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2023-06-06gnu: Add python-decoupler-py.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-decoupler-py): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
2023-06-06gnu: icecat: Update to 102.12.0-guix0-preview1 [security fixes].Mark H Weaver
Includes fixes for CVE-2023-34414 and CVE-2023-34416. * gnu/packages/gnuzilla.scm (%icecat-base-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes.
2023-06-06gnu: nim: Update to 1.6.12.Gruruya
Without the attached patch, Nim is broken on Guix as it searches for its stdlib in /lib while it was placed in /lib/nim. * gnu/packages/nim.scm (nim): Update to 1.6.12. [arguments]: In 'patch-installer phase install stdlib source to the right directory. In 'patch-more-shebangs phase edit substitute* to point to the new osproc source. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-06services: Check if service is #f before applying clause.Josselin Poiret
* gnu/services.scm (apply-clauses): Check if service is #f before trying to apply clause. Follow up of 181951207339508789b28ba7cb914f983319920f.
2023-06-06gnu: python-anaconda-client: Fix build with Python 3.10.Ricardo Wurmus
* gnu/packages/package-management.scm (python-anaconda-client)[build-system]: Use pyproject-bulid-system. [arguments]: Move contents of 'remove-network-tests phase to #:test-flags; drop trailing #T from 'set-HOME phase; add phase 'python3.10-compatibility; disable test_conda_root and test_conda_root_outside_root_environment.
2023-06-06gnu: Add r-caretensemble.Navid Afkhami
* gnu/packages/cran.scm (r-caretensemble): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-06services: 'modify-services' preserves service ordering.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/63921>. The regression was introduced in dbbc7e946131ba257728f1d05b96c4339b7ee88b, which changed the order of services. As a result, someone using 'modify-services' could find themselves with incorrect ordering of expressions in the "boot" script, whereby the cleanup expressions would come after (execl ".../shepherd"). This, in turn, would lead shepherd to error out at boot with EADDRINUSE on /var/run/shepherd/socket. * gnu/services.scm (%delete-service, %apply-clauses): Remove. (clause-alist): New macro. (apply-clauses): New procedure. (modify-services): Use it. Adjust docstring. * tests/services.scm ("modify-services: do nothing"): Remove 'sort' call. ("modify-services: delete service"): Likewise, and add 't4' service. ("modify-services: change value"): Remove 'sort' call and fix expected value.
2023-06-06records: Use SRFI-11 instead of SRFI-71, for Guile 2.0 compatibility.Ludovic Courtès
This fixes a failure of 'tests/packages.scm' introduced in b88e38d4b51b9aa0e857baeb614c000e491ad309: some of the tests import (guix records) on the build side, which uses '%bootstrap-guile' (Guile 2.0) where SRFI-71 is unavailable. * guix/records.scm (match-record-inner): Use SRFI-11 instead of SRFI-71.
2023-06-06doc: Add missing node to the main menu.Ludovic Courtès
This is a followup to 110462bb2f1678fb0147a5845b2b48d0566ce0b4. * doc/guix.texi (Top): Add "Mail Home Services" to the menu.
2023-06-06gnu: sbcl-stmx: Update to 2.0.5-2.f71e742.Guillaume Le Vaillant
* gnu/packages/lisp-xyz.scm (sbcl-stmx): Update to 2.0.5-2.f71e742. [arguments]: Add 'fix-build' phase.
2023-06-06gnu: txr: Update to 287.Guillaume Le Vaillant
* gnu/packages/lisp.scm (txr): Update to 287.
2023-06-06gnu: sbcl: Update to 2.3.5.Guillaume Le Vaillant
* gnu/packages/lisp.scm (sbcl): Update to 2.3.5.
