| Age | Commit message (Expand) | Author |
|---|
| 2017-11-07 | guix: Add archive support for bioconductor-uri....* guix/build-system/r.scm (bioconductor-uri): Also return the archive URL.
* guix/import/cran.scm (latest-bioconductor-release, fetch-description):
Adjust because bioconductor-uri now returns a list.
| Ricardo Wurmus |
| 2017-11-07 | import: cran: Use Bioconductor 3.6 helpers....* guix/import/cran.scm (bioconductor-mirror-url): Remove procedure.
(fetch-description): Extract DESCRIPTION file from tarball for Bioconductor
packages.
(latest-bioconductor-release): Use latest-bioconductor-package-version.
| Ricardo Wurmus |
| 2017-11-07 | import: cran: Add support for Bioconductor 3.6....* guix/import/cran.scm (%bioconductor-version,
%bioconductor-packages-list-url): New variables.
(bioconductor-packages-list, latest-bioconductor-package-version): New
procedures.
| Ricardo Wurmus |
| 2017-11-07 | import: utils: Add string helpers....* guix/import/utils.scm (read-lines, chunk-lines): New procedures.
| Ricardo Wurmus |
| 2017-11-07 | refresh: Account for hidden packages....Suggested by Marius Bakke <mbakke@fastmail.com>
in <https://bugs.gnu.org/29177>.
* guix/scripts/refresh.scm (all-packages): Pass #:select? to
'fold-packages'.
| Ludovic Courtès |
| 2017-11-07 | compile: Fix VPATH builds....Fixes <https://bugs.gnu.org/29091>.
Reported by Eric Bavier <bavier@cray.com>.
* guix/build/compile.scm (relative-file): New procedure.
(load-files): Use it before calling 'file-name->module-name'.
(compile-files): Likewise before calling 'scm->go'.
* guix/build/pull.scm (build-guix): Remove 'with-directory-excursion'
and file name hack from ce33c3af76b0e5c68cc42dddf2b9c4b017386fd8.
Pass OUT to 'all-scheme-files'.
| Ludovic Courtès |
| 2017-11-07 | Fix ambiguous imports....* gnu/packages/ocaml.scm: Hide 'zip' from (srfi srfi-1).
* guix/git.scm: Select 'mkdir-p' from (guix build utils).
| Ludovic Courtès |
| 2017-11-05 | guix: records: Add match-record....* guix/records.scm: New syntax-rule.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| nee |
| 2017-11-01 | download: Refresh the cpan.org mirror list....* guix/download.scm (%mirrors)[cpan]: Update the list of CPAN mirrors (of
which several are dead) with a more-or-less geographically diverse selection.
| Tobias Geerinckx-Rice |
| 2017-10-30 | Revert "import: cpan: Use HTTPS for home pages."...This reverts commit 29f7bf59d5d4d4b848eaedc6766bb4e02cae20d3: HTTPS support
at search.cpan.org is unreliable, at best. Don't rely on it.
| Tobias Geerinckx-Rice |
| 2017-10-29 | import: cpan: Use HTTPS for home pages....* guix/import/cpan.scm (cpan-home): Use HTTPS.
* tests/cpan.scm ("cpan->guix-package"): Expect it.
| Tobias Geerinckx-Rice |
| 2017-10-29 | import: cpan: Actually use CPAN-HOME....* guix/import/cpan.scm (cpan-module->sexp): Use the CPAN-HOME procedure.
| Tobias Geerinckx-Rice |
| 2017-10-29 | import: cpan: Add trailing "/" to CPAN-HOME....Prevent regression after commit e4bc1727302b0e1e255ea5cf4e2ccf33cafe7296.
* guix/import/cpan.scm (cpan-home): Add trailing "/".
| Tobias Geerinckx-Rice |
| 2017-10-28 | import: cpan: Add trailing "/" on home-page....This appeases 'guix lint', which otherwise complains about permanent
redirects.
* guix/import/cpan.scm (cpan-module->sexp): Add trailing "/" on home-page.
* tests/cpan.scm ("cpan->guix-package"): Adjust accordingly.
| Eric Bavier |
| 2017-10-28 | import: cpan: Propagate imported dependencies....This is most often the need for perl module dependencies.
