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authorRicardo Wurmus <rekado@elephly.net>2017-08-03 17:31:27 +0200
committerRicardo Wurmus <rekado@elephly.net>2017-08-03 17:53:54 +0200
commit4e0c847d5965d86d334d04458387cedbd5b4e9d4 (patch)
tree7d108497d4b74974c3c97a7ed3b74605b2e621d9 /gnu/packages/tex.scm
parentc8a9b2bcbff2d78609f8d34ad4d9ca41f17f4602 (diff)
downloadguix-4e0c847d5965d86d334d04458387cedbd5b4e9d4.tar.gz
guix-4e0c847d5965d86d334d04458387cedbd5b4e9d4.zip
gnu: r-wgcna: Update to 1.60.
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.
Diffstat (limited to 'gnu/packages/tex.scm')
0 files changed, 0 insertions, 0 deletions
es peak memory consumption to something less unreasonable. * Makefile.am (make-go): Depend on 'make-*-go' targets; remove body. (guile-compilation-rule): New function. (MODULES_CORE, MODULES_PACKAGES, MODULES_SYSTEM, MODULES_CLI): New variables. <top level>: Call 'guile-compilation-rule' 4 times. * build-aux/compile-all.scm <top level>: Expect "--total" and "--processed". Take them into account when displaying progress reports. Ludovic Courtès 2021-06-18build: Remove Guile 2.2 workaround....* build-aux/compile-all.scm <top level>: Remove Guile 2.2 workaround. Ludovic Courtès 2021-05-11Merge branch 'version-1.3.0'Maxim Cournoyer 2021-05-10maint: update-NEWS: Sort packages prior writing to the data file....* build-aux/update-NEWS.scm (main): Sort packages. Maxim Cournoyer 2021-04-29download: Use Disarchive as a last resort....This is a fixed version of 66b14dccdd0d83c875ce3a8d50ceab8b6f0a3ce2, which was reverted in e74250c3c535b75dd2225a26df51febb7ed94654. * guix/download.scm (%disarchive-mirrors): New variable. (%disarchive-mirror-file): New variable. (built-in-download): Add 'disarchive-mirrors' keyword argument and pass its value along to the 'builtin:download' derivation. (url-fetch): Pass '%disarchive-mirror-file' to 'built-in-download'. * guix/scripts/perform-download.scm (perform-download): Read Disarchive mirrors from the environment and pass them to 'url-fetch'. * guix/build/download.scm (disarchive-fetch/any): New procedure. (url-fetch): Add 'disarchive-mirrors' keyword argument, use it to make a list of URIs, and use the new procedure to fetch the file if all other methods fail. * build-aux/build-self.scm (build-program)[select?]: Exclude '(guix build download)'. * guix/self.scm (compiled-guix)[*core-modules*]: Add 'guile-json' to the list of extensions. Timothy Sample 2021-04-25import: Remove Nix importer....This importer has suffered from bitrot and no longer works with current Nix and Nixpkgs. See <https://bugs.gnu.org/32339> and <https://bugs.gnu.org/36255>. * guix/import/snix.scm, guix/scripts/import/nix.scm, tests/snix.scm: Remove. * Makefile.am (MODULES, SCM_TESTS): Remove them. * guix/scripts/import.scm (importers): Remove "nix". * build-aux/test-env.in: Remove NIXPKGS variable. * configure.ac: Remove '--with-nixpkgs' option. * doc/guix.texi (Invoking guix import): Remove bit about "guix import nix". * etc/completion/fish/guix.fish: Likewise. Ludovic Courtès 2021-04-23build-aux: Relax the regexp used to match NEWS sections....A number of packages doesn't really make sense in the name of the section to be substituted. This change allows using simply '*** new packages' instead of '*** 1999 new packages', for example, and have the update-NEWS.scm script update it. * build-aux/update-NEWS.scm (write-packages-added) <regexp>: Do not care about leading white space in the name of the section. Maxim Cournoyer 2021-04-20import: Remove Nix importer....This importer has suffered from bitrot and no longer works with current Nix and Nixpkgs. See <https://bugs.gnu.org/32339> and <https://bugs.gnu.org/36255>. * guix/import/snix.scm, guix/scripts/import/nix.scm, tests/snix.scm: Remove. * Makefile.am (MODULES, SCM_TESTS): Remove them. * guix/scripts/import.scm (importers): Remove "nix". * build-aux/test-env.in: Remove NIXPKGS variable. * configure.ac: Remove '--with-nixpkgs' option. * doc/guix.texi (Invoking guix import): Remove bit about "guix import nix". * etc/completion/fish/guix.fish: Likewise. Ludovic Courtès 2021-04-01build-self: Take care of the spinner in the parent process....This simplifies code and mostly ensures we don't print a spinner while there's build activity going on. * build-aux/build-self.scm (build-program): Remove 'spin' and 'call-with-new-thread' call from "compute-guix-derivation" body. Remove "Computing Guix derivation" message. (proxy): Pass extra argument to 'select'. Display a spinner when 'select' returns empty lists. (build): Print "Computing Guix derivation" message here. Ludovic Courtès 2021-04-01build-self: Forward sub-process build output to (current-build-output-port)....Fixes <https://bugs.gnu.org/41930>. * build-aux/build-self.scm (build-program): Add extra 'build-output' parameter. Interpret it as a socket name and connect to it; use it as the CURRENT-BUILD-OUTPUT-PORT. (proxy): New procedure. (build): Open a named socket. Accept connections and call 'proxy' on it. Ludovic Courtès 2021-03-19build-self: Silent Guile warnings while computing the derivation....In particular, silence the Guile-Git autoload warnings introduced by c1940fde43c7aca37d67589cc5cb248086d17d56. * build-aux/build-self.scm (build-program): Wrap 'guix-derivation' call in 'parameterize'. Ludovic Courtès 2021-03-10ci: Remove hydra support....This removes