expat + license:bsd-3)))) ; blif2aig + +(define-public lingeling + (let ((commit "72d2b13eea5fbd95557a3d0d199cd98dfbdc76ee") + (revision "1")) + (package + (name "lingeling") + (version (git-version "sc2022" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/arminbiere/lingeling") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16s30x8s2cw6icchwm65zj56ph4qwz6i07g3hwkknvajisvjq85c")))) + (build-system gnu-build-system) + (arguments + (list #:test-target "test" + #:modules `((ice-9 match) + ,@%gnu-build-system-modules) + #:configure-flags #~(list "--aiger=.") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'unpack-aiger + (lambda* (#:key inputs #:allow-other-keys) + (invoke #$(ar-for-target) "x" + (search-input-file inputs "lib/libaiger.a") + "aiger.o") + (copy-file + (search-input-file inputs "include/aiger/aiger.h") + "aiger.h"))) + (add-after 'unpack 'hard-code-commit + (lambda _ + (substitute* "mkconfig.sh" + (("`\\./getgitid`") #$commit)))) + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (substitute* (list "treengeling.c" "lgldimacs.c") + (("\"(gunzip|xz|bzcat|7z)" all cmd) + (string-append + "\"" + (search-input-file inputs (string-append "bin/" cmd))))))) + (replace 'configure + (lambda* (#:key configure-flags #:allow-other-keys) + (apply invoke "./configure.sh" configure-flags))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (for-each + (lambda (file) + (install-file file bin)) + '("blimc" "ilingeling" "lglddtrace" "lglmbt" + "lgluntrace" "lingeling" "plingeling" + "treengeling"))))) + (add-after 'install 'wrap-path + (lambda* (#:key outputs #:allow-other-keys) + (with-directory-excursion (string-append + (assoc-ref outputs "out") + "/bin") + (for-each + (lambda (file) + (wrap-program + file + '("PATH" suffix + #$(map (lambda (input) + (file-append (this-package-input input) "/bin")) + '("gzip" "bzip2" "xz" "p7zip"))))) + ;; These programs use sprintf on buffers with magic + ;; values to construct commands (yes, eww), so we + ;; can't easily substitute* them. + '("lglddtrace" "lgluntrace" "lingeling" "plingeling")))))))) + (inputs (list `(,aiger "static") gzip bzip2 xz p7zip)) + (home-page "http://fmv.jku.at/lingeling") + (synopsis "SAT solver") + (description "This package provides a range of SAT solvers, including +the sequential @command{lingeling} and its parallel variants +@command{plingeling} and @command{treengeling}. A bounded model checker is +also included.") + (license license:expat)))) + +(define-public louvain-community + (let ((commit "8cc5382d4844af127b1c1257373740d7e6b76f1e") + (revision "1")) + (package + (name "louvain-community") + (version (git-version "1.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/meelgroup/louvain-community") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ss00hkdvr9bdkd355hxf8zd7xycb3nm8qpy7s75gjjf6yng0bfj")))) + (build-system cmake-build-system) + (arguments + (list #:tests? #f ; tests appear to require missing files + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'encode-git-hash + (lambda _ + (substitute* "CMakeLists.txt" + (("GIT-hash-notfound") #$commit))))))) + (native-inputs (list python)) + (home-page "https://github.com/meelgroup/louvain-communities") + (synopsis "Multi-criteria community detection") + (description "This package provides a C++ implementation of the Louvain +community detection algorithm.") + (license license:lgpl3+)))) + +(define-public cryptominisat + (package + (name "cryptominisat") + (version "5.11.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/msoos/cryptominisat") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1izjn44phjp9670s7bxrdx4p0r59idqwv3bm6sr0qnlqlha5z4zc")))) + (build-system cmake-build-system) + (arguments + (list + #:build-type "Release" + #:test-target "test" + #:configure-flags #~(list "-DENABLE_TESTING=ON" "-DSTATS=ON") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "CMakeLists.txt" + (("add_subdirectory\\(utils/lingeling-ala\\)") "")) + ;; Transitively included in vendored gtest.h. Fixed in + ;; upstream: + ;; https://github.com/msoos/cryptominisat/pull/686 + (substitute* "tests/assump_test.cpp" + (("#include <vector>") + "#include <vector>\n#include <algorithm>")) + (substitute* "tests/CMakeLists.txt" + (("add_subdirectory\\(\\$\\{GTEST_PREFIX\\} gtest\\)") + "find_package(GTest REQUIRED)") + (("add_subdirectory\\(\\$\\{PROJECT_SOURCE_DIR\\}/utils/.*\\)") + ""))))))) + (inputs (list boost louvain-community python python-numpy sqlite zlib)) + (native-inputs (list googletest lingeling python python-wrapper python-lit)) + (synopsis "Incremental SAT solver") + (description + "CryptoMiniSat is an incremental SAT solver with both command line and +library (C++, C, Python) interfaces. The command-line interface takes a +@acronym{CNF, Conjunctive Normal Form} as an input in the DIMACS format with +the extension of XOR clauses. The library interfaces mimic this and also +allow incremental solving, including assumptions.") + (home-page "https://github.com/msoos/cryptominisat") + (license license:expat))) + (define-public libqalculate (package (name "libqalculate") diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 4e9cb0cb37..e0bd7633bc 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -48,6 +48,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages cdrom) #:use-module (gnu packages cmake) ;for MPD + #:use-module (gnu packages cpp) #:use-module (gnu packages freedesktop) ;elogind #:use-module (gnu packages gettext) #:use-module (gnu packages gnome) @@ -55,6 +56,7 @@ #:use-module (gnu packages gtk) #:use-module (gnu packages icu4c) #:use-module (gnu packages libusb) + #:use-module (gnu packages lua) #:use-module (gnu packages readline) #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -66,15 +68,19 @@ #:use-module (gnu packages music) #:use-module (gnu packages ncurses) #:use-module (gnu packages pcre) + #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pretty-print) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages qt) + #:use-module (gnu packages serialization) #:use-module (gnu packages sphinx) #:use-module (gnu packages sqlite) + #:use-module (gnu packages tls) #:use-module (gnu packages video) + #:use-module (gnu packages web) #:use-module (gnu packages xiph)) (define-public libmpdclient @@ -380,7 +386,7 @@ MPD servers, search and multimedia key support.") (define-public ashuffle (package (name "ashuffle") - (version "2.0.2") + (version "3.13.4") (source (origin (method git-fetch) (uri (git-reference @@ -389,10 +395,20 @@ MPD servers, search and multimedia key support.") (file-name (git-file-name name version)) (sha256 (base32 - "11aa95cg0yca2m2d00sar6wr14g3lc7cfm9bin1h7lk7asdm8azp")))) + "09dvar0aglyy2h9y115ymgryd8l6npc2y2ccdzij0b70f47ncqmf")))) (native-inputs (list pkg-config)) - (inputs (list libmpdclient)) + (inputs + (list abseil-cpp-cxxstd17 + googletest + libmpdclient + yaml-cpp)) (build-system meson-build-system) + (arguments + (list #:configure-flags + #~'("-Dtests=enabled" + "-Dunsupported_use_system_absl=true" + "-Dunsupported_use_system_gtest=true" + "-Dunsupported_use_system_yamlcpp=true"))) (home-page "https://github.com/joshkunz/ashuffle") (synopsis "Automatic library-wide shuffle for mpd") (description "ashuffle is an application for automatically shuffling your @@ -561,3 +577,27 @@ which is focused on playing local music without the need of managing playlists. Instead of maintaining a client side database of your music library, mpdevil loads all tags and covers on demand.") (license license:gpl3+))) + +(define-public mympd + (package + (name "mympd") + (version "10.1.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jcorporation/myMPD") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16cvjwbyb1m88kmgylp95p82a4xdjikmrw9arl6kvmgcbyw317yp")))) + (build-system cmake-build-system) + (arguments + (list #:tests? #f)) ; no test target + (native-inputs (list jq perl)) + (inputs (list flac libid3tag lua openssl pcre2)) + (home-page "https://jcorporation.github.io/") + (synopsis "Web-based MPD client") + (description "MyMPD is a mobile-friendly web client for the MPD music +player daemon.") + (license license:gpl3+))) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 646ea685c3..22b8ca7d68 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2300,10 +2300,10 @@ perform creative live mixes with digital music files.") alsa-lib new-session-manager liblo - qtbase-5 - qtsvg-5)) + qtbase + qtsvg)) (native-inputs - (list pkg-config qttools-5)) + (list pkg-config qttools)) (home-page "https://synthv1.sourceforge.io") (synopsis "Polyphonic subtractive synthesizer") (description @@ -2333,10 +2333,10 @@ oscillators and stereo effects.") alsa-lib new-session-manager liblo - qtbase-5 - qtsvg-5)) + qtbase + qtsvg)) (native-inputs - (list pkg-config qttools-5)) + (list pkg-config qttools)) (home-page "https://drumkv1.sourceforge.io") (synopsis "Drum-kit sampler synthesizer with stereo effects") (description @@ -2366,10 +2366,10 @@ effects.") alsa-lib new-session-manager liblo - qtbase-5 - qtsvg-5)) + qtbase + qtsvg)) (native-inputs - (list pkg-config qttools-5)) + (list pkg-config qttools)) (home-page "https://samplv1.sourceforge.io") (synopsis "Polyphonic sampler synthesizer with stereo effects") (description @@ -2399,10 +2399,10 @@ effects.") new-session-manager liblo fftwf - qtbase-5 - qtsvg-5)) + qtbase + qtsvg)) (native-inputs - (list pkg-config qttools-5)) + (list pkg-config qttools)) (home-page "https://padthv1.sourceforge.io") (synopsis "Polyphonic additive synthesizer") (description @@ -3313,14 +3313,13 @@ from the command line.") libvorbis lilv lv2 - qtbase-5 - qtsvg-5 - qtx11extras + qtbase + qtsvg rubberband suil zlib)) (native-inputs - (list pkg-config qttools-5)) + (list pkg-config qttools)) (home-page "https://qtractor.org/") (synopsis "Audio/MIDI multi-track sequencer") (description @@ -3932,27 +3931,27 @@ with a number of bugfixes and changes to improve IT playback.") (define-public sooperlooper (package (name "sooperlooper") - (version "1.7.6") + (version "1.7.8") (source (origin (method url-fetch) - (uri (string-append "http://essej.net/sooperlooper/sooperlooper-" - version ".tar.gz")) + (uri (string-append "https://sonosaurus.com/sooperlooper" + "/sooperlooper-" version ".tar.gz")) (sha256 - (base32 "0kbb1pj62rl32c88j6p7dg823kvs0gb5s42qy3bl6yg0wn10dksj")))) + (base32 "0dd2kryizwrzndbwafpbddf9w2ghw9gfmb8nyss5hll70b1dx59f")))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'add-sigc++-includes (lambda* (#:key inputs #:allow-other-keys) - (let ((sig (assoc-ref inputs "libsigc++")) - (xml (assoc-ref inputs "libxml2")) + (let ((sig (search-input-directory inputs "include/sigc++-2.0")) + (xml (search-input-directory inputs "include/libxml2")) (cwd (getcwd))) (setenv "CPATH" - (string-append sig "/include/sigc++-2.0:" - sig "/lib/sigc++-2.0/include:" - xml "/include/libxml2/:" + (string-append sig ":" + sig "../../lib/sigc++-2.0/include:" + xml ":" cwd "/libs/pbd:" cwd "/libs/midi++:" (or (getenv "CPATH") "")))) @@ -3979,19 +3978,19 @@ with a number of bugfixes and changes to improve IT playback.") (("static char") "static const char")) #t))))) (inputs - `(("jack" ,jack-1) - ("alsa-lib" ,alsa-lib) - ("wxwidgets" ,wxwidgets-gtk2) - ("libsndfile" ,libsndfile) - ("libsamplerate" ,libsamplerate) - ("liblo" ,liblo) - ("rubberband" ,rubberband) - ("libxml2" ,libxml2) - ("libsigc++" ,libsigc++-2) - ("ncurses" ,ncurses))) + (list jack-1 + alsa-lib + wxwidgets-gtk2 + libsndfile + libsamplerate + liblo + rubberband + libxml2 + libsigc++-2 + ncurses)) (native-inputs (list pkg-config)) - (home-page "http://essej.net/sooperlooper/") + (home-page "https://sonosaurus.com/sooperlooper/") (synopsis "Live looping sampler") (description "SooperLooper is a live looping sampler capable of immediate loop diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 3f44d082fb..f5276e330e 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -593,7 +593,7 @@ supported, including rtmp://, rtmpt://, rtmpe://, rtmpte://, and rtmps://.") (define-public slurm-monitor (package (name "slurm-monitor") - (version "0.4.3") + (version "0.4.4") (source (origin (method git-fetch) @@ -603,9 +603,10 @@ supported, including rtmp://, rtmpt://, rtmpe://, rtmpte://, and rtmps://.") (commit (string-append "upstream/" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1n6pgrcs8gwrcq5fch1q3yk3jipjwrf21s9a13fbjrl903g5zzv9")))) - (build-system cmake-build-system) + (base32 "07q8895bxsajkwip8dgrrwr1m8a10xnl4p0g6wqcrd2wf4hx5gn3")))) + (build-system meson-build-system) (arguments `(#:tests? #f)) ;no tests + (native-inputs (list pkg-config)) (inputs (list ncurses)) (synopsis "Network load monitor") (description @@ -1538,22 +1539,14 @@ Ethernet devices.") (define-public ifstatus (package (name "ifstatus") - (version "1.1.