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2017-10-21Use HTTPS for bioconductor.org.Tobias Geerinckx-Rice
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for bioconductor.org URLs. * gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter) (r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category) (r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews) (r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata) (r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi) (r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray) (r-summarizedexperiment, r-genomicalignments, r-rtracklayer) (r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern) (r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport) (r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid) (r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise. * gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene) (r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db) (r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db) (r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9) (r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene) (r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10) (r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]: Likewise. * gnu/packages/statistics.scm (r-rcurl)[source]: Likewise. * guix/build-system/r.scm (bioconductor-uri): Likewise. * guix/import/cran.scm (%cran-url, bioconductor-package?) (bioconductor-data-package?, bioconductor-experiment-package?): Likewise.
2017-10-19download: Download a nar when a VCS checkout fails.Ludovic Courtès
Fixes <https://bugs.gnu.org/28709>. * guix/build/download-nar.scm: New file. * Makefile.am (MODULES): Add it. * guix/cvs-download.scm (cvs-fetch)[zlib, config.scm, modules]: New variables. [build]: Use MODULES. Add call to 'download-nar'. * guix/git-download.scm (git-fetch): Likewise. * guix/hg-download.scm (hg-fetch): Likewise.
2017-10-19Add (guix progress).Ludovic Courtès
Among other things, this removes (guix utils), (guix ui), (guix config), etc. from the closure of (guix build download), as was the case since 798648515b77507c242752457b4dc17c155bad6e. * guix/utils.scm (<progress-reporter>, call-with-progress-reporter): Move to... * guix/progress.scm: ... here. New file. * Makefile.am (MODULES): Add it. * guix/build/download.scm (current-terminal-columns) (nearest-exact-integer, duration->seconds, seconds->string) (byte-count->string, progress-bar, string-pad-middle) (rate-limited, progress-reporter/file, dump-port*) (time-monotonic): Move to progress.scm. * guix/scripts/download.scm: Adjust accordingly. * guix/scripts/substitute.scm: Likewise.
2017-10-19download: Make 'http-fetch' public.Ludovic Courtès
* guix/build/download.scm (http-fetch): Remove 'file' parameter. Change to return an input port and the content-length. Make public. (url-fetch): Adjust accordingly.
2017-10-19download: Remove old-Guile leftovers.Ludovic Courtès
This is a followup to 36626c556ed75219bce196ac93d148f6b9af984c. * guix/build/download.scm (http-fetch): Rename 'port-or-bv' to 'port'. Assume (port? port) is always true, and remove other branch.
2017-10-17guix: substitute: Report the last progress in the child process.宋文武
Fixes <https://bugs.gnu.org/28756>. * guix/utils.scm (filtered-port): Close the 'input' port for the current process, and close it upon exit in the child process. * guix/scripts/substitute.scm (progress-substitution): Display "\n\n" after the reporter has finished.
2017-10-15emacs-build-system: Change how patch-el-files substitutes commands.Christopher Baines
Previously the regex would match from /bin/ to a closing quote. However, this is greedy, so will match up until the last ". This causes problems when there are several quotes on the same line, for example: org-effectiveness.el: 196: (call-process "/bin/bash" nil t nil "-c" strplot) Therefore, change . to \S so that it doesn't include whitespace characters. Changing to a lazy quantifier would be an option, if that were supported. * guix/build/emacs-build-system.scm (patch-el-files): Change the regular expression used.
2017-10-15emacs-build-system: Handle missing programs when patching.Christopher Baines
Previously the string-append here would error, which isn't useful as it doesn't tell you which command couldn't be found. To make the error actionable, catch it earlier, and explicitly error. * guix/build/emacs-build-system.scm (patch-el-files): Handle (which cmd) returning #f.
2017-10-12build: Add the Go build system.Leo Famulari
* guix/build-system/go.scm, guix/build/go-build-system.scm: New files. * Makefile.am (MODULES): Add new files. * doc/guix.texi (Build Systems): Document the go-build-system.