hydra support to use Cuirass as the only continuous integration system. * build-aux/hydra/gnu-system.scm: Remove it. * build-aux/hydra/guix-modular.scm: Ditto. * build-aux/hydra/guix.scm: Ditto. * build-aux/cuirass/hydra-to-cuirass.scm: Ditto. * Makefile.am (EXTRA_DIST): Update it. (hydra-jobs.scm): Remove it. (cuirass-jobs.scm): Update it. * build-aux/hydra/evaluate.scm: Move it to ... * build-aux/cuirass/evaluate.scm: ... here. * build-aux/cuirass/guix-modular.scm: Remove it. * build-aux/cuirass/gnu-system.scm: Ditto. * guix/packages.scm (%hydra-supported-systems): Rename it to ... (%cuirass-supported-systems): ... this variable. * build-aux/check-final-inputs-self-contained: Adapt it. * etc/release-manifest.scm: Ditto. * gnu/ci.scm (package->alist): Remove it. (derivation->job): New procedure. (package-job, package-cross-job, cross-jobs, image-jobs, system-test-jobs, tarball-jobs): Use it. (guix-jobs): New procedure. (hydra-jobs): Rename it to ... (cuirass-jobs): ... this procedure. Mathieu Othacehe 2021-02-04channels: Record 'guix' channel metadata in (guix config)....Partially fixes <https://bugs.gnu.org/45896>. * guix/config.scm.in (%channel-metadata): New variable. * guix/describe.scm (channel-metadata): Use it. (current-channels): New procedure. (current-profile-entries): Clarify docstring. * guix/self.scm (compiled-guix): Add #:channel-metadata and pass it to 'make-config.scm'. (make-config.scm): Add #:channel-metadata and define '%channel-metadata' in the generated file. (guix-derivation): Add #:channel-metadata and pass it to 'compiled-guix'. * guix/channels.scm (build-from-source): Replace 'name', 'source', and 'commit' parameters with 'instance'. Pass #:channel-metadata to BUILD. (build-channel-instance): Adjust accordingly. * build-aux/build-self.scm (build-program): Add #:channel-metadata and pass it to 'guix-derivation'. (build): Add #:channel-metadata and pass it to 'build-program'. * guix/scripts/describe.scm (display-profile-info): Add optional 'channels' parameter. Pass it to 'display-profile-content'. (display-profile-content): Add optional 'channels' parameter and honor it. Iterate on CHANNELS rather than on the manifest entries of PROFILE. (guix-describe): When PROFILE is #f, call 'current-channels' and pass it to 'display-profile-info', unless it returns the empty list. Ludovic Courtès 2021-02-02build: Add a --show-duration option to the SCM test-driver....* build-aux/test-driver.scm (script-version): Update. (show-help): Document it. (%options): Add the 'show-duration' option. (test-runner-gnu): Pass as a new argument. [test-cases-start-time]: New inner variable. [test-on-test-begin-gnu]: New hook, used to record the start time. [test-on-test-end-gnu]: Conditionally print elapsed time. Record it as the optional metadata in the test result file (.trs). * doc/guix.texi (Running the Test Suite): Document it. Maxim Cournoyer 2021-02-01guix package: Add '--export-channels'....* guix/channels.scm (sexp->channel): Export. * guix/describe.scm: Use (guix channels). (manifest-entry-provenance): New procedure. * guix/scripts/package.scm (channel=?, export-channels): New procedures. (show-help, %options): Add '--export-channels'. (process-query): Honor it. * build-aux/build-self.scm (build-program)[select?]: Exclude (guix channels) to account for the (guix describe) change above. * doc/guix.texi (Invoking guix package): Document it. Ludovic Courtès 2021-01-31build: test-driver.scm: Allow running as a standalone script....* build-aux/test-driver.scm: Add an exec-based shebang and set the script executable bit. (main): Insert a newline after the version string is printed with --version. Maxim Cournoyer 2021-01-31build: test-driver.scm: Add a new '--errors-only' option....* build-aux/test-driver.scm (show-help): Add the help text for the new '--errors-only' option. (%options): Add the errors-only option. (test-runner-gnu): Add the errors-only? parameter and update doc. Move the logging of the test data after the test has completed, so a choice can be made whether to keep it or discard it based on the value of the test result. (main): Pass the errors-only? option to the driver. * doc/guix.texi (Running the Test Suite): Document the new option. Maxim Cournoyer 2021-01-31build: test-driver.scm: Add test cases filtering options....* build-aux/test-driver.scm (show-help): Add help text for the new --select and --exclude options. (%options): Add the new select and exclude options. (test-runner-gnu): Pass them to the test runner. Update doc. (test-match-name*, test-match-name*/negated, %test-match-all): New variables. (main): Compute the test specifier based on the values of the new options and apply it to the current test runner when running the test file. * doc/guix.texi (Running the Test Suite): Document the new options. Maxim Cournoyer 2021-01-31build: test-driver.scm: Enable colored test results by default....The Automake parallel test harness does its own smart detection of the terminal color capability and always provides the --color-tests argument to the driver. This change defaults the --color-tests argument to true when the test driver is run on its own (not via Automake). * build-aux/test-driver.scm (main): Set the default value of the --color-tests argument to true when it's not explicitly provided. Maxim Cournoyer 2021-01-31build: 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