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/ifstatus/ifstatus/" - "ifstatus%20v" version "/ifstatus-v" - version ".tar.gz")) + "ifstatus-v" version ".tar.gz")) (sha256 (base32 - "045cbsq9ps32j24v8y5hpyqxnqn9mpaf3mgvirlhgpqyb9jsia0c")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "Main.h" - (("#include <stdio.h>") - "#include <stdio.h>\n#include <stdlib.h>")) - #t)))) + "0n622f2m3x901hcmad4ns52r2x75csy4nqraagzb8h9fn0j62jkv")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no "check" target diff --git a/gnu/packages/nickle.scm b/gnu/packages/nickle.scm index 95b9915414..6b69d7cb92 100644 --- a/gnu/packages/nickle.scm +++ b/gnu/packages/nickle.scm @@ -28,14 +28,14 @@ (define-public nickle (package (name "nickle") - (version "2.82") + (version "2.90") (source (origin (method url-fetch) (uri (string-append "https://nickle.org/release/nickle-" version ".tar.gz")) (sha256 (base32 - "0jy96z01qbrnmsrywn5mfa14615qdix6b8520qd65c6yjyrk8gs0")))) + "197532b7ghkfnzx9qvxd2qjpnqba7bfl79iff3hk2jxcl0d83czv")))) (build-system gnu-build-system) (native-inputs (list readline)) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 96659632bf..e0bedf74f9 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -1718,7 +1718,7 @@ full_split, cut, rcut, etc..") (define dune-bootstrap (package (name "dune") - (version "3.5.0") + (version "3.6.1") (source (origin (method git-fetch) (uri (git-reference @@ -1727,7 +1727,7 @@ full_split, cut, rcut, etc..") (file-name (git-file-name name version)) (sha256 (base32 - "10fpybiqqkmm7y9xmhy4qs451dydmffcjg13k7w8g2p9dd09jb6l")))) + "0gv851wxbv5ln20429nj7p92spzxgw8vngg9z94q39aawn6q8lx6")))) (build-system ocaml-build-system) (arguments `(#:tests? #f; require odoc @@ -2085,14 +2085,14 @@ defined in this library.") (define-public ocaml-topkg (package (name "ocaml-topkg") - (version "1.0.5") + (version "1.0.6") (source (origin (method url-fetch) (uri (string-append "http://erratique.ch/software/topkg/releases/" "topkg-" version ".tbz")) (sha256 (base32 - "1iyinmcfqpprk7k4cc51nqgypayprbj4larwcfqw86k5dri84825")))) + "11ycfk0prqvifm9jca2308gw8a6cjb1hqlgfslbji2cqpan09kpq")))) (build-system ocaml-build-system) (native-inputs (list opam ocamlbuild)) @@ -4310,7 +4310,7 @@ function that follows the prototype of POSIX's wcwidth.") (define-public ocaml-zed (package (name "ocaml-zed") - (version "3.2.0") + (version "3.2.1") (home-page "https://github.com/ocaml-community/zed") (source (origin @@ -4320,7 +4320,7 @@ function that follows the prototype of POSIX's wcwidth.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1g171kk5wxnk66d4vwz2crh5i19vhqghp78iybl5am17gl9qf8pb")))) + (base32 "17zdbm422y0qznc659civ9bmahhrbffxa50f8dnykiaq8v2ci91l")))) (build-system dune-build-system) (propagated-inputs (list ocaml-react @@ -8456,7 +8456,7 @@ libraries.") (define-public js-of-ocaml (package (name "js-of-ocaml") - (version "4.0.0") + (version "4.1.0") (source (origin (method git-fetch) @@ -8465,7 +8465,7 @@ libraries.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0iyhl9z57j53j2jvyqcwmxhbvy23l6g80aa0abmlgwam14yskspf")))) + (base32 "14ig69iyc9yzniclfsc6cz9g9zqp96bs66y6dy4rzrm78s81w6i1")))) (build-system dune-build-system) (arguments `(#:tests? #f ;tests assume ocaml 4.13 diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 891b504a46..d25e4b999c 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1918,14 +1918,14 @@ the boot loader configuration.") (define-public flatpak (package (name "flatpak") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/flatpak/flatpak/releases/download/" version "/flatpak-" version ".tar.xz")) (sha256 - (base32 "05bqy9kwmaj32y7f94fydcz3k63bsgn4mbcp4pglv8hffxrnj9wf")) + (base32 "17ykbp5lmlbv6241vw55zgqdp34wc12jbj5nhs4wb3018crq4g0a")) (patches (search-patches "flatpak-fix-path.patch" "flatpak-unset-gdk-pixbuf-for-sandbox.patch")))) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index c74ffe5242..aab0a3f2a4 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -218,7 +218,7 @@ algorithms AES or Twofish.") (define-public pwsafe (package (name "pwsafe") - (version "3.54.1") + (version "3.60.0") (home-page "https://www.pwsafe.org/") (source (origin @@ -227,23 +227,20 @@ algorithms AES or Twofish.") (url "https://github.com/pwsafe/pwsafe") (commit version))) (sha256 - (base32 "0d51dlw98mv23nwb0b5jyji8gnb9f5cnig6kivfljl97lmr6lhvf")) + (base32 "064y78sqr8h9mq922spi4r13ga0a1j09mfh4kc4pn7j697nl6b5y")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("gtest" ,googletest) - ("perl" ,perl) - ("zip" ,zip))) - (inputs `(("curl" ,curl) - ("file" ,file) - ("libuuid" ,util-linux "lib") - ("libxt" ,libxt) - ("libxtst" ,libxtst) - ("openssl" ,openssl) - ("qrencode" ,qrencode) - ("wxwidgets" ,wxwidgets) - ("xerces-c" ,xerces-c))) + (list gettext-minimal googletest perl zip)) + (inputs (list curl + file + `(,util-linux "lib") + libxt + libxtst + openssl + qrencode + wxwidgets + xerces-c)) (arguments '(#:configure-flags (list "-DNO_GTEST=YES") #:phases (modify-phases %standard-phases (add-after 'unpack 'add-gtest @@ -1455,3 +1452,43 @@ are not using it. It uses the same GPG key to encrypt passwords and tomb, therefore you don't need to manage more key or secret. Moreover, you can ask pass-tomb to automatically close your store after a given time.") (license license:gpl3+))) + +(define-public xkcdpass + (package + (name "xkcdpass") + (version "1.19.3") + (home-page "https://github.com/redacted/XKCD-password-generator") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "xkcdpass-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xfrmx9k2vinlagv476rfcfdp41aix1ldy6qnzzx26n985gcyk7p")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'install-manpage + (lambda* (#:key outputs #:allow-other-keys) + (install-file + "xkcdpass.1" + (string-append (assoc-ref outputs "out") "/share/man/man1"))))))) + (synopsis + "Generate secure multiword passwords/passphrases, inspired by XKCD") + (description + "This package provides a flexible and scriptable password generator which +generates strong passphrases, inspired by +@url{https://xkcd.com/936/,XKCD 936}.") + (license (list license:bsd-3 ;code + license:cc0 ;spanish, eff_large_de, french word lists + license:cc-by-sa3.0 ;finnish, italian word list + license:cc-by-sa4.0 ;norwegian word list + license:eupl1.1 ;finnish word list + license:gpl2 ;portuguese word list + license:gpl3 ;ger-anix word list + license:lgpl2.0 ;finnish word list + license:lgpl2.1 ;portuguese word list + license:mpl1.1)))) ;portuguese word list diff --git a/gnu/packages/patches/audacity-ffmpeg-fallback.patch b/gnu/packages/patches/audacity-ffmpeg-fallback.patch index b78956070a..d18583c9bd 100644 --- a/gnu/packages/patches/audacity-ffmpeg-fallback.patch +++ b/gnu/packages/patches/audacity-ffmpeg-fallback.patch @@ -8,13 +8,11 @@ it. This dynamic loading mechanism fails to properly locate libraries outside of LD_LIBRARY_PATH. See <https://issues.guix.gnu.org/53591>. ---- - libraries/lib-ffmpeg-support/CMakeLists.txt | 8 ++++++++ - libraries/lib-ffmpeg-support/FFmpegFunctions.cpp | 12 ++++++++++++ - 2 files changed, 20 insertions(+) + +Bugs-added-by: Marius Bakke <marius@gnu.org> diff --git a/libraries/lib-ffmpeg-support/CMakeLists.txt b/libraries/lib-ffmpeg-support/CMakeLists.txt -index 8c5f06d7c..00810e4d0 100644 +index b8803a1f5..f86559cca 100644 --- a/libraries/lib-ffmpeg-support/CMakeLists.txt +++ b/libraries/lib-ffmpeg-support/CMakeLists.txt @@ -1,5 +1,7 @@ @@ -25,7 +23,7 @@ index 8c5f06d7c..00810e4d0 100644 set( SOURCES FFmpegTypes.h -@@ -100,6 +102,12 @@ if (${_OPT}use_ffmpeg) +@@ -107,6 +109,12 @@ if (${_OPT}use_ffmpeg) list(APPEND DEFINITIONS PRIVATE _DARWIN_C_SOURCE ) endif() @@ -39,10 +37,10 @@ index 8c5f06d7c..00810e4d0 100644 "${DEFINITIONS}" "" ) diff --git a/libraries/lib-ffmpeg-support/FFmpegFunctions.cpp b/libraries/lib-ffmpeg-support/FFmpegFunctions.cpp -index 66d085a0b..4eeb4aed3 100644 +index 55d6f676b..46640ef83 100644 --- a/libraries/lib-ffmpeg-support/FFmpegFunctions.cpp +++ b/libraries/lib-ffmpeg-support/FFmpegFunctions.cpp -@@ -238,6 +238,18 @@ struct FFmpegFunctions::Private final +@@ -246,6 +246,18 @@ struct FFmpegFunctions::Private final if (library->IsLoaded()) return library; @@ -58,9 +56,6 @@ index 66d085a0b..4eeb4aed3 100644 + } +#endif + - // Loading has failed. - // wxLogSysError doesn't report errors correctly on *NIX - #if defined(_WIN32) --- -2.34.0 - + return {}; + } + }; diff --git a/gnu/packages/patches/ecl-16-format-directive-limit.patch b/gnu/packages/patches/ecl-16-format-directive-limit.patch deleted file mode 100644 index 237db92722..0000000000 --- a/gnu/packages/patches/ecl-16-format-directive-limit.patch +++ /dev/null @@ -1,83 +0,0 @@ -Patch backported by Sage. - -Fix from upstream that happens to work around -https://trac.sagemath.org/ticket/23011 -diff --git a/src/lsp/format.lsp b/src/lsp/format.lsp -index 77ca799..53b887c 100644 ---- a/src/lsp/format.lsp -+++ b/src/lsp/format.lsp -@@ -307,11 +307,13 @@ - :start (format-directive-start struct) - :end (format-directive-end struct)))) - -+(defconstant +format-directive-limit+ (1+ (char-code #\~))) -+ - #+formatter - (defparameter *format-directive-expanders* -- (make-array char-code-limit :initial-element nil)) -+ (make-array +format-directive-limit+ :initial-element nil)) - (defparameter *format-directive-interpreters* -- (make-array char-code-limit :initial-element nil)) -+ (make-array +format-directive-limit+ :initial-element nil)) - - (defparameter *default-format-error-control-string* nil) - (defparameter *default-format-error-offset* nil) -@@ -550,24 +552,24 @@ - (write-string directive stream) - (interpret-directive-list stream (cdr directives) orig-args args)) - (#-ecl format-directive #+ecl vector -+ (multiple-value-bind -+ (new-directives new-args) -+ (let* ((code (char-code (format-directive-character directive))) -+ (function -+ (and (< code +format-directive-limit+) -+ (svref *format-directive-interpreters* code))) -+ (*default-format-error-offset* -+ (1- (format-directive-end directive)))) -+ (unless function -+ (error 'format-error -+ :complaint "Unknown format directive.")) - (multiple-value-bind - (new-directives new-args) -- (let ((function -- (svref *format-directive-interpreters* -- (char-code (format-directive-character -- directive)))) -- (*default-format-error-offset* -- (1- (format-directive-end directive)))) -- (unless function -- (error 'format-error -- :complaint "Unknown format directive.")) -- (multiple-value-bind -- (new-directives new-args) -- (funcall function stream directive -- (cdr directives) orig-args args) -- (values new-directives new-args))) -- (interpret-directive-list stream new-directives -- orig-args new-args))))) -+ (funcall function stream directive -+ (cdr directives) orig-args args) -+ (values new-directives new-args))) -+ (interpret-directive-list stream new-directives -+ orig-args new-args))))) - args)) - - -@@ -639,11 +641,12 @@ - (values `(write-string ,directive stream) - more-directives)) - (format-directive -- (let ((expander -- (aref *format-directive-expanders* -- (char-code (format-directive-character directive)))) -- (*default-format-error-offset* -- (1- (format-directive-end directive)))) -+ (let* ((code (char-code (format-directive-character directive))) -+ (expander -+ (and (< code +format-directive-limit+) -+ (svref *format-directive-expanders* code))) -+ (*default-format-error-offset* -+ (1- (format-directive-end directive)))) - (if expander - (funcall expander directive more-directives) - (error 'format-error diff --git a/gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch b/gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch deleted file mode 100644 index 42d213c0e9..0000000000 --- a/gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch +++ /dev/null @@ -1,17 +0,0 @@ -Patch adapted from Sage. -diff -Naur ecl-16.1.2.orig/src/c/file.d ecl-16.1.2/src/c/file.d ---- ecl-16.1.2.orig/src/c/file.d 2016-05-11 13:10:51.867673867 +1200 -+++ ecl-16.1.2/src/c/file.d 2016-05-11 14:44:48.121907307 +1200 -@@ -3354,8 +3354,10 @@ - ecl_disable_interrupts(); - do { - out = fwrite(c, sizeof(char), n, IO_STREAM_FILE(strm)); -- } while (out < n && restartable_io_error(strm, "fwrite")); -- ecl_enable_interrupts(); -+ /* Ignore write errors to stderr to avoid an infinite loop */ -+ } while (out < n && (IO_STREAM_FILE(strm) != stderr) && restartable_io_error(strm, "fwrite")); -+ -+ ecl_enable_interrupts(); - return out; - } - diff --git a/gnu/packages/patches/ecl-16-libffi.patch b/gnu/packages/patches/ecl-16-libffi.patch deleted file mode 100644 index fc06a07606..0000000000 --- a/gnu/packages/patches/ecl-16-libffi.patch +++ /dev/null @@ -1,16 +0,0 @@ -Patch adapted from Sage. Allows building ECL on libffi 3.3. -diff --git a/src/c/ffi.d b/src/c/ffi.d -index 8861303e..8a959c23 100644 ---- a/src/c/ffi.d -+++ b/src/c/ffi.d -@@ -133,8 +133,8 @@ static struct { - #elif defined(X86_WIN64) - {@':win64', FFI_WIN64}, - #elif defined(X86_ANY) || defined(X86) || defined(X86_64) -- {@':cdecl', FFI_SYSV}, -- {@':sysv', FFI_SYSV}, -+ {@':cdecl', FFI_UNIX64}, -+ {@':sysv', FFI_UNIX64}, - {@':unix64', FFI_UNIX64}, - #endif - }; diff --git a/gnu/packages/patches/kcontacts-incorrect-country-name.patch b/gnu/packages/patches/kcontacts-incorrect-country-name.patch new file mode 100644 index 0000000000..7e15f9f5eb --- /dev/null +++ b/gnu/packages/patches/kcontacts-incorrect-country-name.patch @@ -0,0 +1,85 @@ +From 5fc2ce8b9f34ea3218a030aeede01b70bedb2546 Mon Sep 17 00:00:00 2001 +From: Petr Hodina <phodina@protonmail.com> +Date: Wed, 28 Sep 2022 20:58:43 +0200 +Subject: [PATCH] autotests: Fix incorrect name of country in comparison. + + +diff --git a/autotests/addresstest.cpp b/autotests/addresstest.cpp +index fc6a9bc7..01e474b6 100644 +--- a/autotests/addresstest.cpp ++++ b/autotests/addresstest.cpp +@@ -157,7 +157,7 @@ void AddressTest::formatTest() + + const QString result( + QStringLiteral("Jim Knopf\nLummerlandstr. 