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2023-04-29gnu: r-annmap: Update to 1.42.0....* gnu/packages/bioconductor.scm (r-annmap): Update to 1.42.0. Ricardo Wurmus
2023-04-29gnu: r-anf: Update to 1.22.0....* gnu/packages/bioconductor.scm (r-anf): Update to 1.22.0. Ricardo Wurmus
2023-04-29gnu: r-aneufinder: Update to 1.28.0....* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.28.0. [propagated-inputs]: Remove r-reordercluster. Ricardo Wurmus
2023-04-29gnu: r-altcdfenvs: Update to 2.62.0....* gnu/packages/bioconductor.scm (r-altcdfenvs): Update to 2.62.0. Ricardo Wurmus
2023-04-29gnu: r-alpsnmr: Update to 4.2.0....* gnu/packages/bioconductor.scm (r-alpsnmr): Update to 4.2.0. Ricardo Wurmus
2023-04-29gnu: r-alpine: Update to 1.25.0....* gnu/packages/bioconductor.scm (r-alpine): Update to 1.25.0. Ricardo Wurmus
2023-04-29gnu: r-alphabeta: Update to 1.14.0....* gnu/packages/bioconductor.scm (r-alphabeta): Update to 1.14.0. Ricardo Wurmus
2023-04-29gnu: r-alevinqc: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.16.0. Ricardo Wurmus
2023-04-29gnu: r-aldex2: Update to 1.32.0....* gnu/packages/bioconductor.scm (r-aldex2): Update to 1.32.0. Ricardo Wurmus
2023-04-29gnu: r-anvil: Update to 1.12.0....* gnu/packages/bioconductor.scm (r-anvil): Update to 1.12.0. Ricardo Wurmus
2023-04-29gnu: r-annotationhubdata: Update to 1.30.0....* gnu/packages/bioconductor.scm (r-annotationhubdata): Update to 1.30.0. Ricardo Wurmus
2023-04-29gnu: r-animalcules: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-animalcules): Update to 1.16.0. Ricardo Wurmus
2023-04-29gnu: r-ancombc: Update to 2.2.0....* gnu/packages/bioconductor.scm (r-ancombc): Update to 2.2.0. Ricardo Wurmus
2023-04-29gnu: r-anaquin: Update to 2.24.0....* gnu/packages/bioconductor.scm (r-anaquin): Update to 2.24.0. Ricardo Wurmus
2023-04-29gnu: r-amaretto: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-amaretto): Update to 1.16.0. Ricardo Wurmus
2023-04-29gnu: r-amplican: Update to 1.21.0....* gnu/packages/bioconductor.scm (r-amplican): Update to 1.21.0. Ricardo Wurmus
2023-04-29gnu: r-amountain: Update to 1.26.0....* gnu/packages/bioconductor.scm (r-amountain): Update to 1.26.0. Ricardo Wurmus
2023-04-29gnu: r-airpart: Update to 1.8.0....* gnu/packages/bioconductor.scm (r-airpart): Update to 1.8.0. Ricardo Wurmus
2023-04-29gnu: r-aims: Update to 1.32.0....* gnu/packages/bioconductor.scm (r-aims): Update to 1.32.0. Ricardo Wurmus
2023-04-29gnu: r-agimicrorna: Update to 2.50.0....* gnu/packages/bioconductor.scm (r-agimicrorna): Update to 2.50.0. Ricardo Wurmus
2023-04-29gnu: r-adductomicsr: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-adductomicsr): Update to 1.16.0. Ricardo Wurmus
2023-04-29gnu: r-agilp: Update to 3.32.0....* gnu/packages/bioconductor.scm (r-agilp): Update to 3.32.0. Ricardo Wurmus
2023-04-29gnu: r-aggregatebiovar: Update to 1.10.0....* gnu/packages/bioconductor.scm (r-aggregatebiovar): Update to 1.10.0. Ricardo Wurmus
2023-04-29gnu: r-agdex: Update to 1.48.0....* gnu/packages/bioconductor.scm (r-agdex): Update to 1.48.0. Ricardo Wurmus
2023-04-29gnu: r-affyrnadegradation: Update to 1.46.0....* gnu/packages/bioconductor.scm (r-affyrnadegradation): Update to 1.46.0. Ricardo Wurmus
2023-04-29gnu: r-affyplm: Update to 1.76.0....* gnu/packages/bioconductor.scm (r-affyplm): Update to 1.76.0. Ricardo Wurmus
2023-04-29gnu: r-affylmgui: Update to 1.74.0....* gnu/packages/bioconductor.scm (r-affylmgui): Update to 1.74.0. Ricardo Wurmus