* guix/import/cpan.scm (cpan-module->sexp): 'inputs -> 'propagated-inputs.
* tests/cpan.scm ("cpan->guix-package"): Adjust accordingly.
| Eric Bavier |
| 2017-10-28 | graph: Remove mention of Graphviz from the summary line....* guix/scripts/graph.scm (show-help): Remove mention of Graphviz from
the summary line.
| Ludovic Courtès |
| 2017-10-28 | import: elpa: Do not abort when failing to download the archive....* guix/import/elpa.scm (elpa-fetch-archive): Use 'http-fetch/cached'
directly instead of 'call-with-downloaded-file'. This ensures we don't
just abort when networking access is lacking, which is required to allow
'guix refresh -c refresh' to proceed.
| Ludovic Courtès |
| 2017-10-28 | import: github: Gracefully handle multiple-URL origins....* guix/import/github.scm (latest-release)[origin-github-uri]: New
procedure. Use it.
| Ludovic Courtès |
| 2017-10-28 | lint: 'refresh' gracefully handles lack of networking access....* guix/scripts/lint.scm (check-for-updates): Wrap
'package-latest-release*' call in 'with-networking-fail-safe'.
| Ludovic Courtès |
| 2017-10-28 | lint: Extract network-related exception handling....* guix/scripts/lint.scm (call-with-networking-fail-safe): New procedure.
(with-networking-fail-safe): New macro.
(current-vulnerabilities*): Rewrite in terms of 'with-networking-fail-safe'.
| Ludovic Courtès |
| 2017-10-28 | scripts: Factorize option parsing sans 'GUIX_BUILD_OPTIONS'....* guix/scripts.scm (parse-command-line): Add #:build-options? parameter
and honor it.
* guix/scripts/challenge.scm (guix-challenge): Use 'parse-command-line'
with #:build-options? #f instead of 'args-fold*'.
* guix/scripts/gc.scm (guix-gc): Likewise.
* guix/scripts/graph.scm (guix-graph): Likewise.
* guix/scripts/hash.scm (guix-hash): Likewise.
* guix/scripts/lint.scm (guix-lint): Likewise.
* guix/scripts/refresh.scm (guix-refresh): Likewise.
* guix/scripts/size.scm (guix-size): Likewise.
* guix/scripts/weather.scm (guix-weather): Likewise.
| Ludovic Courtès |
| 2017-10-27 | scripts: Use 'args-fold*' for command that do not honor build flags....Fixes <https://bugs.gnu.org/28984>.
Reported by Eric Bavier.
* guix/scripts/challenge.scm (guix-challenge): Use 'args-fold*' instead
of 'parse-command-line'.
* guix/scripts/size.scm (guix-size): Likewise.
* guix/scripts/weather.scm (guix-weather): Likewise.
| Ludovic Courtès |
| 2017-10-26 | build-system/go: Fix installation path of executable files....* guix/build/go-build-system.scm (setup-environment): Set GOBIN correctly.
| Leo Famulari |
| 2017-10-25 | challenge: Display an overall summary....* guix/scripts/challenge.scm (summarize-report-list): New procedure.
(guix-challenge): Use it.
* doc/guix.texi (Invoking guix challenge): Adjust command output in
example.
| Ludovic Courtès |
| 2017-10-25 | substitute: Don't send more than 1000 requests in a row....Fixes <https://bugs.gnu.org/28731>.
Reported by Jan Nieuwenhuizen <janneke@gnu.org>.
* guix/scripts/substitute.scm (at-most): New procedure.
(http-multiple-get): Use it to send at most 1000 requests at once.
| Ludovic Courtès |
| 2017-10-25 | guix package: '--list-available' does not show superseded packages....* guix/scripts/package.scm (process-query) <'list-available>: Filter out
P if it matches 'package-superseded'.
| Ludovic Courtès |
| 2017-10-24 | build-system/go: Parameterize installing the source code....* guix/build-system/go.scm (go-build): Add install-source? key.