1\n" +- "12345 Lummerstadt\n\nGERMANIA")); ++ "12345 Lummerstadt\n\nGERMANY")); + + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QStringLiteral("Jim Knopf")), result); + #if KCONTACTS_BUILD_DEPRECATED_SINCE(5, 92) +@@ -175,7 +175,7 @@ void AddressTest::formatTest() + + const QString result( + QStringLiteral("Huck Finn\n457 Foobar Ave\nNERVOUSBREAKTOWN," +- " DC 1A2B3C\n\nSTATI UNITI")); ++ " DC 1A2B3C\n\nUNITED STATES")); + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QStringLiteral("Huck Finn")), result); + } + +@@ -188,7 +188,7 @@ void AddressTest::formatTest() + + const QString result( + QStringLiteral("Jim Knopf\nLummerlandstr. 1\n" +- "12345 Lummerstadt\n\nGERMANIA")); ++ "12345 Lummerstadt\n\nGERMANY")); + + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QStringLiteral("Jim Knopf")), result); + } +@@ -214,7 +214,7 @@ void AddressTest::formatTest() + address.setCountry(QStringLiteral("Schweiz")); + + // we want the Italian variant of the Swiss format for it_CH +- const QString result(QStringLiteral("Dr. Konqui\nCasella postale 5678\nHaus Randa\n1234 Randa\n\nSVIZZERA")); ++ const QString result(QStringLiteral("Dr. Konqui\nCasella postale 5678\nHaus Randa\n1234 Randa\n\nSWITZERLAND")); + + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QStringLiteral("Dr. Konqui")), result); + } +@@ -228,14 +228,14 @@ void AddressTest::formatTest() + address.setCountry(QStringLiteral("CH")); + + // we want the Italian variant of the Swiss format for it_CH +- const QString result(QStringLiteral("Dr. Konqui\nCasella postale 5678\nHaus Randa\n1234 Randa\n\nSVIZZERA")); ++ const QString result(QStringLiteral("Dr. Konqui\nCasella postale 5678\nHaus Randa\n1234 Randa\n\nSWITZERLAND")); + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QStringLiteral("Dr. Konqui")), result); + } + + { + KContacts::Address address; + address.setCountry(QStringLiteral("CH")); +- QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QString()), QLatin1String("SVIZZERA")); ++ QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal, QString()), QLatin1String("SWITZERLAND")); + } + + { +@@ -257,14 +257,14 @@ void AddressTest::formatTest() + address.setLocality(QStringLiteral("Minato-ku")); + address.setPostalCode(QStringLiteral("106-0047")); + address.setStreet(QStringLiteral("4-6-28 Minami-Azabu")); +- auto result = QString::fromUtf8("4-6-28 Minami-Azabu, Minato-ku\nTOKYO 106-0047\n\nGIAPPONE"); ++ auto result = QString::fromUtf8("4-6-28 Minami-Azabu, Minato-ku\nTOKYO 106-0047\n\nJAPAN"); + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal), result); + + address.setRegion(QStringLiteral("東京")); + address.setLocality(QStringLiteral("都港区")); + address.setPostalCode(QStringLiteral("106-0047")); + address.setStreet(QStringLiteral("南麻布 4-6-28")); +- result = QString::fromUtf8("〒106-0047\n東京都港区南麻布 4-6-28\n\nGIAPPONE"); ++ result = QString::fromUtf8("〒106-0047\n東京都港区南麻布 4-6-28\n\nJAPAN"); + QCOMPARE(address.formatted(KContacts::AddressFormatStyle::Postal), result); + } + } + +base-commit: 1d757eba019718cab5d3b33a231d19daf31eb8ba +-- +2.37.2 + diff --git a/gnu/packages/patches/kde-cli-tools-delay-mime-db.patch b/gnu/packages/patches/kde-cli-tools-delay-mime-db.patch new file mode 100644 index 0000000000..e29b3b192d --- /dev/null +++ b/gnu/packages/patches/kde-cli-tools-delay-mime-db.patch @@ -0,0 +1,26 @@ +From f8cfb96a1540fc3256af95adf8003b75c305183c Mon Sep 17 00:00:00 2001 +From: Petr Hodina <phodina@protonmail.com> +Date: Fri, 30 Sep 2022 21:55:55 +0200 +Subject: [PATCH] Add delay to update the mime db in testCreateMimeType test + function. + + +diff --git a/keditfiletype/tests/filetypestest.cpp b/keditfiletype/tests/filetypestest.cpp +index e58e6f2..a41d4ad 100644 +--- a/keditfiletype/tests/filetypestest.cpp ++++ b/keditfiletype/tests/filetypestest.cpp +@@ -315,6 +315,9 @@ private Q_SLOTS: + QVERIFY(data.isDirty()); + QVERIFY(data.sync()); + MimeTypeWriter::runUpdateMimeDatabase(); ++ // QMimeDatabase doesn't even try to update the cache if less than ++ // 5000 ms have passed (can't use qmime_secondsBetweenChecks) ++ QTest::qSleep(5000); + QMimeType mime = db.mimeTypeForName(mimeTypeName); + QVERIFY(mime.isValid()); + QCOMPARE(mime.comment(), fakeComment); + +base-commit: b5911cda17521156b22429436e19b508aa442a57 +-- +2.37.2 + diff --git a/gnu/packages/patches/libksysguard-qdiriterator-follow-symlinks.patch b/gnu/packages/patches/libksysguard-qdiriterator-follow-symlinks.patch new file mode 100644 index 0000000000..ec4a34037d --- /dev/null +++ b/gnu/packages/patches/libksysguard-qdiriterator-follow-symlinks.patch @@ -0,0 +1,24 @@ +From 46164a50de4102d02ae9d1d480acdd4b12303db8 Mon Sep 17 00:00:00 2001 +From: Thomas Tuegel <ttuegel@gmail.com> +Date: Wed, 14 Oct 2015 07:07:22 -0500 +Subject: [PATCH] qdiriterator follow symlinks + +--- + processui/scripting.cpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/processui/scripting.cpp b/processui/scripting.cpp +index efed8ff..841761a 100644 +--- a/processui/scripting.cpp ++++ b/processui/scripting.cpp +@@ -293,7 +293,7 @@ void Scripting::loadContextMenu() + const QStringList dirs = + QStandardPaths::locateAll(QStandardPaths::GenericDataLocation, QStringLiteral("ksysguard/scripts/"), QStandardPaths::LocateDirectory); + for (const QString &dir : dirs) { +- QDirIterator it(dir, QStringList() << QStringLiteral("*.desktop"), QDir::NoFilter, QDirIterator::Subdirectories); ++ QDirIterator it(dir, QStringList() << QStringLiteral("*.desktop"), QDir::NoFilter, QDirIterator::Subdirectories | QDirIterator::FollowSymlinks); + while (it.hasNext()) { + scripts.append(it.next()); + } +-- +2.5.2 diff --git a/gnu/packages/patches/linux-libre-infodocs-target.patch b/gnu/packages/patches/linux-libre-infodocs-target.patch new file mode 100644 index 0000000000..e9e6495c26 --- /dev/null +++ b/gnu/packages/patches/linux-libre-infodocs-target.patch @@ -0,0 +1,88 @@ +Upstream status: https://marc.info/?l=linux-doc&m=166861669723994&w=2 + +From 7edb5b278ee383ff9bed525329b2cdbe22317bf2 Mon Sep 17 00:00:00 2001 +From: Maxim Cournoyer <maxim.cournoyer@gmail.com> +Date: Mon, 14 Nov 2022 22:51:11 -0500 +Subject: [PATCH] doc: add texinfodocs and infodocs targets + +Sphinx supports generating Texinfo sources and Info documentation, +which can be navigated easily and is convenient to search (via the +indexed nodes or anchors, for example). + +This change also causes the html output to appear under its own output +sub-directory, which makes it easier to install, since it's clean from +.doctrees or other output formats. + +Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> +--- + Documentation/Makefile | 13 ++++++++++++- + Documentation/userspace-api/media/Makefile | 3 ++- + Makefile | 2 +- + 3 files changed, 15 insertions(+), 3 deletions(-) + +diff --git a/Documentation/Makefile b/Documentation/Makefile +index 64d44c1ecad3..bd8dac560633 100644 +--- a/Documentation/Makefile ++++ b/Documentation/Makefile +@@ -93,7 +93,16 @@ quiet_cmd_sphinx = SPHINX $@ --> file://$(abspath $(BUILDDIR)/$3/$4) + + htmldocs: + @$(srctree)/scripts/sphinx-pre-install --version-check +- @+$(foreach var,$(SPHINXDIRS),$(call loop_cmd,sphinx,html,$(var),,$(var))) ++ @+$(foreach var,$(SPHINXDIRS),$(call loop_cmd,sphinx,html,$(var),html,$(var))) ++ ++texinfodocs: ++ @$(srctree)/scripts/sphinx-pre-install --version-check ++ @+$(foreach var,$(SPHINXDIRS),$(call loop_cmd,sphinx,texinfo,$(var),texinfo,$(var))) ++ ++# Note: the 'info' Make target is generated by sphinx itself when ++# running the texinfodocs target define above. ++infodocs: texinfodocs ++ $(MAKE) -C $(BUILDDIR)/texinfo info + + linkcheckdocs: + @$(foreach var,$(SPHINXDIRS),$(call loop_cmd,sphinx,linkcheck,$(var),,$(var))) +@@ -143,6 +152,8 @@ cleandocs: + dochelp: + @echo ' Linux kernel internal documentation in different formats from ReST:' + @echo ' htmldocs - HTML' ++ @echo ' texinfodocs - Texinfo' ++ @echo ' infodocs - Info' + @echo ' latexdocs - LaTeX' + @echo ' pdfdocs - PDF' + @echo ' epubdocs - EPUB' +diff --git a/Documentation/userspace-api/media/Makefile b/Documentation/userspace-api/media/Makefile +index 00922aa7efde..3d8aaf5c253b 100644 +--- a/Documentation/userspace-api/media/Makefile ++++ b/Documentation/userspace-api/media/Makefile +@@ -47,10 +47,11 @@ $(BUILDDIR)/lirc.h.rst: ${UAPI}/lirc.h ${PARSER} $(SRC_DIR)/lirc.h.rst.exception + + # Media build rules + +-.PHONY: all html epub xml latex ++.PHONY: all html texinfo epub xml latex + + all: $(IMGDOT) $(BUILDDIR) ${TARGETS} + html: all ++texinfo: all + epub: all + xml: all + latex: $(IMGPDF) all +diff --git a/Makefile b/Makefile +index 58cd4f5e1c3a..b3266c408b6c 100644 +--- a/Makefile ++++ b/Makefile +@@ -1785,7 +1785,7 @@ $(help-board-dirs): help-%: + # Documentation targets + # --------------------------------------------------------------------------- + DOC_TARGETS := xmldocs latexdocs pdfdocs htmldocs epubdocs cleandocs \ +- linkcheckdocs dochelp refcheckdocs ++ linkcheckdocs dochelp refcheckdocs texinfodocs infodocs + PHONY += $(DOC_TARGETS) + $(DOC_TARGETS): + $(Q)$(MAKE) $(build)=Documentation $@ + +base-commit: 81e7cfa3a9eb4ba6993a9c71772fdab21bc5d870 +-- +2.38.1 + diff --git a/gnu/packages/patches/wacomtablet-add-missing-includes.patch b/gnu/packages/patches/wacomtablet-add-missing-includes.patch new file mode 100644 index 0000000000..cd93938075 --- /dev/null +++ b/gnu/packages/patches/wacomtablet-add-missing-includes.patch @@ -0,0 +1,11 @@ +diff -rup wacomtablet-3.1.0/src/kcmodule/styluspagewidget.cpp wacomtablet-3.1.0.new/src/kcmodule/styluspagewidget.cpp +--- wacomtablet-3.1.0/src/kcmodule/styluspagewidget.cpp 2018-06-22 15:07:58.000000000 +0200 ++++ wacomtablet-3.1.0.new/src/kcmodule/styluspagewidget.cpp 2018-07-10 17:38:09.239242847 +0200 +@@ -25,6 +25,7 @@ + #include "profilemanagement.h" + + // common includes ++#include "logging.h" + #include "property.h" + #include "deviceprofile.h" + #include "dbustabletinterface.h" diff --git a/gnu/packages/patches/wacomtablet-qt5.15.patch b/gnu/packages/patches/wacomtablet-qt5.15.patch new file mode 100644 index 0000000000..598ac939e8 --- /dev/null +++ b/gnu/packages/patches/wacomtablet-qt5.15.patch @@ -0,0 +1,23 @@ +From 4f73ff02b3efd5e8728b18fcf1067eca166704ee Mon Sep 17 00:00:00 2001 +From: Christophe Giboudeaux <christophe@krop.fr> +Date: Thu, 4 Jun 2020 16:00:38 +0200 +Subject: [PATCH] Fix build with Qt 5.15 + +--- + src/kcmodule/pressurecurvewidget.cpp | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/src/kcmodule/pressurecurvewidget.cpp b/src/kcmodule/pressurecurvewidget.cpp +index 0c943b3..f047a6c 100644 +--- a/src/kcmodule/pressurecurvewidget.cpp ++++ b/src/kcmodule/pressurecurvewidget.cpp +@@ -22,6 +22,7 @@ + //Qt includes + #include <QDebug> + #include <QPainter> ++#include <QPainterPath> + #include <QMouseEvent> + #include <QResizeEvent> + #include <QTabletEvent> +-- +GitLab diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index b6c33b2a36..0e21176751 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -1899,14 +1899,14 @@ as defined by two typical specimens of Perl coders.") (define-public perl-conf-libconfig (package (name "perl-conf-libconfig") - (version "0.100") + (version "0.101") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/C/CN/CNANGEL/" "Conf-Libconfig-" version ".tar.gz")) (sha256 - (base32 "0qdypqd7mx96bwdjlv13fn6p96bs4w0yv94yv94xa7z5lqkdj4rg")))) + (base32 "11dd3kb0k45gqahnnwz50x3b4b25c5jgykkwgf74rcyr0dsy0n5a")))) (build-system perl-build-system) (native-inputs (list perl-extutils-pkgconfig perl-test-deep perl-test-exception diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm index a052a38853..f7184bd49a 100644 --- a/gnu/packages/protobuf.scm +++ b/gnu/packages/protobuf.scm @@ -189,7 +189,7 @@ internal RPC protocols and file formats.") ;; The 3.5 series are the last versions that do not require C++ 11. (define-public