2023-04-29gnu: r-affyilm: Update to 1.52.0....* gnu/packages/bioconductor.scm (r-affyilm): Update to 1.52.0. Ricardo Wurmus
2023-04-29gnu: r-affixcan: Update to 1.18.0....* gnu/packages/bioconductor.scm (r-affixcan): Update to 1.18.0. Ricardo Wurmus
2023-04-29gnu: r-adsplit: Update to 1.70.0....* gnu/packages/bioconductor.scm (r-adsplit): Update to 1.70.0. Ricardo Wurmus
2023-04-29gnu: r-adimpute: Update to 1.10.0....* gnu/packages/bioconductor.scm (r-adimpute): Update to 1.10.0. Ricardo Wurmus
2023-04-29gnu: r-adamgui: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-adamgui): Update to 1.16.0. Ricardo Wurmus
2023-04-29gnu: r-adam: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-adam): Update to 1.16.0. Ricardo Wurmus
2023-04-29gnu: r-adacgh2: Update to 2.40.0....* gnu/packages/bioconductor.scm (r-adacgh2): Update to 2.40.0. Ricardo Wurmus
2023-04-29gnu: r-absseq: Update to 1.54.0....* gnu/packages/bioconductor.scm (r-absseq): Update to 1.54.0. Ricardo Wurmus
2023-04-29gnu: r-abarray: Update to 1.68.0....* gnu/packages/bioconductor.scm (r-abarray): Update to 1.68.0. Ricardo Wurmus
2023-04-29gnu: r-missmethyl: Update to 1.34.0....* gnu/packages/bioconductor.scm (r-missmethyl): Update to 1.34.0. Ricardo Wurmus
2023-04-29gnu: r-shiny: Update to 1.7.4....* gnu/packages/cran.scm (r-shiny): Update to 1.7.4. Ricardo Wurmus
2023-04-29gnu: r-glimma: Update to 2.10.0....* gnu/packages/bioconductor.scm (r-glimma): Update to 2.10.0. [source]: Delete minified JavaScript files. [arguments]: Add 'process-javascript phase. [native-inputs]: Add esbuild. Ricardo Wurmus
2023-04-29gnu: r-reportingtools: Update to 2.39.0....* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.39.0. [source]: Delete minified JavaScript files. [arguments]: Add 'process-javascript phase. [native-inputs]: Add source code for jquery 1.8.0. Ricardo Wurmus
2023-04-29gnu: Add r-densvis....* gnu/packages/bioconductor.scm (r-densvis): New variable. Ricardo Wurmus
2023-04-29gnu: r-with-tests: Update to 4.3.0....* gnu/packages/statistics.scm (r-with-tests): Update to 4.3.0. [arguments]: Move 'set-timezone before 'configure. Ricardo Wurmus
2023-04-29gnu: libpotassco: Unbundle catch....This patch incidentally fixes a build failure caused by the bundled catch. * gnu/packages/potassco.scm (libpotassco)[source]: Unbundle catch. [native-inputs]: Add catch2-1. Liliana Marie Prikler
2023-04-28gnu: libexpected: Update to 1.1.0....* gnu/packages/patches/libexpected-use-provided-catch2.patch: Add new patch. * gnu/packages/patches/libexpected-nofetch.patch: Remove unused patch. * gnu/local.mk (dist_patch_DATA): Register changes. * gnu/packages/cpp.scm (libexpected): Update to 1.1.0, and use new patch. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Josselin Poiret
2023-04-28gnu: fwupd: Update to 1.8.14....* gnu/packages/firmware.scm (fwupd): Update to 1.8.14. Also, change two files' timestamp because they are zipped up by Python. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Josselin Poiret
2023-04-28gnu: maven-embedder: Fix build....* gnu/packages/maven (maven-embedder)[arguments]: Add the'add-sisu-shebang phase after unpack. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Aleksandr Vityazev
2023-04-28gnu: maven-core-bootstrap: Fix build....* gnu/packages/maven (maven-core-bootstrap)[arguments]: Add the'add-sisu-shebang phase after unpack. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Aleksandr Vityazev
