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2021-11-18gnu: r-rsubread: Update to 2.8.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.8.1.
2021-11-18gnu: r-geoquery: Update to 2.62.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-geoquery): Update to 2.62.1. [propagated-inputs]: Add r-r-utils.
2021-11-18gnu: r-icobra: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-icobra): Update to 1.22.1.
2021-11-18gnu: r-ggtree: Update to 3.2.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ggtree): Update to 3.2.1.
2021-11-18gnu: r-treeio: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-treeio): Update to 1.18.1.
2021-11-18gnu: r-systempiper: Update to 2.0.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.0.1.
2021-11-18gnu: r-msnbase: Update to 2.20.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msnbase): Update to 2.20.1.
2021-11-18gnu: r-ensembldb: Update to 2.18.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.18.2.
2021-11-18gnu: r-chipseeker: Update to 1.30.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.30.2.
2021-11-18gnu: r-annotationdbi: Update to 1.56.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.56.2.
2021-11-18tests: Replace texlive importer tests.Ricardo Wurmus
* tests/texlive.scm (xml, sxml): Remove variables. ("fetch-sxml: returns SXML for valid XML", "sxml->package"): Remove tests. ("texlive->guix-package"): Add new test.
2021-11-18import: texlive: Take different package database as optional argument.Ricardo Wurmus
* guix/import/texlive.scm (tlpdb->package): Expect PACKAGE-DATABASE as argument. (texlive->guix-package): Accept PACKAGE-DATABASE keyword.
2021-11-18import: texlive: Print inputs with labels and guixified names.Ricardo Wurmus
* guix/import/texlive.scm (tlpdb->package): Improve handling of propagated-inputs.
2021-11-18gnu: wireshark: Update to 3.4.10.Nicolas Goaziou
* gnu/packages/networking.scm (wireshark): Update to 3.4.10.
2021-11-18gnu: emacs-elfeed-score: Update to 1.2.0.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-elfeed-score): Update to 1.2.0.
2021-11-18gnu: coq-stdpp: Adjust '#:make-flags'.zimoun
* gnu/packages/coq.scm (coq-stdpp)[arguments]<#:make-flags>: Set install destination. <#:phases>: Remove replace 'install. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
2021-11-18gnu: coq-equations: Adjust '#:make-flags'.zimoun
* gnu/packages/coq.scm (coq-equations)[arguments]<#:make-flags>: Set install destination. <#:phases>: Remove replace 'install. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
2021-11-18gnu: coq-autosubst: Adjust '#:make-flags'.zimoun
* gnu/packages/coq.scm (coq-autosubst)[arguments]<#:make-flags>: Set install destination. <#:phases>: Remove replace 'install. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
2021-11-18gnu: coq-mathcomp: Adjust '#:make-flags'.zimoun
* gnu/packages/coq.scm (coq-mathcomp)[arguments]<#:make-flags>: Set install destination. <#:phases>: Remove replace 'install. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
2021-11-18gnu: Add coq-semantics.zimoun
* gnu/packages/coq.scm (coq-semantics): New variable. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
2021-11-17gnu: perl-tie-handle-offset: Fix typo.Vagrant Cascadian
* gnu/packages/perl.scm (perl-tie-handle-offset)[description]: Fix "This module" typo.
2021-11-17gnu: perl-business-ismn: Fix typo.Vagrant Cascadian
* gnu/packages/perl.scm (perl-business-ismn)[description]: Fix "This module" typo.
2021-11-17gnu: perl-business-issn: Fix typo.Vagrant Cascadian
* gnu/packages/perl.scm (perl-business-issn)[description]: Fix "This module" typo.
2021-11-17gnu: perl-business-isbn: Fix typo.Vagrant Cascadian
* gnu/packages/perl.scm (perl-business-isbn)[description]: Fix "This module" typo.
2021-11-17gnu: perl-test-dir: Fix typo.Vagrant Cascadian
* gnu/packages/perl-check.scm (perl-test-dir)[description]: Fix "This module" typo.
2021-11-17gnu: python-sgmllib3k: Fix typo.Vagrant Cascadian
* gnu/packages/python-xyz.scm (python-sgmllib3k)[description]: Fix "This package" typo.
2021-11-17gnu: rust-fever-api-0.2: Fix typo.Vagrant Cascadian
* gnu/packages/crates-io.scm (rust-fever-api-0.2)[description]: Fix "This package" typo.
2021-11-17gnu: perl-test-nowarnings: Fix typo.Vagrant Cascadian
* gnu/packages/perl-check.scm (perl-test-nowarnings)[description]: Fix "This module" typo.
2021-11-18gnu: foo2zjs: Use archived home page.Tobias Geerinckx-Rice
* gnu/packages/cups.scm (foo2zjs)[home-page]: Link to the Web Archive'd URL.