protobuf-3.5 (package - (inherit protobuf) + (inherit protobuf-3.6) (version "3.5.1") (source (origin (method url-fetch) diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm index 1426ad9f09..c483d68b5f 100644 --- a/gnu/packages/python-compression.scm +++ b/gnu/packages/python-compression.scm @@ -1,9 +1,9 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> -;;; Copyright © 2017, 2019, 2021 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2017, 2019, 2021, 2022 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2017 Nikita <nikita@n0.is> ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu> -;;; Copyright © 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2018-2020, 2022 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr> ;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2021 Brendan Tildesley <mail@brendan.scot> @@ -31,6 +31,7 @@ #:use-module (guix gexp) #:use-module (guix build-system gnu) #:use-module (guix build-system python) + #:use-module (guix build-system pyproject) #:use-module (gnu packages) #:use-module (gnu packages libffi) #:use-module (gnu packages compression) @@ -47,21 +48,20 @@ (define-public python-multivolumefile (package (name "python-multivolumefile") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (pypi-uri "multivolumefile" version)) (sha256 (base32 - "0j46wab4b09s3favjzp3zs1cn2sn8pr7qyngs5wn31hpqqxbbz76")))) - (build-system python-build-system) + "1mh9sz50s1p8ik83a455pqd57syprad7xhfmk28yb5mwmw58sr50")))) + (build-system pyproject-build-system) (native-inputs - (list python-pep517 - python-setuptools - python-setuptools-scm + (list python-setuptools-scm python-coverage python-coveralls + python-hypothesis python-pyannotate python-pytest python-pytest-cov)) @@ -72,6 +72,36 @@ file-object abstraction, making it possible to use multiple files as if they were a single file.") (license license:lgpl2.1+))) +(define-public python-pybcj + (package + (name "python-pybcj") + (version "1.0.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pybcj" version)) + (sha256 + (base32 + "1hvm3c3mb20z25kmbzyyn6pr5inx50z0ignl8b0bggxaik82ws4b")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-importlib-metadata)) + (native-inputs + (list python-coverage + python-hypothesis + python-pytest + python-pytest-cov + python-setuptools-scm)) + (home-page "https://codeberg.org/miurahr/pybcj") + (synopsis "BCJ filter library") + (description "In data compression, BCJ, short for Branch-Call-Jump, refers +to a technique that improves the compression of machine code of executable +binaries by replacing relative branch addresses with absolute ones. This +allows a LZMA compressor to identify duplicate targets and archive higher +compression rate. BCJ is used in the 7-zip compression utility as the default +filter for executable binaries. + +pybcj provides Python bindings to a BCJ implementation in C.") + (license license:lgpl2.1+))) + (define-public python-bcj-cffi (package (name "python-bcj-cffi") @@ -95,6 +125,59 @@ were a single file.") Jump conversion filter by CFFI for Python.") (license license:lgpl2.1+))) +(define-public python-brotlicffi + (package + (name "python-brotlicffi") + (version "1.0.9.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "brotlicffi" version)) + (sha256 + (base32 + "15kxgdiqcg0cm6h5xq3vkbhw7674673hcx3n2yicd3wx29l8l90c")) + (snippet + #~(begin + (use-modules (guix build utils)) + (delete-file-recursively "libbrotli"))))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'use-shared-brotli + (lambda _ + (setenv "USE_SHARED_BROTLI" "1")))))) + (propagated-inputs (list python-cffi)) + (inputs (list brotli)) + (home-page "https://github.com/python-hyper/brotlicffi") + (synopsis "Python CFFI bindings to the Brotli library") + (description "This package provides Python CFFI bindings to the Brotli +library.") + (license license:expat))) + +(define-public python-inflate64 + (package + (name "python-inflate64") + (version "0.3.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "inflate64" version)) + (sha256 + (base32 + "0767j35gkwaykl1iq9qn8rc25j1ggv56x3d1vzjpk89bzpzdhbdm")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-importlib-metadata)) + (native-inputs + (list python-pyannotate + python-pytest + python-setuptools-scm)) + (home-page "https://pypi.org/project/inflate64/") + (synopsis "deflate64 compression/decompression library") + (description "The @code{inflate64} package provides @code{Deflater} and +@code{Inflater} classes to compress and decompress with the Enhanced Deflate +compression algorithm.") + (license license:lgpl2.1+))) + (define-public python-isal (package (name "python-isal") @@ -124,24 +207,50 @@ Jump conversion filter by CFFI for Python.") and decompression by implementing Python bindings for the ISA-L library.") (license license:expat))) +(define-public python-pyppmd + (package + (name "python-pyppmd") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "pyppmd" version)) + (sha256 + (base32 + "03w4x26mar0ha73c3v39psn1i0k6xrzwmaxfsxysic73jz99np07")))) + (build-system pyproject-build-system) + (native-inputs + (list python-coverage + python-hypothesis + python-pytest + python-pytest-benchmark + python-pytest-cov + python-pytest-timeout + python-setuptools-scm)) + (home-page "https://github.com/miurahr/pyppmd") + (synopsis "PPMd compression/decompression library") + (description "Pyppmd provides classes and functions for compressing and +decompressing text data, using the @dfn{Prediction by partial matching} (PPM) +compression algorithm variation H and I.2. It provides an API similar to +Python's zlib/bz2/lzma modules.") + (license license:lgpl2.1+))) + (define-public python-ppmd-cffi (package (name "python-ppmd-cffi") - (version "0.3.3") + (version "0.5.0") (source (origin (method url-fetch) (uri (pypi-uri "ppmd-cffi" version)) (sha256 (base32 - "01wcd9l6pp6hivdmd275qh9dhcwficjqfl67hxix5n07vvq7jzz0")))) + "0vprpl29fkflqx0m6anfpx7q7i4cw0d0qxcdm91k4pl82dcad81g")))) (build-system python-build-system) (propagated-inputs (list python-cffi)) (native-inputs - (list python-setuptools + (list python-hypothesis python-setuptools-scm - python-pep517 python-coverage python-pytest python-pytest-cov)) @@ -155,23 +264,27 @@ several possible methods.") (define-public python-py7zr (package (name "python-py7zr") - (version "0.14.1") + (version "0.20.2") (source (origin (method url-fetch) (uri (pypi-uri "py7zr" version)) (sha256 (base32 - "1zmgp7yax328fj8yj8pj4l7yh78hp727j6wk12vfi6nmi82wl32i")))) - (build-system python-build-system) + "0lwniinfr3rb10n0c203a09vz06vxnnj637yqn8ipdlml89gj7kr")))) + (build-system pyproject-build-system) (propagated-inputs - (list python-bcj-cffi + (list python-brotli + python-brotlicffi + python-importlib-metadata + python-inflate64 python-multivolumefile - python-ppmd-cffi - python-pycryptodome + python-psutil + python-pybcj + python-pycryptodomex + python-pyppmd python-pyzstd - python-texttable - python-zstandard)) + python-texttable)) (native-inputs (list python-setuptools python-setuptools-scm @@ -429,14 +542,16 @@ wrapper. It provides a backport of the @code{Path} object.") (define-public python-zstandard (package (name "python-zstandard") - (version "0.15.2") + (version "0.19.0") (source (origin (method url-fetch) (uri (pypi-uri "zstandard" version)) (sha256 - (base32 "0by9z7nxnkzhmza075q6q91rs8lnpf91129k8ppv7kymbwshipjj")))) + (base32 "0qvqhs121spk7yc1l20samflxx47waxv3xm55ksxpn1djk6jzl9i")))) (build-system python-build-system) + (propagated-inputs + (list python-cffi)) (native-inputs (list python-hypothesis)) (home-page "https://github.com/indygreg/python-zstandard") @@ -449,17 +564,18 @@ provided.") (define-public python-pyzstd (package (name "python-pyzstd") - (version "0.14.3") + (version "0.15.3") (source (origin (method url-fetch) (uri (pypi-uri "pyzstd" version)) (sha256 (base32 - "1d3mngs45w2p490vrq5ymd2wz4lp15phmks1ilcx4k7amgibml3d")))) + "0wkli2i4my79l43b996bdga0fac8s8nfd1zjyzl46lwmsfsxlkmc")))) (build-system python-build-system) (home-page "https://github.com/animalize/pyzstd") (synopsis "Zstandard bindings for Python") - (description "This package provides Python bindings to the Zstandard (zstd) + (description "This package provides Python bindings to the +Zstandard (zstd) compression library. The API is similar to Python's bz2/lzma/zlib module.") (license license:bsd-3))) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 905d79886f..4f3a587c6a 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -4743,6 +4743,65 @@ Google search engine. Its module is called @code{googlesearch}.") (description "Python client library for Google's discovery based APIs") (license license:asl2.0))) +(define-public whoogle-search + (package + (name "whoogle-search") + (version "0.8.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "whoogle-search" version)) + (sha256 + (base32 + "0h8cl9bkd3vx17kbvcnmc8cy6pc29lxr0drxm84kj37ka788cj2g")))) + (build-system python-build-system) + (arguments + (list + ;; The tests need network access + #:tests? #f)) + (propagated-inputs + (list python-attrs + python-beautifulsoup4 + python-cachelib + python-certifi + python-cffi + python-brotli + python-chardet + python-click + python-cryptography + python-cssutils + python-defusedxml + python-flask + python-flask-session + python-idna + python-itsdangerous + python-jinja2 + python-markupsafe + python-more-itertools + python-packaging + python-pluggy + python-py + python-pycodestyle + python-pycparser + python-pyopenssl + python-pyparsing + python-pysocks + python-dateutil + python-requests + python-soupsieve + python-stem + python-urllib3 + python-waitress + python-wcwidth + python-werkzeug + python-dotenv)) + (home-page "https://github.com/benbusby/whoogle-search") + (synopsis "Self-hosted, ad-free, privacy-respecting metasearch engine") + (description + "Get Google results, but without any ads, javascript, AMP links, +cookies, or IP address tracking. Quick and simple to implement as a primary +search engine replacement on both desktop and mobile.") + (license license:expat))) + (define-public python-hawkauthlib (package (name "python-hawkauthlib") diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 509d57964f..87963f9f19 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -104,7 +104,7 @@ ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be> ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr> ;;; Copyright © 2021 Franck Pérignon <franck.perignon@univ-grenoble-alpes.fr> -;;; Copyright © 2021 Petr Hodina <phodina@protonmail.com> +;;; Copyright © 2021, 2022 Petr Hodina <phodina@protonmail.com> ;;; Copyright © 2021 Simon Streit <simon@netpanic.org> ;;; Copyright © 2021 Daniel Meißner <daniel.meissner-i4k@ruhr-uni-bochum.de> ;;; Copyright © 2021, 2022 Pradana Aumars <paumars@courrier.dev> @@ -3075,6 +3075,41 @@ applications. dogtail scripts are written in Python and executed like any other Python program.") (license license:gpl2+))) +(define-public python-doxyqml + (package + (name "python-doxyqml") + (version "0.5.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "doxyqml" version)) + (sha256 + (base32 + "1f0jjqvamly4hn7f1palvq27z6yr694rfzyxrb6g0ysbbawxkvq9")))) + (build-system python-build-system) + (home-page "http://agateau.com/projects/doxyqml") + (synopsis "Doxygen input filter for QML files") + (description + "This package provides a Doxygen input filter for QML files.") + (license license:bsd-3))) + +(define-public python-doxypypy + (package + (name "python-doxypypy") + (version "0.8.8.6") + (source (origin + (method url-fetch) + (uri (pypi-uri "doxypypy" version)) + (sha256 + (base32 + "06z0vbh975g42z5szbfvn9i3bif3xwr5pncqd4fvjzjkbi2p2xb2")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ;no test suite + (home-page "https://github.com/Feneric/doxypypy") + (synopsis "Doxygen filter for Python") + (description + "This package provides a Doxygen filter for Python.") + (license license:gpl2+))) + (define-public python-empy (package (name "python-empy") @@ -3105,25 +3140,6 @@ system is highly configurable via command line options and embedded commands.") (license license:lgpl2.1+))) -(define-public python-enum34 - (package - (name "python-enum34") - (version "1.1.6") - (source - (origin - (method url-fetch) - (uri (pypi-uri "enum34" version)) - (sha256 - (base32 - "1cgm5ng2gcfrkrm3hc22brl6chdmv67b9zvva9sfs7gn7dwc9n4a")))) - (build-system python-build-system) - (home-page "https://pypi.org/project/enum34/") - (synopsis "Backported Python 3.4 Enum") - (description - "Enum34 is the new Python stdlib enum module available in Python 3.4 -backported for previous versions of Python from 2.4 to 3.3.") - (license license:bsd-3))) - (define-public python-parse-type (package (name "python-parse-type") @@ -7031,6 +7047,8 @@ as the original project seems to have been abandoned circa 2007.") (build-system python-build-system) (arguments `(#:tests? #f)) ; Tests try to access the network. + (propagated-inputs + (list python-six)) (home-page "http://pagekite.net/wiki/Floss/PySocksipyChain/") (synopsis "Python SOCKS module with chained proxies support") (description @@ -10254,16 +10272,18 @@ more advanced mathematics.") (define-public python-bigfloat (package (name "python-bigfloat") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (pypi-uri "bigfloat" version)) (sha256 - (base32 "0xd7q4l7v0f463diznjv4k9wlaks80pn9drdqmfifi7zx8qvybi6")))) + (base32 "1f0c1hdr39bbl5rds5r1waa1papjmjiyp0ixs64mkjiahzg6pfaq")))) (build-system python-build-system) (inputs (list mpfr)) + (propagated-inputs + (list python-six)) (home-page "https://github.com/mdickinson/bigfloat") (synopsis "Arbitrary precision floating-point arithmetic for Python") (description @@ -16025,6 +16045,20 @@ way.") (sha256 (base32 "00yvj8bxmhhhhd74v7j0x673is7vizmxwgb3dd5xmnkr74ybyi7w")))) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'disable-test + (lambda _ + ;; See https://github.com/bmc/munkres/issues/40 + (substitute* "test/test_munkres.py" + (("^def test_profit_float" m) + (string-append "\ +import platform +@pytest.mark.skipif(platform.architecture()[0] == \"32bit\", + reason=\"Fails on 32 bit architectures\") +" m)))))))) (build-system python-build-system) (native-inputs (list python-pytest-6)) (home-page "https://software.clapper.org/munkres/") @@ -17613,8 +17647,10 @@ It supports TSIG authenticated messages and EDNS0.") (lambda _ (substitute* "setup.py" (("import DNS") "") - (("DNS.