2023-04-28gnu: maven-resolver-provider: Fix build....* gnu/packages/maven (maven-resolver-provider)[arguments]: Add the'add-sisu-shebang phase after unpack. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Aleksandr Vityazev
2023-04-28gnu: maven-model-builder: Fix build....* gnu/packages/maven (maven-model-builder)[arguments]: Add the'add-sisu-shebang phase after unpack. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Aleksandr Vityazev
2023-04-28gnu: maven-settings-builder: Fix build....* gnu/packages/maven (maven-settings-builder)[arguments]: Add the'add-sisu-shebang phase after unpack. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Aleksandr Vityazev
generated by cgit
?id=13f299b2c98cce0ede3a8a37dd11832fdb3827bb'>build: test-driver.scm: Make output redirection optional....This makes it easier (and less surprising) for users to experiment with the custom Scheme test driver directly. The behavior is unchanged from Automake's point of view. * build-aux/test-driver.scm (main): Make the --log-file and --trs-file arguments optional and update doc. Only open, redirect and close a port to a log file when the --log-file option is provided. Only open and close a port to a trs file when the --trs-file option is provided. (test-runner-gnu): Set OUT-PORT parameter default value to the current output port. Set the TRS-PORT parameter default value to a void port. Update doc. Maxim Cournoyer 2020-11-12maint: update-guix-package: Optionally add sources to store....Following discussions in <https://issues.guix.gnu.org/43893>, keeping a copy of the updated package source is desirable when generating a release. * build-aux/update-guix-package.scm (version-controlled?): Remove variable. (call-with-temporary-git-worktree): Renamed from 'with-temporary-git-worktree'. Update doc. Do not change directory implicitly. Define as a procedure, not a syntax. (keep-source-in-store): New procedure. (main): Adjust to use with call-with-temporary-git-worktree. Add the sources to the store when GUIX_ALLOW_ME_TO_USE_PRIVATE_COMMIT is set. Exit gracefully when FIND-ORIGIN-REMOTE returns #f. (%savannah-guix-git-repo-push-url-regexp): Adjust match for a potential colon separator. * Makefile.am (GUIX_ALLOW_ME_TO_USE_PRIVATE_COMMIT): Adjust. * .dir-locals.el (scheme-mode): Remove entry for with-temporary-git-worktree. * doc/contributing.texi (Updating the Guix Package): Update doc. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Maxim Cournoyer 2020-10-25maint: update-guix-package: Include the git.sv.gnu.org alias....* build-aux/update-guix-package.scm (%savannah-guix-git-repo-push-url): Rename to... (%savannah-guix-git-repo-push-url-regexp): ...this. Add the 'sv' alternative to 'savannah' and the (push) suffix in the URL regexp. (find-origin-remote): Adjust accordingly. Reported-by: Ludovic Courtès <ludo@gnu.org> Maxim Cournoyer 2020-10-19maint: update-guix-package: Prevent accidentally breaking guix pull....Fixes <https://issues.guix.gnu.org/43893>. This changes the 'update-guix-package' tool so that it: 1. Always uses a clean checkout to compute the hash of the updated 'guix' package. 2. Ensures the commit used in the updated 'guix' package definition has already been pushed upstream. * build-aux/update-guix-package.scm (%savannah-guix-git-repo-push-url): New variable. (with-input-pipe-to-string, with-temporary-git-worktree): New syntaxes. (find-origin-remote, git-add-worktree): New procedures. (commit-already-pushed?): New predicate. (main): Check the commit used has already been pushed upstream and compute the hash from a clean checkout. * doc/contributing.texi (Updating the Guix Package): Document it. * .dir-locals.el (scheme-mode): Fix indentation of with-temporary-git-worktree. Maxim Cournoyer 2020-10-04cuirass: Add hurd-manifest....