2023-06-06gnu: openocd: Update to 0.12.0.Jean-Pierre De Jesus DIAZ
* gnu/packages/embedded.scm (openocd): Update to 0.12.0. [inputs]: Remove libusb-compat as openocd dropped support for libusb0. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-06gnu: jimtcl: Update to 0.82.Jean-Pierre De Jesus DIAZ
* gnu/packages/embedded (jimtcl): Update to 0.82. [arguments]: Use G-Expressions and update failing test, TTY test doesn't fail anymore. [inputs]: Add openssl as an input as now by default jimtcl enables the SSL configuration option. * gnu/packages/embedded (openocd): Support jimtcl 0.82. [arguments]: Link against libssl and libcrypto. [inputs]: Add openssl. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-06gnu: libjaylink: Update to 0.3.1.Jean-Pierre De Jesus DIAZ
* gnu/packages/embedded (libjaylink): Update to 0.3.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-06gnu: thc-ipv6: Do not build with "-march=native".Z572
* gnu/packages/networking.scm (thc-ipv6)[origin]: Add 'snippet'. [properties]: New field. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-05gnu: linux-libre 5.4: Update to 5.4.245.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.245. (linux-libre-5.4-pristine-source): Update hash.
2023-06-05gnu: linux-libre 5.10: Update to 5.10.182.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.182. (linux-libre-5.10-pristine-source): Update hash.
2023-06-05gnu: linux-libre 5.15: Update to 5.15.115.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.115. (linux-libre-5.15-pristine-source): Update hash.
2023-06-05gnu: linux-libre 6.1: Update to 6.1.32.Leo Famulari
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.32. (linux-libre-6.1-pristine-source): Update hash.
2023-06-05gnu: linux-libre: Update to 6.3.6.Leo Famulari
* gnu/packages/linux.scm (linux-libre-6.3-version): Update to 6.3.6. (linux-libre-6.3-pristine-source): Update hash.
2023-06-05gnu: blurhash: Update to 0.2.0.Efraim Flashner
* gnu/packages/image.scm (blurhash): Update to 0.2.0. [native-inputs]: Remove cmake. Add pkg-config.
2023-06-05gnu: cpp-httplib: Update to 0.12.5.Efraim Flashner
* gnu/packages/cpp.scm (cpp-httplib): Update to 0.12.5. [arguments]: Adjust configure-flags to build the tests. Add a make-flag to set CXX. Adjust custom 'disable-network-tests phase to skip more network tests. Remove custom 'check phase. [native-inputs]: Add googletest.
2023-06-05doc: Fix some typos in the manual.Efraim Flashner
* doc/guix.texi (Invoking guix pull): Correct followings to following. (Using Guix Interactively): Correct expresssion to expression. (Base Services): Correct overriden to overridden. (Audio Services): Correct Supress to Suppress. (Setuid Programs): Correct goup to group. (Essential Home Services): Correct apropiate to appropriate, similiar to similar. (Messaging Home Services): Correct seperately to separately. (image Reference): Correct instanciated to instantiated. (Full-Source Bootstrap): Correct udpate to update, Frome to From.
2023-06-05gnu: python-codespell: Update to 2.2.4.Efraim Flashner
* gnu/packages/python-xyz.scm (python-codespell): Update to 2.2.4. [build-system]: Switch to pyproject-build-system. [native-inputs]: Remove python-check-manifest; add python-pygments and python-tomli.
2023-06-05doc: cookbook: Update example my-libgit2 package.Efraim Flashner
* doc/guix-cookbook.texi (Packaging Tutorial): Improve the code quality of the example my-libgit2 package.
2023-06-05import/cran: Ensure current package is not among inputs.Ricardo Wurmus
* guix/import/cran.scm (cran-package-inputs): Remove the current package from the result.
2023-06-05gnu: proj-7: Add upstream patch.Ricardo Wurmus
* gnu/packages/patches/proj-7-initialize-memory.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/geo.scm (proj-7)[source]: Add it.
2023-06-05gnu: python-bulkvis: Reference upstream issue.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bulkvis)[arguments]: Add comment with link to upstream issue for bokeh compatibility patch.
2023-06-05gnu: python-tenacity: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-tenacity)[build-system]: Use pyproject-build-system. [arguments]: Remove.
2023-06-05gnu: python-tenacity: Use Tornado 6.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-tenacity)[native-inputs]: Replace python-tornado with python-tornado-6.