2017-10-12lint: 'home-page' checker reports permanent redirects.Ludovic Courtès
* guix/scripts/lint.scm (probe-uri): Add special case for HTTP 301. (validate-uri): Likewise. * tests/lint.scm ("home-page: 301, invalid") ("home-page: 301 -> 200", "home-page: 301 -> 404") ("source: 301 -> 200", "source: 301 -> 404"): New tests.
2017-10-12tests: Support multiple HTTP server instances.Ludovic Courtès
* guix/tests/http.scm (%http-server-socket): Turn into... (open-http-server-socket): ... this procedure. (http-server-can-listen?): New procedure. (http-write, %http-server-lock, %http-server-ready) (http-open, stub-http-server): Move to 'call-with-http-server' body. (call-with-http-server): Add #:headers parameter. (with-http-server): Add an additional pattern with headers. * tests/derivations.scm: Use (http-server-can-listen?) instead of (force %http-server-socket). * tests/lint.scm: Likewise.
2017-10-12offload: Reduce the number of calls to 'machine-load'.Ludovic Courtès
Previously we would call 'machine-load' once per machine, which was very costly when there were many machines. Now we arrange to call it only once on average (when all the machines have the same 'speed' value). * guix/scripts/offload.scm (random-seed, shuffle): New procedures. (choose-build-machine)[machines+slots+loads]: Rename to... [machines+slots]: ... this. Remove load from the tuples therein. [undecorate]: Adjust accordingly. [machine-less-loaded-or-faster?]: Remove. [machine-faster?]: New procedure. Sort MACHINES+SLOTS according to 'machine-faster?'. Call 'machine-load?' as the last thing.
2017-10-12substitute: Close the progress port after substitute finished.宋文武
Fixes <https://bugs.gnu.org/28756>. * guix/scripts/substitute.scm (progress-substitution): Call '(close-port progress)'.
2017-10-11zlib: Fix memory leak due to revealed ports not being GC'd.Ludovic Courtès
Fixes <https://bugs.gnu.org/28784>. This mostly reverts 81a0f1cdf12e7bcc34c1203f034a323fa8f52cf5, which introduced a regression: revealed ports are *never* GC'd (contrary to what Guile's manual suggests). In addition to the revert, 'close-procedure' now explicitly swallows EBADF errors when 'close-port' is called. * guix/zlib.scm (close-procedure): New procedure. (make-gzip-input-port)[gzfile]: Use 'fileno' instead of 'port->fdes'. Use 'close-procedure' instead of 'gzclose'. (make-gzip-output-port): Likewise. * tests/zlib.scm ("compression/decompression pipe"): Use 'port-closed?' to determine whether PARENT has been closed.
2017-10-10import: cpan: Load (gnu packages perl) lazily.Ludovic Courtès
* guix/import/cpan.scm: Remove dependency on (gnu packages perl). (perl-package): New procedure. (%corelist, core-module?): Use it instead of referring to 'perl'.
2017-10-10import: pypi: Remove unneeded import.Ludovic Courtès
* guix/import/pypi.scm: Remove unneeded import.
2017-10-10ui: Improve reporting of missing closing parentheses.Ludovic Courtès
Suggested by Ricardo Wurmus. Works around <https://bugs.gnu.org/28295>. * guix/ui.scm (report-load-error): Add case for 'read-error'. * tests/guix-system.sh: Test missing-closing-paren errors.
2017-10-10guix: mirrors: Add kde archive mirror.Efraim Flashner
* guix/download.scm (%mirrors)[kde]: Add kde-attic mirror.
2017-10-09syscalls: clone: Define syscall-id for aarch64.Eric Bavier
* guix/build/syscalls.scm (clone): Define syscall-id for aarch64 machines.
2017-10-09lint: Remove extra newline.Ludovic Courtès
* guix/scripts/lint.scm (check-for-updates): Remove trailing "~%".
2017-10-09guix: lint: Add checker for new upstream versions.Efraim Flashner
* guix/scripts/lint.scm (check-for-updates): New procedure. (%checkers): Add it. * guix/scripts/refresh.scm (importer-modules, %updaters): Move from here ... * guix/upstream.scm: ... to here.