2021-11-18gnu: sg3-utils: Omit static library.Tobias Geerinckx-Rice
* gnu/packages/scsi.scm (sg3-utils)[arguments]: Add "--disable-static" to #:configure-flags.
2021-11-18gnu: sg3-utils: Update to 1.47.Tobias Geerinckx-Rice
* gnu/packages/scsi.scm (sg3-utils): Update to 1.47.
2021-11-17gnu: ungoogled-chromium: Update to 96.0.4664.45-0.Marius Bakke
* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for M96. (%chromium-version): Set to 96.0.4664.45. (%ungoogled-origin, ungoogled-chromium): Update hashes.
2021-11-17gnu: libtorrent-rasterbar: Update to 1.2.14.Marius Bakke
* gnu/packages/bittorrent.scm (libtorrent-rasterbar): Update to 1.2.14. [source](uri): Adjust tag name. [build-system]: Change to CMAKE-BUILD-SYSTEM. [arguments]: Adjust accordingly. Override the check phase to fake the time for one test, and disable another. [native-inputs]: Add LIBFAKETIME.
2021-11-17gnu: Add rcs-blame.Foo Chuan Wei
* gnu/packages/version-control.scm (rcs-blame): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17gnu: rcs: Install rcsfreeze.Foo Chuan Wei
* gnu/packages/version-control.scm (rcs): Install rcsfreeze. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17gnu: system: Improve location of some configuration warnings.Josselin Poiret
* gnu/bootloader.scm (%warn-target-field-deprecation): Remove it. * gnu/bootloader.scm (warn-target-field-deprecation): Use define-with-syntax-properties. * gnu/system.scm (ensure-setuid-program-list): Ditto. Also rename the 'location' variable to 'properties'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17diagnostics: Add syntax to capture arguments' syntax-properties.Josselin Poiret
* guix/diagnostics.scm (define-with-syntax-properties): Add it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17doc: Improve wording for param spec of `./configure`.Rostislav Svoboda
* doc/contributing.texi (Running Guix Before It Is Installed): Writing "Do <this>. But it won't work unless ..." is a bad practice. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17gnu: tidy-html: Update to 5.8.0.Philip McGrath
* gnu/packages/web.scm (tidy-html): Update to 5.8.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17scripts: home: Make ‘guix home import’ write home-configuration.scm.Xinglu Chen
* guix/scripts/home.scm (process-command): Populate ‘home-configuration.scm’ in the destination directory instead of printing to stdout. * doc/guix.texi (Declaring the Home Environment): Adjust accordingly. (Invoking guix home): Likewise. Suggested-by: Ludovic Courtès <ludo@gnu.org> Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17gnu: xfce4-whiskermenu-plugin: Update to 2.6.1.Michael Rohleder
* gnu/packages/xfce.scm (xfce4-whiskermenu-plugin): Update to 2.6.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17gnu: ristretto: Update to 0.12.0.Michael Rohleder
* gnu/packages/xfce.scm (ristretto): Update to 0.12.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17gnu: xfce4-cpugraph-plugin: Update to 1.2.5.Michael Rohleder
* gnu/packages/xfce.scm (xfce4-cpugraph-plugin): Update to 1.2.5. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17gnu: shellcheck: Update to 0.8.0.jgart
* gnu/packages/haskell-apps.scm (shellcheck): Update to 0.8.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17gnu: perl-inline-c: Patch paths to ‘make’.Xinglu Chen
* gnu/packages/perl.scm (perl-inline-c)[arguments]<#:phases>{patch-paths}: New phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17services: docker: Add 'environment-variables' configuration field.Alexey Abramov
* gnu/services/docker.scm (docker-configuration): Add the field (docker-shepherd-service): Pass the list of defined variables to make-forkexec-constructor. * doc/guix.texi (Miscellaneous Services): Update doc. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-11-17gnu: perl-log-message: Fix typo.Vagrant Cascadian
* gnu/packages/perl.scm (perl-log-message)[description]: Correctly use "lets you".
2021-11-17gnu: emacs-eldev: Update to 0.10.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-eldev): Update to 0.10. [arguments]: Enable some tests, disable some others. Remove #t at the end of phases.
2021-11-17gnu: home: services: Fix typo.Vagrant Cascadian
* gnu/home/services.scm (compute-on-first-login-script): Fix spelling of "appropriate".
2021-11-17gnu: python-numcodecs: Unbundle c-blosc.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-numcodecs)[source]: Add snippet to remove bundled c-blosc sources and pre-built Cython files. [arguments]: Add build phase 'disable-avx2 and 'unbundle; replace 'check phase to run pytest; disable tests. [inputs]: Add c-blosc, lz4, zlib, and zstd. [native-inputs]: Add python-cython.
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