__version__") (string-append "\"" ,version "\""))) - #t))) + (("DNS.__version__") (string-append "\"" ,version "\""))))) + ;; For the same reason, drop the sanity check because the library + ;; fails to load without /etc/resolv.conf. + (delete 'sanity-check)) #:tests? #f)) ; Also skip the tests. (home-page "https://launchpad.net/py3dns") (synopsis "Python 3 DNS library") @@ -19629,6 +19665,27 @@ from the header, as well as section details and data available.") and bit flag values.") (license license:expat))) +(define-public python-attrdict + (package + (name "python-attrdict") + (version "2.0.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "attrdict" version)) + (sha256 + (base32 + "0w3vsz64j9npxfgh83hghsh161wwkrx1fxqi1533js2wnnc0dj9m")))) + (build-system python-build-system) + ;; The package is no longer maintained and tests need some work. + (arguments '(#:tests? #f)) + (propagated-inputs (list python-six)) + (home-page "https://github.com/bcj/AttrDict") + (synopsis "Attribute-style access dictionaries") + (description + "This package provides mapping objects whose elements can be accessed +both as keys and as attributes.") + (license license:expat))) + (define-public python-attrs (package (name "python-attrs") @@ -27371,14 +27428,14 @@ and pandoc-citeproc.") (define-public python-rnc2rng (package (name "python-rnc2rng") - (version "2.6.4") + (version "2.6.6") (source (origin (method url-fetch) (uri (pypi-uri "rnc2rng" version)) (sha256 (base32 - "1kmp3iwxxyzjsd47j2sprd47ihhkwhb3yydih3af5bbfq0ibh1w8")))) + "1wbqvz2bhq2f5kqi7q2q3m9y5vs9rj970zhnjh502pvvhmbx20as")))) (build-system python-build-system) (propagated-inputs (list python-rply)) @@ -27575,6 +27632,8 @@ module patches @code{asyncio} to allow nested use of @code{asyncio.run} and "1mzk4yabxj6r149fswhis18hd8dnag5sj8i4wb06450zq3pi8dh7")))) (native-inputs (list unzip)) + (propagated-inputs + (list python-six)) (build-system python-build-system) (arguments '(#:tests? #f)) ; No test suite. (home-page "https://www.parallelpython.com") @@ -29603,7 +29662,7 @@ development, testing, production]}; (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "pytest" "-vv"))))))) - (native-inputs (list python-pytest python-pytest-mock)) + (native-inputs (list python-pytest python-pytest-mock python-numpy)) (propagated-inputs (list python-jedi python-pygments python-urwid python-urwid-readline)) (home-page "https://documen.tician.de/pudb/") diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 8cbb2c6a07..a0ced6451b 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -25,6 +25,7 @@ ;;; Copyright © 2021 Nicolò Balzarotti <nicolo@nixo.xyz> ;;; Copyright © 2022 Foo Chuan Wei <chuanwei.foo@hotmail.com> ;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com> +;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -48,6 +49,7 @@ #:use-module (guix git-download) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module (guix build-system meson) #:use-module (guix build-system trivial) #:use-module (guix build-system python) #:use-module (guix build-system qt) @@ -59,17 +61,21 @@ #:use-module (gnu packages bash) #:use-module (gnu packages base) #:use-module (gnu packages bison) + #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages cpp) #:use-module (gnu packages cups) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages documentation) + #:use-module (gnu packages elf) #:use-module (gnu packages enchant) #:use-module (gnu packages fontutils) #:use-module (gnu packages flex) #:use-module (gnu packages freedesktop) #:use-module (gnu packages gcc) + #:use-module (gnu packages gdb) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages glib) @@ -140,8 +146,7 @@ (modify-phases %standard-phases (add-after 'unpack 'chdir (lambda _ - (chdir "libqite") - #t))))) + (chdir "libqite")))))) (inputs (list qtbase-5 qtmultimedia-5)) (home-page "https://github.com/Ri0n/qite/") @@ -219,10 +224,10 @@ window managers, that don't provide Qt integration by themselves.") (native-inputs (list cmake-shared extra-cmake-modules pkg-config)) (inputs - `(("qtbase" ,qtbase-5) - ("qtwayland" ,qtwayland-5) - ("wayland" ,wayland) - ("xkbcommon" ,libxkbcommon))) + (list qtbase-5 + qtwayland-5 + wayland + libxkbcommon)) (synopsis "Material Decoration for Qt") (description "MaterialDecoration is a client-side decoration for Qt applications on Wayland.") @@ -254,8 +259,7 @@ applications on Wayland.") (add-before 'check 'check-setup (lambda _ ;; make Qt render "offscreen", required for tests - (setenv "QT_QPA_PLATFORM" "offscreen") - #t))))) + (setenv "QT_QPA_PLATFORM" "offscreen")))))) (home-page "https://github.com/steveire/grantlee") (synopsis "Libraries for text templating with Qt") (description "Grantlee Templates can be used for theming and generation of @@ -820,6 +824,69 @@ developers using C++ or QML, a CSS & JavaScript like language.") (variable "XDG_CONFIG_DIRS") (files '("etc/xdg"))))))) +(define-public qt3d-5 + (package + (inherit qtbase-5) + (name "qt3d") + (version "5.15.5") + (source (origin + (method url-fetch) + (uri (qt-urls name version)) + (sha256 + (base32 + "1m3y7d58crn0qgfwkimxcggssn2pbs8nj5b9diwns6rwqg4aqk20")))) + (propagated-inputs `()) + (native-inputs (list perl)) + (inputs (list mesa qtbase-5 vulkan-headers zlib)) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-before 'configure 'configure-qmake + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((tmpdir (string-append (getenv "TMPDIR"))) + (qmake (string-append tmpdir "/qmake")) + (qt.conf (string-append tmpdir "/qt.conf"))) + (symlink (which "qmake") qmake) + (setenv "PATH" + (string-append tmpdir ":" + (getenv "PATH"))) + (with-output-to-file qt.conf + (lambda () + (format #t "[Paths] +Prefix=~a +ArchData=lib/qt5 +Data=share/qt5 +Documentation=share/doc/qt5 +Headers=include/qt5 +Libraries=lib +LibraryExecutables=lib/qt5/libexec +Binaries=bin +Tests=tests +Plugins=lib/qt5/plugins +Imports=lib/qt5/imports +Qml2Imports=lib/qt5/qml +Translations=share/qt5/translations +Settings=etc/xdg +Examples=share/doc/qt5/examples +HostPrefix=~a +HostData=lib/qt5 +HostBinaries=bin +HostLibraries=lib + +[EffectiveSourcePaths] +HostPrefix=~a +HostData=lib/qt5" + #$output #$output #$(this-package-input + "qtbase"))))))) + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (invoke "qmake" + "QT_BUILD_PARTS = libs tools tests"))) + (add-before 'check 'set-display + (lambda _ + (setenv "QT_QPA_PLATFORM" "offscreen")))))) + (synopsis "Qt module for 3D") + (description "The Qt3d module provides classes for displaying 3D."))) + (define-public qt5compat (package (name "qt5compat") @@ -1802,9 +1869,22 @@ that helps in Qt development."))) (list ;; The build system attempts to fetch online resources and fails when ;; building the test suite. - #:configure-flags #~(list "-DQT_BUILD_TESTS=OFF"))) + #:configure-flags #~(list "-DQT_BUILD_TESTS=OFF") + #:phases #~(modify-phases %standard-phases + (add-after 'install 'sanity-check + (lambda* (#:key outputs #:allow-other-keys) + ;; This validation exists to validate that the dynamic + ;; library for Clang works as intended; there was + ;; originally problems due to left-overs patching the + ;; value of BUILD_SHARED_LIBS in CLANG-FROM-LLVM that + ;; would cause the following error: "CommandLine Error: + ;; Option 'filter' registered more than once!" + (invoke/quiet (search-input-file outputs "bin/qdoc") + "--help")))))) (native-inputs (list perl qtdeclarative vulkan-headers)) - (inputs (list libxkbcommon mesa qtbase)) + ;; Use clang-15, which is built using as a single shared library, which is + ;; what the build system of qttools expects. + (inputs (list clang-15 libxkbcommon mesa qtbase)) (home-page (package-home-page qtbase)) (synopsis "Qt Tools and Designer modules") (description "The Qt Tools module provides a set of applications to browse @@ -1814,6 +1894,27 @@ that helps in Qt development.") ;; LICENSES/Qt-GPL-exception-1.0.txt). (license (list license:gpl3)))) +(define-public qttranslations + (package + (name "qttranslations") + (version "6.3.1") + (source (origin + (method url-fetch) + (uri (qt-urls name version)) + (sha256 + (base32 + "15yvvxw1vngnjlly6cady05ljamg01qiaqn2vh0xkph855gdbgfp")))) + (build-system cmake-build-system) + (arguments (list #:tests? #f)) + (native-inputs (list qtbase qttools)) + (home-page (package-home-page qtbase)) + (synopsis "Qt translation catalogs") + (description "This package contains the translations for Qt contributed by +the Qt community.") + ;; GPL 3 only with Qt GPL exception 1.0 (see: + ;; LICENSES/Qt-GPL-exception-1.0.txt). + (license (list license:gpl3)))) + (define-public qtscript (package (inherit qtsvg-5) (name "qtscript") @@ -1917,12 +2018,12 @@ coloring, and many more."))) (native-inputs (list perl pkg-config)) (inputs - `(("fontconfig" ,fontconfig) - ("freetype" ,freetype) - ("libxrender" ,libxrender) - ("sdl2" ,sdl2) - ("qtbase" ,qtbase-5) - ("qtdeclarative-5" ,qtdeclarative-5))) + (list fontconfig + freetype + libxrender + sdl2 + qtbase-5 + qtdeclarative-5)) (synopsis "Qt Gamepad module") (description "The Qt Gamepad module is an add-on library that enables Qt applications to support the use of gamepad hardware and in some cases remote @@ -2478,16 +2579,16 @@ using the Enchant spell-checking library.") pciutils protobuf pulseaudio - qtbase-5 - qtdeclarative-5 qtmultimedia-5 - qtwebchannel-5 re2 snappy eudev valgrind vulkan-headers xcb-util)) + (propagated-inputs + ;; Required by Qt5WebEngineCoreConfig.cmake. + (list qtbase-5 qtdeclarative-5 qtwebchannel-5)) (arguments (substitute-keyword-arguments (package-arguments qtsvg-5) ((#:modules modules '()) @@ -2882,11 +2983,13 @@ linux/libcurl_wrapper.h" python-html5lib))) (inputs (modify-inputs (package-inputs qtwebengine-5) - (replace "qtbase" qtbase) - (replace "qtdeclarative" qtdeclarative) (replace "qtmultimedia" qtmultimedia) - (replace "qtwebchannel" qtwebchannel) (append libxkbfile xkeyboard-config))) + (propagated-inputs + (modify-inputs (package-propagated-inputs qtwebengine-5) + (replace "qtbase" qtbase) + (replace "qtdeclarative" qtdeclarative) + (replace "qtwebchannel" qtwebchannel))) (native-search-paths (list (search-path-specification (file-type 'regular) @@ -2941,8 +3044,7 @@ system libraries.") (string-append source "/" file) (string-append out "/include"))) '("SingleApplication" - "singleapplication.h" "singleapplication_p.h")) - #t)))))) + "singleapplication.h" "singleapplication_p.h")))))))) (inputs (list qtbase-5)) (home-page "https://github.com/itay-grudev/SingleApplication") @@ -3088,9 +3190,7 @@ module provides support functions to the automatically generated code.") (let* ((qtbase (assoc-ref inputs "qtbase")) (qtprinter.h (string-append "\"" qtbase "/include/qt5/QtPrintSupport/qprinter.h\""))) (substitute* "sip/QtPrintSupport/qprinter.sip" - (("<qprinter.h>") - qtprinter.h)) - #t))) + (("<qprinter.h>") qtprinter.h))))) (replace 'configure (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -3215,8 +3315,7 @@ contain over 620 classes.") (lambda _ (display " from pkgutil import extend_path __path__ = extend_path(__path__, __name__) -"))) - #t)))))) +"))))))))) (home-page "https://www.riverbankcomputing.com/software/pyqtwebengine/intro") (synopsis "Python bindings for QtWebEngine") (description @@ -3376,8 +3475,7 @@ indicators, code completion and call tips.") (string-append out "/lib"))) ;; And fix the installed.txt file (substitute* "installed.txt" - (("/gnu/store/[^/]+") out))) - #t))))) + (("/gnu/store/[^/]+") out)))))))) (inputs `(("qscintilla" ,qscintilla) ("python" ,python) @@ -3405,8 +3503,7 @@ This package provides the Python bindings."))) (match %build-inputs (((names . directories) ...) (union-build (assoc-ref %outputs "out") - directories) - #t))))) + directories)))))) (inputs `(("python-pyqt" ,python-pyqt) ("python-qscintilla" ,python-qscintilla))) @@ -3484,8 +3581,7 @@ securely. It will not store any data unencrypted unless explicitly requested.") (("#include \"qtlockedfile.