2017-10-07pull: Add GUIX_PULL_URL environment variable.Oleg Pykhalov
* guix/scripts/pull.scm (%repository-url): Add GUIX_PULL_URL environment variable. * doc/guix.texi (Invoking guix pull): Mention GUIX_PULL_URL. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-10-07pull: Honor 'parallel-job-count'.Ludovic Courtès
* guix/build/pull.scm (build-guix): Use 'n-par-for-each' and honor 'parallel-job-count'.
2017-10-07store: Add missing import.Ludovic Courtès
* guix/store.scm: Use (ice-9 format).
2017-10-07guix package: '--upgrade' no longer reverses package order.Ludovic Courtès
Reported by Oleg Pykhalov <go.wigust@gmail.com> at <https://lists.gnu.org/archive/html/help-guix/2017-10/msg00000.html>. * guix/scripts/package.scm (options->installable)[upgraded]: Use 'fold-right' instead of 'fold'.
2017-10-05publish: Cache uncompressed nars as well.Ludovic Courtès
Fixes <https://bugs.gnu.org/28664>. Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>. * guix/scripts/publish.scm (bake-narinfo+nar): When COMPRESSION is 'none, write NAR instead of doing nothing. (make-request-handler): Use 'render-nar/cached' for /nar URLs with no compression. * tests/publish.scm ("with cache", "with cache, uncompressed"): Adjust expected result accordingly.
2017-10-05guix system: Error out when passed a wrong file system UUID/label.Ludovic Courtès
* guix/scripts/system.scm (check-file-system-availability): New procedure. (perform-action): Use it.
2017-10-03guix: ant-build-system: Add #:test-include and #:test-exclude arguments.Julien Lepiller
* guix/build-system/ant.scm: Add #:test-include and #:test-exclude arguments. * guix/build/ant-build-system.scm: Generate test list from arguments. * doc/guix.texi (Build Systems): Document it.
2017-10-03guix: ant-build-system: Add main-class support.Julien Lepiller
* guix/build-system/ant.scm: New #:main-class argument * guix/build/ant-build-system.scm: Generate a manifest file with additional properties. * doc/guix.texi (Build Systems): Document it.
2017-09-28guix: Revert accidentally committed changes.Ricardo Wurmus
This is a follow-up to commit fb1db385476bc4548d3eadea93b5dd6a346839f2. * guix/scripts/build.scm (lazy-util): Remove procedure. (options->things-to-build): Remove special case for files with ".json" extension.
2017-09-28import: Add JSON importer.Ricardo Wurmus
* doc/guix.texi (Invoking guix import): Document it. * guix/scripts/import/json.scm: New file. * Makefile.am (MODULES): Add it. * guix/scripts/import.scm (importers): Add json importer.
2017-09-28import: Add generic data to package converter.Ricardo Wurmus
* guix/import/utils.scm (build-system-modules, lookup-build-system-by-name, specs->package-lists, source-spec->object, alist->package): New procedures. * tests/import-utils.scm: Add tests for alist->package.
2017-09-28import: Add package->code.Ricardo Wurmus
* guix/import/print.scm: New file. * tests/print.scm: New file. * Makefile.am (SCM_TESTS): Add new test file. (MODULES): Add print.scm.
2017-09-26build-system: meson: Fix typo in variable name.Mohammed Sadiq
* guix/build-system/meson.scm (lower): fix typo in glib-or-gtk?.
2017-09-26http-client: Reset cache TTL upon 304 "Not Modified" responses.Ludovic Courtès
* guix/http-client.scm (http-fetch/cached)[update-cache]: Add call to 'utime' in the 304 case.
2017-09-26upstream: Add new GNOME updater.Ludovic Courtès
Partly fixes <https://bugs.gnu.org/28159>. Reported by Hartmut Goebel <h.goebel@crazy-compilers.com>. * guix/import/gnome.scm: New file. * Makefile.am (MODULES): Add it. * guix/gnu-maintenance.scm (latest-gnome-release) (%gnome-updater): Remove.