* build-aux/cuirass/hurd-manifest.scm: New file. Jan (janneke) Nieuwenhuizen 2020-10-01ci: Add log and outputs keys....Add 'log and 'outputs properties to hydra objects. This way Cuirass won't have to go through every derivation to add those properties. * gnu/ci.scm (package->alist, image-jobs, system-test-jobs, tarball-jobs): Add 'log and 'outputs properties. * build-aux/hydra/guix-modular.scm (build-job): Ditto. Mathieu Othacehe 2020-10-01ci: Add nix-name and system keys....Add 'nix-name and 'system properties to hydra objects. This way Cuirass won't have to go through every derivation to add those properties. * gnu/ci.scm (package->alist, image-jobs, system-test-jobs, tarball-jobs): Add 'nix-name and 'system properties. * build-aux/hydra/guix-modular.scm (build-job): Ditto. Mathieu Othacehe 2020-08-29build: Remove references to the 'nix-hash' program....* configure.ac: Remove check for 'nix-hash'. * tests/base32.scm (%nix-hash, %have-nix-hash?): Remove. ("sha256 & bytevector->nix-base32-string"): Remove test. * build-aux/pre-inst-env.in: Do not set 'NIX_HASH' environment variable. Ludovic Courtès 2020-08-24Use "guile-zlib" and "guile-lzlib" instead of (guix config)....* Makefile.am (MODULES): Remove guix/zlib.scm and guix/lzlib.scm, (SCM_TESTS): remove tests/zlib.scm, tests/lzlib.scm. * build-aux/build-self.scm (make-config.scm): Remove unused %libz variable. * configure.ac: Remove LIBZ and LIBLZ variables and check instead for Guile-zlib and Guile-lzlib. * doc/guix.texi ("Requirements"): Remove zlib requirement and add Guile-zlib and Guile-lzlib instead. * gnu/packages/package-management.scm (guix)[native-inputs]: Add "guile-zlib" and "guile-lzlib", [inputs]: remove "zlib" and "lzlib", [propagated-inputs]: ditto, [arguments]: add "guile-zlib" and "guile-lzlib" to Guile load path. * guix/config.scm.in (%libz, %liblz): Remove them. * guix/lzlib.scm: Remove it. * guix/man-db.scm: Use (zlib) instead of (guix zlib). * guix/profiles.scm (manual-database): Do not stub (guix config) in imported modules list, instead add "guile-zlib" to the extension list. * guix/scripts/publish.scm: Use (zlib) instead of (guix zlib) and (lzlib) instead of (guix lzlib), (string->compression-type, effective-compression): do not check for zlib and lzlib availability. * guix/scripts/substitute.scm (%compression-methods): Do not check for lzlib availability. * guix/self.scm (specification->package): Add "guile-zlib" and "guile-lzlib" and remove "zlib" and "lzlib", (compiled-guix): remove "zlib" and "lzlib" arguments and add guile-zlib and guile-lzlib to the dependencies, also do not pass "zlib" and "lzlib" to "make-config.scm" procedure, (make-config.scm): remove "zlib" and "lzlib" arguments as well as %libz and %liblz variables. * guix/utils.scm (lzip-port): Use (lzlib) instead of (guix lzlib) and do not check for lzlib availability. * guix/zlib.scm: Remove it. * m4/guix.m4 (GUIX_LIBZ_LIBDIR, GUIX_LIBLZ_FILE_NAME): Remove them. * tests/lzlib.scm: Use (zlib) instead of (guix zlib) and (lzlib) instead of (guix lzlib), and do not check for zlib and lzlib availability. * tests/publish.scm: Ditto. * tests/substitute.scm: Do not check for lzlib availability. * tests/utils.scm: Ditto. * tests/zlib.scm: Remove it. Mathieu Othacehe