*\\.cpp\"") "") ;; Unwrap namespace added in the vendoring process. (("QtLP_Private::QtLockedFile") - "QtLockedFile"))) - #t)))) + "QtLockedFile"))))))) (build-system gnu-build-system) (arguments `(#:tests? #f ; No target @@ -3509,8 +3605,7 @@ securely. It will not store any data unencrypted unless explicitly requested.") (("SUBDIRS\\+=examples") "")) ;; Fix deprecated functions. (substitute* "qtsoap/src/qtsoap.cpp" - (("toAscii") "toUtf8")) - #t)) + (("toAscii") "toUtf8")))) (replace 'configure (lambda _ (for-each (lambda (solution) @@ -3518,16 +3613,14 @@ securely. It will not store any data unencrypted unless explicitly requested.") (invoke "./configure" "-library") (invoke "qmake"))) '("qtlockedfile" "qtpropertybrowser" "qtservice" - "qtsingleapplication" "qtsoap")) - #t)) + "qtsingleapplication" "qtsoap")))) (replace 'build (lambda _ (for-each (lambda (solution) (with-directory-excursion solution (invoke "make"))) '("qtlockedfile" "qtpropertybrowser" "qtservice" - "qtsingleapplication" "qtsoap")) - #t)) + "qtsingleapplication" "qtsoap")))) (replace 'install (lambda args (for-each (lambda (solution) @@ -3607,8 +3700,7 @@ that can be only started once per user. ;; Remove some incomplete manual pages. (for-each delete-file (find-files "doc/man/man3" "^_tmp.*")) (mkdir-p man) - (copy-recursively "doc/man" man) - #t)))))) + (copy-recursively "doc/man" man))))))) (home-page "http://qwt.sourceforge.net") (synopsis "Qt widgets for plots, scales, dials and other technical software GUI components") @@ -3850,7 +3942,7 @@ color-related widgets.") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'use-shiboken-dir-only - (lambda _ (chdir "sources/shiboken2") #t)) + (lambda _ (chdir "sources/shiboken2"))) (add-before 'configure 'make-files-writable-and-update-timestamps (lambda _ ;; The build scripts need to modify some files in @@ -3861,13 +3953,11 @@ color-related widgets.") (for-each (lambda (file) (make-file-writable file) (utime file circa-1980 circa-1980)) - (find-files "."))) - #t)) + (find-files "."))))) (add-before 'configure 'set-build-env (lambda _ (let ((llvm #$(this-package-input "clang-toolchain"))) - (setenv "CLANG_INSTALL_DIR" llvm) - #t)))))) + (setenv "CLANG_INSTALL_DIR" llvm))))))) (home-page "https://wiki.qt.io/Qt_for_Python") (synopsis "Shiboken generates bindings for C++ libraries using CPython source code") @@ -3905,7 +3995,7 @@ color-related widgets.") ((#:phases p) #~(modify-phases #$p (replace 'use-shiboken-dir-only - (lambda _ (chdir "sources/shiboken6") #t)))) + (lambda _ (chdir "sources/shiboken6"))))) ((#:configure-flags flags) #~(cons* ;; The RUNPATH of shibokenmodule contains the entry in build @@ -3959,7 +4049,7 @@ color-related widgets.") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'go-to-source-dir - (lambda _ (chdir "sources/pyside2") #t)) + (lambda _ (chdir "sources/pyside2"))) (add-after 'go-to-source-dir 'fix-qt-module-detection (lambda _ ;; Activate qt module support even if it not in the same @@ -4054,7 +4144,7 @@ generate Python bindings for your C or C++ code.") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'go-to-source-dir - (lambda _ (chdir "sources/pyside6") #t)) + (lambda _ (chdir "sources/pyside6"))) (add-after 'go-to-source-dir 'fix-qt-module-detection (lambda _ (substitute* "cmake/PySideHelpers.cmake" @@ -4114,7 +4204,7 @@ generate Python bindings for your C or C++ code."))) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'go-to-source-dir - (lambda _ (chdir "sources/pyside2-tools") #t))))) + (lambda _ (chdir "sources/pyside2-tools")))))) (home-page "https://wiki.qt.io/Qt_for_Python") (synopsis "Command line tools for PySide2") @@ -4291,8 +4381,7 @@ and import their menus over DBus.") (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "ctest" "-E" ;; These tests try connect to the internet. - "(kdsoap-webcalls|kdsoap-webcalls_wsdl|kdsoap-test_calc)")) - #t))))) + "(kdsoap-webcalls|kdsoap-webcalls_wsdl|kdsoap-test_calc)"))))))) (home-page "https://www.kdab.com/development-resources/qt-tools/kd-soap/") (synopsis "Qt SOAP component") (description "KD SOAP is a tool for creating client applications for web @@ -4300,6 +4389,349 @@ services using the XML based SOAP protocol and without the need for a dedicated web server.") (license (list license:gpl2 license:gpl3)))) +(define-public libaccounts-qt + (package + (name "libaccounts-qt") + (version "1.16") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/accounts-sso/libaccounts-qt") + (commit (string-append "VERSION_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1vmpjvysm0ld8dqnx8msa15hlhrkny02cqycsh4k2azrnijg0xjz")))) + (build-system gnu-build-system) + (arguments + (list #:tests? #f ;TODO + #:phases + #~(modify-phases %standard-phases + (replace 'configure + (lambda _ + (substitute* "tests/tst_libaccounts.pro" + (("QMAKE_RPATHDIR = \\$\\$\\{QMAKE_LIBDIR\\}") + (string-append "QMAKE_RPATHDIR =" + #$output "/lib"))) + (invoke "qmake" + (string-append "PREFIX=" #$output) + (string-append "LIBDIR=" #$output "/lib"))))))) + ;; * SignOnQt5 (required version >= 8.55), D-Bus service which performs + ;; user authentication on behalf of its clients, + ;; <https://gitlab.com/accounts-sso/signond> + (native-inputs (list doxygen pkg-config qtbase-5 qttools-5)) + (inputs (list glib signond libaccounts-glib)) + (home-page "https://accounts-sso.gitlab.io/") + (synopsis "Qt5 bindings for libaccounts-glib") + (description + "Accounts SSO is a framework for application developers who +wish to acquire, use and store web account details and credentials. It +handles the authentication process of an account and securely stores the +credentials and service-specific settings.") + (license license:lgpl2.1+))) + +(define-public libsignon-glib + (package + (name "libsignon-glib") + (version "2.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/accounts-sso/libsignon-glib") + (commit (string-append "VERSION_" version)) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gnx9gqsh0hcfm1lk7w60g64mkn1iicga5f5xcy1j9a9byacsfd0")))) + (build-system meson-build-system) + (arguments + (list #:tests? #f ;TODO: ninja: no work to do. + #:imported-modules `((guix build python-build-system) + ,@%meson-build-system-modules) + #:modules '(((guix build python-build-system) + #:select (python-version)) + (guix build meson-build-system) + (guix build utils)) + #:configure-flags + #~(list "-Dtests=true" + (string-append "-Dpy-overrides-dir=" + #$output "/lib/python" + (python-version #$(this-package-input + "python")) + "/site-packages/gi/overrides")))) + (native-inputs (list dbus + dbus-test-runner + `(,glib "bin") + gobject-introspection + gtk-doc + pkg-config + vala)) + (inputs (list check signond python python-pygobject)) + (propagated-inputs (list glib)) + (home-page "https://accounts-sso.gitlab.io/libsignon-glib/") + (synopsis "Single signon authentication library for GLib applications") + (description + "This package provides single signon authentication library for +GLib applications.") + (license license:lgpl2.1+))) + +(define-public packagekit-qt5 + (package + (name "packagekit-qt5") + (version "1.0.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hughsie/PackageKit-Qt") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1d20r503msw1vix3nb6a8bmdqld7fj8k9jk33bkqsc610a2zsms6")))) + (build-system cmake-build-system) + (arguments '(#:tests? #f)) ;no test suite + (native-inputs (list pkg-config)) + (inputs (list packagekit qtbase-5)) + (home-page "https://www.freedesktop.org/software/PackageKit/pk-intro.html") + (synopsis "Qt5 bindings for PackageKit") + (description "Provides Qt5 bindings to PackageKit which is a DBUS +abstraction layer that allows the session user to manage packages in +a secure way.") + (license license:lgpl2.1+))) + +(define-public signond + (package + (name "signond") + (version "8.61") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/accounts-sso/signond") + (commit (string-append "VERSION_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0k6saz5spys4a4p6ws0ayrjks2gqdqvz7zfmlhdpz5axha0gbqq4")))) + (build-system qt-build-system) + (native-inputs (list doxygen pkg-config qtbase-5 qttools-5)) + (inputs (list dbus glib libaccounts-glib)) + (arguments + (list #:tests? #f ; Figure out how to run tests + #:phases + #~(modify-phases %standard-phases + (delete 'validate-runpath) + (replace 'configure + (lambda _ + (substitute* "src/signond/signond.pro" + (("/etc/") + (string-append #$output "/etc/"))) + (substitute* + '("tests/extensions/extensions.pri" + "tests/signond-tests/mock-ac-plugin/plugin.pro" + "tests/signond-tests/identity-tool.pro" + "tests/signond-tests/mock-ac-plugin/identity-ac-helper.pro" + "tests/libsignon-qt-tests/libsignon-qt-tests.pro" + "tests/signond-tests/signond-tests.pri") + (("QMAKE_RPATHDIR = \\$\\$\\{QMAKE_LIBDIR\\}") + (string-append "QMAKE_RPATHDIR = " + #$output "/lib:" + #$output "/lib/signon"))) + (invoke "qmake" + (string-append "PREFIX=" #$output) + (string-append "LIBDIR=" #$output "/lib"))))))) + (home-page "http://accounts-sso.gitlab.io/signond/index.html") + (synopsis "Perform user authentication over D-Bus") + (description "This package provides a D-Bus service which performs user +authentication on behalf of its clients.") + (license license:lgpl2.1+))) + +(define-public signon-plugin-oauth2 + (package + (name "signon-plugin-oauth2") + (version "0.25") + (home-page "https://gitlab.com/accounts-sso/signon-plugin-oauth2") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "VERSION_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16aslnyk8jdg03zcg97rp6qzd0gmclj14hyhliksz8jgfz1l0w7c")))) + (build-system qt-build-system) + (native-inputs (list doxygen pkg-config)) + (inputs (list signond)) + (arguments + (list #:tests? #f ;no tests + #:make-flags #~(list (string-append "INSTALL_ROOT=" #$output)) + #:phases + #~(modify-phases %standard-phases + (replace 'configure + (lambda _ + (substitute* "common-project-config.pri" + (("-Werror") + "")) + (invoke "qmake" + (string-append "PREFIX=" #$output) + (string-append "LIBDIR=" #$output "/lib"))))))) + (synopsis "OAuth 2 plugin for signon") + (description + "This plugin for the Accounts-SSO SignOn daemon handles the OAuth +1.0 and 2.0 authentication protocols.") + (license license:lgpl2.1+))) + +(define-public clazy + (package + (name "clazy") + (version "1.11") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/KDE/clazy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1y0n1jknq566z1rifkgdm1yqb0mw564lp51jidfz7q9w91spijci")))) + (build-system cmake-build-system) + (native-inputs (list python)) + (inputs (list clang llvm)) + (home-page "https://github.com/KDE/clazy/") + (synopsis "Qt-oriented static code analyzer") + (description "clazy is a compiler plugin which allows @command{clang} to +understand Qt semantics. It can emit more than fifty (50) Qt-related compiler +warnings, ranging from unneeded memory allocations to misuses of the API, +including @i{fix-its} for automatic refactoring.") + (license license:lgpl2.0+))) + +(define-public qt-creator + (package + (name "qt-creator") + (version "9.0.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://download.qt.io/official_releases/qtcreator/" + (version-major+minor version) "/" version + "/qt-creator-opensource-src-" version ".tar.gz")) + (modules '((guix build utils))) + (snippet '(begin + (for-each + delete-file-recursively + ;; Remove bundled libraries, where supported. + ;; TODO: package and unbundle litehtml + '("src/libs/3rdparty/yaml-cpp" + "src/shared/qbs/src/shared/qtscript/src/3rdparty" + "tests/unit/unittest/3rdparty" + ;; Marketplace recommends nonfree extensions; + ;; remove it. + "src/plugins/marketplace")) + (substitute* "src/plugins/CMakeLists.txt" + (("add_subdirectory\\(marketplace).*") "")) + (substitute* "src/plugins/plugins.qbs" + ((".*marketplace/marketplace.qbs.