2017-09-26upstream: Add 'url-prefix-predicate'.Ludovic Courtès
* guix/gnu-maintenance.scm (url-prefix-predicate): Move to... * guix/upstream.scm (url-prefix-predicate): ... here.
2017-09-22licenses: Add CC-Sampling+ 1.0.Arun Isaac
* guix/licenses.scm (cc-sampling-plus-1.0): New variable. Signed-off-by: Kei Kebreau <kkebreau@posteo.net>
2017-09-20download: Don't report the progress too fast.宋文武
* guix/utils.scm (<progress-reporter>): New record type. (call-with-progress-reporter): New procedure. * guix/build/download.scm (dump-port*, rate-limited, progress-reporter/file): New procedures. (ftp-fetch, http-fetch): Use 'dump-port*'. (progress-proc): Remove procedure. * guix/scripts/substitute.scm (progress-report-port): Rewrite in terms of <progress-reporter>. (process-substitution): Adjust accordingly.
2017-09-19cve: Disable position recording while reading the CVE list.Ludovic Courtès
* guix/cve.scm (fetch-vulnerabilities)[read*]: New procedure. Use it in lieu of 'read'.
2017-09-19http-client: 'http-client/cached' uses 'If-Modified-Since'.Ludovic Courtès
* guix/http-client.scm (http-fetch/cached)[update-cache]: Add 'cache-port' parameter. Check its mtime and compute 'if-modified-since' header accordingly. Guard 'http-get-error?' and honor 304. Adjust callers of 'update-cache'. * guix/gnu-maintenance.scm (ftp.gnu.org-files): Set #:ttl to 15m.
2017-09-19utils: 'current-source-directory' gracefully deals with lack of location info.Ludovic Courtès
* guix/utils.scm (current-source-directory): Adjust for when 'syntax-source' returns #f.
2017-09-18substitute: Close the download port after substitution finished.宋文武
* guix/scripts/substitute.scm (progress-substitution): Call 'close-port' after 'restore-file'.
2017-09-16build-system: Add 'meson-build-system'.Peter Mikkelsen
* Makefile.am (MODULES): Add 'guix/build-system/meson.scm' and 'guix/build/meson-build-system.scm'. * guix/build-system/meson.scm: New file. * guix/build/meson-build-system.scm: New file. * doc/guix.texi (Build Systems): Add 'meson-build-system'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-09-16guix system: Add 'search' command.Ludovic Courtès
* guix/scripts/system.scm (resolve-subcommand): New procedure. (process-command): Handle 'search'. (guix-system): Likewise. (show-help): Augment. * guix/scripts/system/search.scm: New file. * po/guix/POTFILES.in: Add it. * Makefile.am (MODULES): Add it. * guix/ui.scm (%text-width): Export. * doc/guix.texi (Invoking guix system): Document it. (Service Types and Services): Mention 'guix system search'. * tests/guix-system.sh: Test it.
2017-09-16ui: Generalize relevance computation.Ludovic Courtès
* guix/ui.scm (relevance, package-relevance): New procedures. (%package-metrics): New variable. * guix/scripts/package.scm (find-packages-by-description)[score] [package-score]: Remove. Use 'package-relevance' instead.
2017-09-14guix download: Honor mirrors when using '-o'.Ludovic Courtès
Previously "guix download -o x mirror://gnu/…" would fail. * guix/scripts/download.scm (download-to-file): Pass #:mirrors to 'url-fetch'.
2017-09-12import: cpan: Replace '(package-license perl) with 'perl-license.Christopher Baines
The perl-license definition is intended to avoid circular dependencies, so use this as a default when importing packages from CPAN. * guix/import/cpan.scm (string->license): Replace '(package-license perl) with 'perl-license.
2017-09-12store: 'run-with-store' has a #:target parameter.Ludovic Courtès
* guix/store.scm (run-with-store): Add #:target and honor it.
2017-09-12guix system: Pretty-print device UUIDs.Ludovic Courtès
* guix/scripts/system.scm (display-system-generation): Check if ROOT-DEVICE is a UUID and pretty-print it if it is.
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