2023-06-05gnu: python-bokeh: Use Tornado 6.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-bokeh)[propagated-inputs]: Replace python-tornado with python-tornado-6.
2023-06-05gnu: Add python-bulkvis.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-bulkvis): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-05gnu: Add python-readpaf.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-readpaf): New variable.
2023-06-05gnu: gcompris-qt: Update to 3.2.Efraim Flashner
* gnu/packages/education.scm (gcompris-qt): Update to 3.2. [inputs]: Add qtcharts, qtquickcontrols2-5. Remove qtquickcontrols-5, qtxml-5.
2023-06-05gnu: mupdf: Update to 1.22.1.Timotej Lazar
* gnu/packages/pdf.scm (mupdf): Update to 1.22.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04gnu: lagrange: Update to 1.16.3.Efraim Flashner
* gnu/packages/web-browsers.scm (lagrange): Update to 1.16.3.
2023-06-04gnu: keepassxc: Update to 2.7.5.Efraim Flashner
* gnu/packages/password-utils.scm (keepassxc): Update to 2.7.5.
2023-06-04gnu: urlscan: Update to 1.0.0.Efraim Flashner
* gnu/packages/mail.scm (urlscan): Update to 1.0.0. [arguments]: Skip the test phase. [build-system]: Switch to the pyproject-build-system. [native-inputs]: Add python-hatch-vcs, python-hatchling.
2023-06-04gnu: tree: Update to 2.1.1.Efraim Flashner
* gnu/packages/admin.scm (tree): Update to 2.1.1. [arguments]: Remove unneeded 'fix-manpage-version phase.
2023-06-04gnu: jpegoptim: Fix cross-compiling to riscv64.Zheng Junjie
* gnu/packages/image.scm (jpegoptim)[arguments]: When cross-compiling t riscv64, add phase to update-config-scripts. [native-inputs]: When cross-compiling to riscv64, add config. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04gnu: libicns: Fix cross-compiling to riscv64.Zheng Junjie
* gnu/packages/image.scm (libicns)[arguments]: When cross-compiling to riscv64, add phase to update-config-scripts. [native-inputs]: When cross-compiling to riscv64, add config. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04gnu: gsettings-desktop-schemas: Fix cross-compiling.Zheng Junjie
* gnu/packages/gnome.scm(gsettings-desktop-schemas)[inputs]: Add gobject-introspection. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04gnu: gobject-introspection: Fix cross-compiling.Zheng Junjie
* gnu/packages/glib.scm(gobject-introspection)[native-inputs]: When cross-compiling add python. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04gnu: mtdev: Fix cross-compiling to riscv64.Zheng Junjie
* gnu/packages/xdisorg.scm (mtdev)[arguments]: When cross-compiling to riscv64 add a phase to update config.{guess,sub}. [native-inputs]: When cross-compiling to riscv64 add config.
2023-06-04gnu: xcb-util-wm: Fix cross-compiling to riscv64.Zheng Junjie
* gnu/packages/xorg.scm (xcb-util-wm)[arguments]: Add update-config-scripts phase when cross-compiling to riscv64. [native-inputs]: Add config when cross-compiling to riscv64. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04gnu: libxtst: Fix cross-compiling to riscv64.Zheng Junjie
* gnu/packages/xorg.scm (libxtst)[arguments]: When cross-compiling to riscv64, add phase to update config.{guess,sub}. [native-inputs]: When cross-compiling to riscv64, add config. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-04gnu: libdeflate: Use default tests.Efraim Flashner
* gnu/packages/compression.scm (libdeflate)[arguments]: Adjust configure-flags to build the test suite. Remove custom 'check phase.
2023-06-04channels: Raise an error if dependency's introduction is malformedJosselin Poiret
* guix/channels.scm (sexp->channel-introduction): Do it.
2023-06-04gnu: agda-ial: Update to ded30c410d5d40142249686572aa1acd1b2f8cc7.Josselin Poiret
* gnu/packages/agda.scm (agda-ial): Update to ded30c410d5d40142249686572aa1acd1b2f8cc7, use agda-build-system, switch to G-Exps, reorder fields.
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