*") "")))) + (sha256 + (base32 + "1adyxs0cnqx14gwzkvh909c52449ia6y87n1r4qf6wwydhch43cs")))) + (build-system qt-build-system) + (arguments + (list + #:qtbase qtbase + #:configure-flags + #~(list "-DWITH_DOCS=ON" + "-DBUILD_DEVELOPER_DOCS=ON" + "-DCMAKE_VERBOSE_MAKEFILE=ON" + "-DWITH_TESTS=ON" + ;; Extend the RUNPATH with lib/qtcreator, which contains + ;; multiple shared objects. + (string-append "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath=" + #$output "/lib/qtcreator")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-tests-build + (lambda _ + ;; Add a missing link directive (see: + ;; https://bugreports.qt.io/browse/QTCREATORBUG-28434). + (substitute* "src/libs/tracing/CMakeLists.txt" + (("DEPENDS Utils Qt5::Qml Qt5::Quick") + "DEPENDS Utils Qt5::Quick") + (("PUBLIC_DEPENDS Qt5::Widgets") + "PUBLIC_DEPENDS Qt5::Widgets Qt5::Qml")))) + (add-after 'unpack 'patch-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("src/libs/utils/commandline.cpp" + "src/libs/utils/deviceshell.cpp") + (("/bin/sh") + (search-input-file inputs "bin/sh"))) + (substitute* "src/libs/utils/qtcprocess.cpp" + (("/usr/bin/env") + (search-input-file inputs "bin/env"))) + (substitute* "tests/auto/utils/qtcprocess/tst_qtcprocess.cpp" + (("/bin/sh") + (which "sh"))))) + (add-before 'build 'build-doc + (lambda _ + (invoke "cmake" "--build" "." "--target=docs" "-v"))) + (add-after 'build-doc 'install-doc + (lambda _ + (invoke "cmake" "--install" "." "--prefix" #$output + "--component=qch_docs") + (invoke "cmake" "--install" "." "--prefix" #$output + "--component=html_docs"))) + (replace 'check + ;; Loosely based on .github/workflows/build_cmake.yml. + (lambda* (#:key tests? parallel-tests? #:allow-other-keys) + (when tests? + (invoke "xvfb-run" ;for the 'renderpass' tests + "ctest" "-j" (if parallel-tests? + (number->string (parallel-job-count)) + "1") + "--label-exclude" "exclude_from_precheck" + "--exclude-regex" "tst_perfdata")))) + (add-after 'qt-wrap 'wrap-bin + ;; Make a few well-integrated tools readily available. + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (search-input-file outputs "bin/qtcreator") + `("PATH" suffix ,(map (lambda (c) + (dirname (search-input-file inputs c))) + '("bin/clang-tidy" + "bin/clazy-standalone" + "bin/gdb" + "bin/valgrind"))))))))) + (native-inputs + (list googletest + pkg-config + python + qttools + qttranslations + vulkan-headers + xvfb-run)) + (inputs + (list bash-minimal + coreutils-minimal + clang + clazy + elfutils + gdb + libxkbcommon + llvm + qt5compat + qtdeclarative + qtshadertools + qtsvg + yaml-cpp + valgrind + vulkan-loader + `(,zstd "lib"))) + (home-page "https://www.qt.io/") + (synopsis "Integrated development environment (IDE) for Qt") + (description "Qt Creator is an IDE tailored to the needs of Qt developers. +It includes features such as an advanced code editor, a visual debugger and a +@acronym{GUI, Graphical User Interface} designer.") + (license license:gpl3+))) ;with the Qt Company GPL Exception 1.0 + ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index e36dc55795..3834599cfc 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -175,7 +175,7 @@ used as a drop-in substitute for @code{libfec}.") (define-public liquid-dsp (package (name "liquid-dsp") - (version "1.4.0") + (version "1.5.0") (source (origin (method git-fetch) (uri (git-reference @@ -183,21 +183,25 @@ used as a drop-in substitute for @code{libfec}.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0mr86z37yycrqwbrmsiayi1vqrgpjq0pn1c3p1qrngipkw45jnn0")))) + (base32 "0m0bhj80rs9yhfwnrlx960lii1cqijz1wr8q93i7m2z91h3v3w0j")))) (build-system gnu-build-system) (native-inputs (list autoconf automake)) (inputs (list fftwf libfec)) (arguments - `(;; For reproducibility, disable use of SSE3, SSE4.1, etc. - #:configure-flags '("--enable-simdoverride") - #:phases - (modify-phases %standard-phases - (add-after 'install 'delete-static-library - (lambda* (#:key outputs #:allow-other-keys) - (delete-file (string-append (assoc-ref outputs "out") - "/lib/libliquid.a"))))))) + (list + ;; For reproducibility, disable use of SSE3, SSE4.1, etc. + #:configure-flags #~(list "--enable-simdoverride") + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'delete-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((version #$(version-major+minor + (package-version this-package)))) + (delete-file (string-append #$output + "/lib/libliquid.a." + version)))))))) (home-page "https://liquidsdr.org") (synopsis "Signal processing library for software-defined radios") (description diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index b53aa02ef3..9cf57a325a 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -194,7 +194,7 @@ a focus on simplicity and productivity.") (define ruby-2.7-fixed (package (inherit ruby-2.7) - (version "2.7.6") + (version "2.7.7") (source (origin (inherit (package-source ruby-2.7)) @@ -203,12 +203,12 @@ a focus on simplicity and productivity.") "/ruby-" version ".tar.gz")) (sha256 (base32 - "042xrdk7hsv4072bayz3f8ffqh61i8zlhvck10nfshllq063n877")))))) + "143vih5jzmrd2r5h94pa3qzml0ldii0qzs6g09jg6zqxd7djf0g1")))))) (define-public ruby-3.0 (package (inherit ruby-2.7) - (version "3.0.4") + (version "3.0.5") (source (origin (method url-fetch) @@ -217,7 +217,7 @@ a focus on simplicity and productivity.") "/ruby-" version ".tar.xz")) (sha256 (base32 - "1w7jpq3flnm007z5kj8kixgm8l4smb80w8ak4993a12j0irzq8lf")))) + "1pnxbdkkh2miq9nqfq2qscvh76nprzg0r620d9ckdzih42xbaz6g")))) (inputs (modify-inputs (package-inputs ruby-2.7) (replace "openssl" openssl))))) diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm index 4542bc1c88..3d8c07b813 100644 --- a/gnu/packages/sagemath.scm +++ b/gnu/packages/sagemath.scm @@ -170,27 +170,6 @@ represented as strings.") (license license:public-domain) (home-page "https://github.com/miguelmarco/libhomfly"))) -;; Sage 9.1 doesn't build with ECL 20. This won't be necessary once 9.2 is -;; released. See https://trac.sagemath.org/ticket/22191 -(define-public ecl-16 - (package - (inherit ecl) - (version "16.1.3") - (source - (origin - (method url-fetch) - (uri (string-append - "https://common-lisp.net/project/ecl/static/files/release/ecl" - "-" version ".tgz")) - (sha256 - (base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn")) - (patches (search-patches - "ecl-16-libffi.patch" - "ecl-16-ignore-stderr-write-error.patch" - "ecl-16-format-directive-limit.patch")))) - ;; Current ECL uses LGPL 2.1+ - (license license:lgpl2.0+))) - (define-public pynac (package (name "pynac") diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm index 307a0d4cb0..16099a4da7 100644 --- a/gnu/packages/security-token.scm +++ b/gnu/packages/security-token.scm @@ -891,7 +891,7 @@ phone is required.") (define-public libfido2 (package (name "libfido2") - (version "1.11.0") + (version "1.12.0") (source (origin (method git-fetch) @@ -899,21 +899,21 @@ phone is required.") (url "https://github.com/Yubico/libfido2") (commit version))) (file-name (git-file-name name version)) - (sha256 (base32 "1nk4irmdg36930lgc892qmlmd4whz4fq37wknkdx5ap57i5x18i6")))) + (sha256 (base32 "123rysl21bmgk6rmpgg5s21a5ksmxnn1hc32ws88h7z0q4icvj87")))) (native-inputs (list pkg-config)) (inputs (list eudev libcbor openssl zlib)) (build-system cmake-build-system) (arguments (list - #:configure-flags - #~(list (string-append - "-DPKG_CONFIG_EXECUTABLE=" - (search-input-file %build-inputs - (string-append - "/bin/" #$(pkg-config-for-target)))) - (string-append "-DUDEV_RULES_DIR=" #$output "/lib/udev/rules.d")) - ;; regress tests enabled only for debug builds - #:tests? #f)) + #:configure-flags + #~(list (string-append + "-DPKG_CONFIG_EXECUTABLE=" + (search-input-file %build-inputs + (string-append + "/bin/" #$(pkg-config-for-target)))) + (string-append "-DUDEV_RULES_DIR=" #$output "/lib/udev/rules.d")) + ;; regress tests enabled only for debug builds + #:tests? #f)) (synopsis "Library functionality and command-line tools for FIDO devices") (description "libfido2 provides library functionality and command-line tools to communicate with a FIDO device over USB, and to verify attestation diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 79c55e2b2f..8ab1efd311 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -578,27 +578,6 @@ object, without whitespace.") RPC system. Think JSON, except binary. Or think Protocol Buffers, except faster.") (license license:expat))) -(define-public libbson - (package - (name "libbson") - (version "1.6.2") - (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/mongodb/libbson/releases/" - "download/" version "/libbson-" version ".tar.gz")) - (sha256 - (base32 - "1fj4554msq0rrz14snbj908dzqj46gh7jg9w9j0akn2b7q911m5a")))) - (build-system gnu-build-system) - (native-inputs (list perl)) - (home-page "http://mongoc.org/libbson/current/index.html") - (synopsis "C BSON library") - (description "Libbson can create and parse BSON documents. It can also -convert JSON documents to BSON and the opposite. BSON stands for Binary JSON, -it is comparable to protobuf.") - (license license:asl2.0))) - (define-public python-ruamel.yaml (package (name "python-ruamel.yaml") diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2d4dbe4a31..6196d6bd69 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -206,7 +206,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.2.1") + (version "4.2.2") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -214,7 +214,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "0gv4di1x835i4nsy21vqw66c0blmmmvyjkixc5a8x117dm4dnljd")))) + "1x9xjl6fyzs8r72zigirp905ki50wzyw9rxf7iqsbbsixi12pxhg")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -310,7 +310,11 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ (("\\(2008\\)\n") "(2008) ") ((" ``Software") "``Software") (("Data Analysis:.") "Data Analysis:\n") - (("Programming with R") " Programming with R")))) + (("Programming with R") " Programming with R")) + (substitute* "src/library/tools/DESCRIPTION.in" + (("codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr") + "codetools, methods, xml2, curl, commonmark, + knitr, xfun, mathjaxr")))) (add-before 'build 'set-locales (lambda _ (setlocale LC_ALL "C") @@ -366,48 +370,48 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ;; As the JDK is a rather large input with only very limited effects on R, ;; we decided to drop it. (native-inputs - `(("bzip2" ,bzip2) - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("texinfo" ,texinfo) ; for building HTML manuals - ("texlive" ,(texlive-updmap.cfg (list texlive-ae - texlive-inconsolata - texlive-fonts-ec - texlive-grfext - texlive-amsfonts - texlive-latex-base - texlive-latex-fancyvrb - texlive-latex-graphics - texlive-hyperref - texlive-oberdiek - texlive-latex-tools - texlive-latex-upquote - texlive-url - texlive-latex-xkeyval))) - ("tzdata" ,tzdata-for-tests) - ("xz" ,xz))) + (list bzip2 + perl + pkg-config + texinfo ; for building HTML manuals + (texlive-updmap.cfg (list texlive-ae + texlive-inconsolata + texlive-fonts-ec + texlive-grfext + texlive-amsfonts + texlive-latex-base + texlive-latex-fancyvrb + texlive-latex-graphics + texlive-hyperref + texlive-oberdiek + texlive-latex-tools + texlive-latex-upquote + texlive-url + texlive-latex-xkeyval)) + tzdata-for-tests + xz)) (inputs - `(;; We need not only cairo here, but pango to ensure that tests for the - ;; "cairo" bitmapType plotting backend succeed. - ("pango" ,pango) - ("coreutils" ,coreutils) - ("curl" ,curl) - ("openblas" ,openblas) - ("gfortran" ,gfortran) - ("icu4c" ,icu4c) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libtiff" ,libtiff) - ("libxt" ,libxt) - ("pcre2" ,pcre2) - ("readline" ,readline) - ;; This avoids a reference to the ungraftable static bash. R uses the - ;; detected shell for the "system" procedure. - ("bash" ,bash-minimal) - ("tcl" ,tcl) - ("tk" ,tk) - ("which" ,which) - ("zlib" ,zlib))) + (list coreutils + curl + openblas + gfortran + icu4c + libjpeg-turbo + libpng + libtiff + libxt + ;; We need not only cairo here, but pango to ensure that tests for the + ;; "cairo" bitmapType plotting backend succeed. + pango + pcre2 + readline + tcl + tk + which + zlib + ;; This avoids a reference to the ungraftable static bash. R uses the + ;; detected shell for the "system" procedure. + bash-minimal)) (native-search-paths (list (search-path-specification (variable "R_LIBS_SITE") @@ -448,29 +452,23 @@ available, greatly increasing its breadth and scope.") (substitute* (string-append out "/lib/R/bin/libtool") (((string-append "(-L)?(" - (assoc-ref inputs "bzip2") - "|" - (assoc-ref inputs "perl") - "|" - (assoc-ref inputs "texlive") - "|" - (assoc-ref inputs "texlive-bin") - "|" - (assoc-ref inputs "texinfo") - "|" - (assoc-ref inputs "xz") - "|" (format #false - "/gnu/store/[^-]+-(~{~a~^|~})-[^/]+" - '("glibc-utf8-locales" + "~a/[^-]+-(~{~a~^|~})-[^/]+" + (%store-directory) + '("bzip2" + "file" + "glibc-utf8-locales" + "graphite2" "libselinux" "libsepol" - "file" + "perl" + "texinfo" "texlive-bin" "util-macros" - "graphite2")) + "xz")) "|" - "/gnu/store/[^-]+-glibc-[^-]+-static" + (format #false "~a/[^-]+-glibc-[^-]+-static" + (%store-directory)) ")/lib")) "")))))))))))) (define-public rmath-standalone @@ -1236,25 +1234,28 @@ using just two functions: melt and dcast (or acast).") