| Commit message (Collapse) | Author | Age |
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* guix/utils.scm (&error-location, &fix-hint): New condition types.
* guix/ui.scm (report-load-error): Handle them.
(call-with-error-handling): Honor '&error-location'.
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* guix/ui.scm (G_, N_, _P, %gettext-domain, %package-text-domain): Move
to...
* guix/i18n.scm: ... here. New file.
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* 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.
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* 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.
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* guix/import/cran.scm (%bioconductor-version,
%bioconductor-packages-list-url): New variables.
(bioconductor-packages-list, latest-bioconductor-package-version): New
procedures.
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* guix/import/utils.scm (read-lines, chunk-lines): New procedures.
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Suggested by Marius Bakke <mbakke@fastmail.com>
in <https://bugs.gnu.org/29177>.
* guix/scripts/refresh.scm (all-packages): Pass #:select? to
'fold-packages'.
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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'.
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* gnu/packages/ocaml.scm: Hide 'zip' from (srfi srfi-1).
* guix/git.scm: Select 'mkdir-p' from (guix build utils).
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* guix/records.scm: New syntax-rule.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* guix/download.scm (%mirrors)[cpan]: Update the list of CPAN mirrors (of
which several are dead) with a more-or-less geographically diverse selection.
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This reverts commit 29f7bf59d5d4d4b848eaedc6766bb4e02cae20d3: HTTPS support
at search.cpan.org is unreliable, at best. Don't rely on it.
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* guix/import/cpan.scm (cpan-home): Use HTTPS.
* tests/cpan.scm ("cpan->guix-package"): Expect it.
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* guix/import/cpan.scm (cpan-module->sexp): Use the CPAN-HOME procedure.
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Prevent regression after commit e4bc1727302b0e1e255ea5cf4e2ccf33cafe7296.
* guix/import/cpan.scm (cpan-home): Add trailing "/".
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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.
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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.
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* guix/scripts/graph.scm (show-help): Remove mention of Graphviz from
the summary line.
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* 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.
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* guix/import/github.scm (latest-release)[origin-github-uri]: New
procedure. Use it.
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* guix/scripts/lint.scm (check-for-updates): Wrap
'package-latest-release*' call in 'with-networking-fail-safe'.
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* 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'.
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* 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.
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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.
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* guix/build/go-build-system.scm (setup-environment): Set GOBIN correctly.
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* guix/scripts/challenge.scm (summarize-report-list): New procedure.
(guix-challenge): Use it.
* doc/guix.texi (Invoking guix challenge): Adjust command output in
example.
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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.
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* guix/scripts/package.scm (process-query) <'list-available>: Filter out
P if it matches 'package-superseded'.
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* 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.
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* guix/build/go-build-system.scm (build): Tell the Go linker to strip some
symbol tables and debugging information.
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* guix/build/pull.scm (build-guix): Bind 'current-warning-port' to a
void port.
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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'.
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* gnu/services.scm (directory-union): Move to...
* guix/gexp.scm (directory-union): ... here. New procedure.
* doc/guix.texi (G-Expressions): Document it.
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* gnu/services.scm (file-union): Move to...
* guix/gexp.scm (file-union): ... here. New procedure.
* doc/guix.texi (G-Expressions): Document it.
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* 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).
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* 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.
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* 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.
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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.
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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.
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* 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.
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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.
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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.
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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.
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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.
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* 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.
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* 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.
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* 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.
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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.
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Fixes <https://bugs.gnu.org/28756>.
* guix/scripts/substitute.scm (progress-substitution):
Call '(close-port progress)'.
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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.
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