* guix/build/go-build-system.scm (install-source): Check if
install-source? is true.
| Leo Famulari |
| 2017-10-24 | build-system/go: Strip the Go binaries with the native tool....* guix/build/go-build-system.scm (build): Tell the Go linker to strip some
symbol tables and debugging information.
| Leo Famulari |
| 2017-10-23 | pull: Hide compilation warnings....* guix/build/pull.scm (build-guix): Bind 'current-warning-port' to a
void port.
| Ludovic Courtès |
| 2017-10-23 | pull: Add (guix build compile) to the mix....Fixes <https://bugs.gnu.org/28956>.
Reported by Leo Famulari <leo@famulari.name>.
* build-aux/build-self.scm (build): Add (guix build compile) to
#:modules.
* guix/build/pull.scm (build-guix): Wrap 'compile-files' call in
'with-directory-excursion'. Strip "./" from FILES when passing it to
'compile-files'.
| Ludovic Courtès |
| 2017-10-22 | gexp: Add 'directory-union'....* gnu/services.scm (directory-union): Move to...
* guix/gexp.scm (directory-union): ... here. New procedure.
* doc/guix.texi (G-Expressions): Document it.
| Ludovic Courtès |
| 2017-10-22 | gexp: Add 'file-union'....* gnu/services.scm (file-union): Move to...
* guix/gexp.scm (file-union): ... here. New procedure.
* doc/guix.texi (G-Expressions): Document it.
| Ludovic Courtès |
| 2017-10-22 | discovery: Move 'file-name->module-name' to (guix modules)....* guix/discovery.scm (file-name->module-name): Move to...
* guix/modules.scm (file-name->module-name): ... here.
* guix/build/compile.scm: Use (guix modules) instead of (guix discovery).
| Ludovic Courtès |
| 2017-10-22 | build: Factorize module compilation in (guix build compile)....* guix/build/compile.scm: New file.
* Makefile.am (MODULES): Add it.
* build-aux/compile-all.scm: Use it.
(warnings, file->module, load-module-file)
(%default-optimizations, %lightweight-optimizations)
(optimization-options, compile-file*): Remove.
<top level>: Use 'compile-files'.
* guix/build/pull.scm (%default-optimizations)
(%lightweight-optimizations, optimization-options): Remove.
(build-guix): Rewrite as a call to 'compile-files'.
* guix/discovery.scm (file-name->module-name): Export.
| Ludovic Courtès |
| 2017-10-21 | Use HTTPS for bioconductor.org....* 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.
| Tobias Geerinckx-Rice |
| 2017-10-19 | download: Download a nar when a VCS checkout fails....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.
| Ludovic Courtès |
| 2017-10-19 | Add (guix progress)....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.
| Ludovic Courtès |
| 2017-10-19 | download: Make 'http-fetch' public....* 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.
| Ludovic Courtès |
| 2017-10-19 | download: Remove old-Guile leftovers....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.
| Ludovic Courtès |
| 2017-10-17 | guix: substitute: Report the last progress in the child process....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.
| 宋文武 |
| 2017-10-15 | emacs-build-system: Change how patch-el-files substitutes commands....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.
| Christopher Baines |
| 2017-10-15 | emacs-build-system: Handle missing programs when patching....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.
| Christopher Baines |
| 2017-10-12 | build: Add the Go build system....* 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.
| Leo Famulari |
| 2017-10-12 | lint: 'home-page' checker reports permanent redirects....* 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.
| Ludovic Courtès |
| 2017-10-12 | tests: Support multiple HTTP server instances....* 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.
| Ludovic Courtès |
| 2017-10-12 | offload: Reduce the number of calls to 'machine-load'....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.
| Ludovic Courtès |
| 2017-10-12 | substitute: Close the progress port after substitute finished....Fixes <https://bugs.gnu.org/28756>.
* guix/scripts/substitute.scm (progress-substitution):
Call '(close-port progress)'.
| 宋文武 |
| 2017-10-11 | zlib: Fix memory leak due to revealed ports not being GC'd....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.
| Ludovic Courtès |
| 2017-10-10 | import: cpan: Load (gnu packages perl) lazily....* guix/import/cpan.scm: Remove dependency on (gnu packages perl).
(perl-package): New procedure.
(%corelist, core-module?): Use it instead of referring to 'perl'.
| Ludovic Courtès |
| 2017-10-10 | import: pypi: Remove unneeded import....* guix/import/pypi.scm: Remove unneeded import.
| Ludovic Courtès |