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.3.6") + (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "1aa377jdfajj8ld2fh159y8havlibsr4pjisf6mkzk8g5awlxjxz")))) + (base32 "0gj7n2y8msnmhk3x4r481biknvn2dqhahwazfqwr8f3lz599wbx8")))) (build-system r-build-system) (propagated-inputs - (list r-digest + (list r-cli + r-digest r-glue r-gtable r-isoband + r-lifecycle r-mass r-mgcv r-tibble r-rlang r-scales r-svglite ; Needed for 'ggsave' + r-vctrs r-withr)) (native-inputs (list r-knitr)) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 81f74f17df..a600bcae58 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3993,6 +3993,47 @@ definitions.") (define-deprecated-package texlive-latex-amsmath texlive-amsmath) +(define-public texlive-mathdots + (let ((template + (simple-texlive-package + "texlive-mathdots" + (list "doc/generic/mathdots/" + "source/generic/mathdots/" + "tex/generic/mathdots/") + (base32"1jaffj343p1chdxs2g7s6lpckvihk0jfw22nw0vmijyjxfiy9yg0")))) + (package + (inherit template) + (outputs '("out" "doc")) + (arguments + (substitute-keyword-arguments (package-arguments template) + ((#:tex-directory _ '()) + "generic/mathdots") + ((#:build-targets _ '()) + '(list "mathdots.ins")) + ((#:phases phases) + #~(modify-phases #$phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "source/generic/mathdots"))) + (replace 'copy-files + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((origin (assoc-ref inputs "source")) + (source (string-append (assoc-ref outputs "out") + "/share/texmf-dist/source")) + (doc (string-append (assoc-ref outputs "doc") + "/share/texmf-dist/doc"))) + (copy-recursively (string-append origin "/source") source) + (copy-recursively (string-append origin "/doc") doc)))))))) + (home-page "https://ctan.org/macros/generic/mathdots") + (synopsis "Commands to produce dots in math that respect font size") + (description + "Mathdots redefines @code{\\ddots} and @code{\\vdots}, and defines +@code{\\iddots}. The dots produced by @code{\\iddots} slant in the opposite +direction to @code{\\ddots}. All the commands are designed to change size +appropriately in scripts, as well as in response to LaTeX size changing +commands. The commands may also be used in plain TeX.") + (license license:lppl)))) + (define-public texlive-amscls (let ((template (simple-texlive-package "texlive-amscls" diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index ed77113726..4d472575fa 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -49,6 +49,7 @@ #:use-module (guix build-system glib-or-gtk) #:use-module (guix build-system meson) #:use-module (guix build-system python) + #:use-module (guix build-system qt) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages aspell) @@ -59,6 +60,7 @@ #:use-module (gnu packages code) #:use-module (gnu packages cpp) #:use-module (gnu packages crates-io) + #:use-module (gnu packages curl) #:use-module (gnu packages datastructures) #:use-module (gnu packages documentation) #:use-module (gnu packages fontutils) @@ -494,7 +496,7 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings. e3 can be used on (define-public mg (package (name "mg") - (version "20220614") + (version "20221112") (source (origin (method git-fetch) (uri (git-reference @@ -503,7 +505,7 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings. e3 can be used on (file-name (git-file-name name version)) (sha256 (base32 - "145qk4bzys4igv98645vikswv9hqym46chh6xb9d82ihsvjq1wjk")) + "1wsib91f277xsx3qi8zmjcd9r9cm078rcf8hii0rwipyn04vxy83")) (modules '((guix build utils))) (snippet '(begin (substitute* "GNUmakefile" @@ -895,6 +897,39 @@ Octave. TeXmacs is completely extensible via Guile.") (license license:gpl3+) (home-page "https://www.texmacs.org/tmweb/home/welcome.en.html"))) +(define-public mogan + (package + (inherit texmacs) + (name "mogan") + (version "1.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/XmacsLabs/mogan") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "04wz6xmimjv2l6baxgzm8vyq5grg102m3l4wq8i6bglv529yp4ff")))) + (build-system qt-build-system) + (inputs + (modify-inputs (package-inputs texmacs) + ;; Replaced by S7 scheme + ;; TODO: Maybe unbundle S7 + (delete "guile") + (prepend curl))) + (arguments + (substitute-keyword-arguments (package-arguments texmacs) + ((#:phases orig) + #~(modify-phases #$orig + ;; The non-deterministic compression issue is solved in Mogan. + (delete 'gzip-flags))))) + (home-page "https://github.com/XmacsLabs/mogan") + (synopsis "Scientific structural text editor") + (description + "Mogan is a scientific structural text editor, a fork of GNU TeXmacs.") + (license license:gpl3+))) + (define-public textpieces (package (name "textpieces") diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 3aceb349bf..f1e844b608 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -995,47 +995,6 @@ correct OpenSSL include path. It is intended for use in your number generator") (license license:perl-license))) -(define-public acme-client - (package - (name "acme-client") - (version "0.1.16") - (source (origin - (method url-fetch) - (uri (string-append "https://kristaps.bsd.lv/" name "/" - "snapshots/" name "-portable-" - version ".tgz")) - (sha256 - (base32 - "00q05b3b1dfnfp7sr1nbd212n0mqrycl3cr9lbs51m7ncaihbrz9")))) - (build-system gnu-build-system) - (arguments - '(#:tests? #f ; no test suite - #:make-flags - (list "CC=gcc" - (string-append "PREFIX=" (assoc-ref %outputs "out"))) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-paths - (lambda* (#:key inputs #:allow-other-keys) - (let ((pem (search-input-file inputs "/etc/ssl/cert.pem"))) - (substitute* "http.c" - (("/etc/ssl/cert.pem") pem)) - #t))) - (delete 'configure)))) ; no './configure' script - (native-inputs - (list pkg-config)) - (inputs - (list libbsd libressl)) - (synopsis "Let's Encrypt client by the OpenBSD project") - (description "acme-client is a Let's Encrypt client implemented in C. It -uses a modular design, and attempts to secure itself by dropping privileges and -operating in a chroot where possible. acme-client is developed on OpenBSD and -then ported to the GNU / Linux environment.") - (home-page "https://kristaps.bsd.lv/acme-client/") - ;; acme-client is distributed under the ISC license, but the files 'jsmn.h' - ;; and 'jsmn.c' are distributed under the Expat license. - (license (list license:isc license:expat)))) - ;; The "-apache" variant is the upstreamed prefered variant. A "-gpl" ;; variant exists in addition to the "-apache" one. (define-public mbedtls-apache diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index c394c65442..70a9cd4033 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2242,6 +2242,7 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.") libxext libxkbcommon libxinerama + libxpresent libxrandr libxscrnsaver libxv @@ -2529,7 +2530,7 @@ YouTube.com and many more sites.") (define-public yt-dlp (package/inherit youtube-dl (name "yt-dlp") - (version "2022.10.04") + (version "2022.11.11") (source (origin (method git-fetch) @@ -2538,7 +2539,7 @@ YouTube.com and many more sites.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0g2nvslzb9yx2axv6yqxdcdh49ckyipyy9apx1lx6bg6y9rjvx6v")))) + (base32 "00dng4x7xbxp6w76dqkfzzhf2dh3s9pgfd0axs7qar20clj717py")))) (arguments (substitute-keyword-arguments (package-arguments youtube-dl) ((#:tests? _) (not (%current-target-system))) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index 957f00a92e..9a4a2ce235 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -78,7 +78,7 @@ (define-public vim (package (name "vim") - (version "9.0.0820") + (version "9.0.0954") (source (origin (method git-fetch) (uri (git-reference @@ -87,7 +87,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "00zl1g4m6hcwzdla2m770wcq3p5amh3pr7y88hi852x8dn74gssp")))) + "098fiqw6hz0cc5zzy934alqxgwp01180vz3v9wm9i6x6fhdnhxxn")))) (build-system gnu-build-system) (arguments `(#:test-target "test" diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index 31885fcbe0..a2d6e399e9 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -705,7 +705,7 @@ is fully configurable and extensible in Common Lisp.") (define-public lagrange (package (name "lagrange") - (version "1.13.8") + (version "1.14.1") (source (origin (method url-fetch) @@ -713,7 +713,7 @@ is fully configurable and extensible in Common Lisp.") (string-append "https://git.skyjake.fi/skyjake/lagrange/releases/" "download/v" version "/lagrange-" version ".tar.gz")) (sha256 - (base32 "1l6cfvmmw2g30qsxmn5jma17kxgmfknlgji4pbdj1flv8p73bvza")) + (base32 "0dhynq5pn6xjis0bpnam89km9qbrdxkbv76mfsx6jzda934iyy2n")) (modules '((guix build utils))) (snippet '(begin diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index d2c406915c..61e1d1f1bc 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -5847,13 +5847,13 @@ deployments.") (package (name "varnish") (home-page "https://varnish-cache.org/") - (version "7.1.1") + (version "7.2.1") (source (origin (method url-fetch) (uri (string-append home-page "_downloads/varnish-" version ".tgz")) (sha256 (base32 - "14512fjjzwini3fics6sib9y83s45vlrpncamixqmmg7j0jvxbrc")))) + "0h590kr7rhp57a4kfx6apyvqk60w78qdjwpr6g2ikv5840bpv4sd")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list (string-append "LDFLAGS=-Wl,-rpath=" %output "/lib") diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index 73338c73b3..083cf27212 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -77,7 +77,7 @@ in downloaded documents to relative links.") (define-public wgetpaste (package (name "wgetpaste") - (version "2.32") + (version "2.33") (source (origin (method git-fetch) @@ -86,7 +86,7 @@ in downloaded documents to relative links.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "13zdqfnbpymwz2f04icw92flj50227n5r0dcms84qxswfxrarnas")))) + (base32 "0gx5y3f0qf3hrah1z0q243hyldshaq6mvbg1lnjzciviv1vc8zx0")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 298e6f3e47..9cc7cc652a 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -516,7 +516,12 @@ avoiding password prompts when X11 forwarding has already been setup.") wayland-protocols xkeyboard-config)) (native-inputs - (list bison doxygen pkg-config python)) + (append (list bison doxygen pkg-config python) + (if (%current-target-system) + ;; wayland-scanner is required at build time. + ;; TODO: Remove this conditional on core-updates. + (list pkg-config-for-build wayland) + '()))) (arguments `(#:configure-flags (list (string-append "-Dxkb-config-root=" @@ -1140,19 +1145,19 @@ transparent text on your screen.") (define-public wob (package (name "wob") - (version "0.13") + (version "0.14.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/francma/wob/releases/download/" version "/wob-" version ".tar.gz")) (sha256 - (base32 "0i8y6kq37qcgdq85ll4rapisjl7zw6aa11yx2f2xw2d3j93kdxh8")))) + (base32 "12s9pc0dhqgawq6jiqhamj1zq9753kgpswny1rcsdx1lkpzrgaq1")))) (build-system meson-build-system) (native-inputs (list pkg-config scdoc)) (inputs - (list libseccomp wayland wayland-protocols)) + (list libinih libseccomp wayland wayland-protocols)) (home-page "https://github.com/francma/wob") (synopsis "Lightweight overlay bar for Wayland") (description diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index 6840867612..720a36e3b9 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -681,7 +681,7 @@ allows you to shut down the computer from Xfce.") (define-public xfce4-settings (package (name "xfce4-settings") - (version "4.16.4") + (version "4.16.5") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/xfce/" @@ -689,7 +689,7 @@ allows you to shut down the computer from Xfce.") name "-" version ".tar.bz2")) (sha256 (base32 - "1vd3l20myjfbq53x8sywy989zd557adyv3bb2y0nhh2is8ps9aqq")) + "13nj80mshkz3czrp8l1yxj6qmz0kkfhzv94z3ixfgmw64j078kvs")) (patches (search-patches "xfce4-settings-defaults.patch")))) (build-system gnu-build-system) (arguments @@ -1335,7 +1335,7 @@ of data to either CD/DVD/BD.") (define-public xfce4-screenshooter (package (name "xfce4-screenshooter") - (version "1.9.11") + (version "1.10.0") (source (origin (method url-fetch) (uri (string-append "https://archive.xfce.org/src/apps/" @@ -1345,7 +1345,7 @@ of data to either CD/DVD/BD.") version ".tar.bz2")) (sha256 (base32 - "1d7qyc2w4962crmkz5n0mma2qmyp9hhq455karyzacjbb6z0cgg7")))) + "0lvv6iam348n7l3md94lanxyyn87xmrivzdvfi0fa3vgjfk88j56")))) (build-system gnu-build-system) (native-inputs (list pkg-config intltool diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index a6b7b71d1d..7767a35afe 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -1217,7 +1217,7 @@ hit when running single-threaded.") "1p0flwb67xawyv6yhri9w17m1i4lji5qnd0gq8v1vsfb8zw7rw15")))) (build-system gnu-build-system) (inputs - (list xorgproto libxext libx11)) + (list xorgproto libxext libx11 windowswmproto)) (native-inputs (list pkg-config)) (home-page "https://www.x.org/wiki/") |