9f8605958e
download: Pass the timeout to 'ftp-retr'.
...
This ensures the timeout applies when connecting to the port returned by
PASV.
* guix/ftp-client.scm (ftp-list): Add #:timeout parameter. Use
'connect*' instead of 'connect' and pass TIMEOUT.
(ftp-retr): Likewise.
* guix/build/download.scm (ftp-fetch): Pass TIMEOUT to 'ftp-retr'.
2017-11-14 23:46:53 +01:00
412716eff2
grafts: Clarify the status of the workaround for < http://bugs.gnu.org/24659 >.
...
* guix/build/graft.scm (mkdir-p*): Annotate.
2017-11-14 16:38:02 -05:00
d0b87779f0
download: Use HTTPS for the first ImageMagick mirror.
...
* guix/download.scm (%mirrors)[imagemagick]: Use HTTPS for <sunsite.icm.edu.pl>.
2017-11-12 17:50:01 -05:00
ecc585711e
download: Try FTP servers last.
...
* guix/download.scm (%mirrors)[savannah, kernel.org, apache, xorg, imagemagick]:
Re-arrange so that FTP is last.
2017-11-12 17:50:01 -05:00
b1488c7653
git: Check whether 'clone-init-options' is defined.
...
This is a followup to 195f0d05c3
2017-11-11 20:09:25 +01:00
65a19abf3f
download: Work around more bogus HTTP handling in Guile 2.2 <= 2.2.2.
...
Reported by Mark H Weaver <mhw@netris.org>
at <https://lists.gnu.org/archive/html/guix-devel/2017-11/msg00190.html >.
* guix/build/download.scm (guile-2.2) [write-request-line]: Backport
Guile commit 6ad28ae3bc6a6d9e95ab7d70510d12c97673a143.
2017-11-11 15:20:02 +01:00
59da6f04f4
download: Work around bogus HTTP handling in Guile 2.2 <= 2.2.2.
...
Reported by Konrad Hinsen <konrad.hinsen@fastmail.net>
at <https://lists.gnu.org/archive/html/guix-devel/2017-11/msg00070.html >.
* guix/build/download.scm (write-request-line) [guile-2.2]: New
procedure.
2017-11-10 23:11:52 +01:00
195f0d05c3
git: Work around wrong default argument of 'clone'.
...
Fixes <https://bugs.gnu.org/29238 >.
Reported by Benjamin Andresen <benny@in-ulm.de>.
* guix/git.scm (clone*): Pass second argument to 'clone'.
2017-11-10 13:07:54 +01:00
dc856223f5
ui: Add an 'unbound-variable' exception printer.
...
* guix/ui.scm (print-unbound-variable-error): New variable.
Use it as the 'unbound-variable' printer.
2017-11-09 23:54:47 +01:00
a2985bb101
ui: Provide hints for unbound-variable errors.
...
* guix/ui.scm (known-variable-definition): New procedure.
(report-load-error): Handle 'unbound-variable'.
2017-11-09 23:54:47 +01:00
935542fbde
ui: Add 'display-hint'.
...
* guix/ui.scm (known-variable-definition): New procedure.
(report-load-error): Use it.
2017-11-09 23:54:47 +01:00
23735137eb
ui: Define and honor '&error-location' and '&fix-hint' conditions.
...
* 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'.
2017-11-08 22:31:58 +01:00
37eed374d9
ui: Introduce (guix i18n).
...
* guix/ui.scm (G_, N_, _P, %gettext-domain, %package-text-domain): Move
to...
* guix/i18n.scm: ... here. New file.
2017-11-08 22:31:58 +01:00
25e51b1c45
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.
2017-11-07 08:14:09 +01:00
27baf50956
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.
2017-11-07 08:13:35 +01:00
84dfdc5759
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.
2017-11-07 08:13:34 +01:00
6b46b04f91
import: utils: Add string helpers.
...
* guix/import/utils.scm (read-lines, chunk-lines): New procedures.
2017-11-07 08:07:51 +01:00
8e57e416c0
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'.
2017-11-07 00:12:10 +01:00
c9405c461b
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 ce33c3af76
2017-11-07 00:12:10 +01:00
0ad5f80982
Fix ambiguous imports.
...
* gnu/packages/ocaml.scm: Hide 'zip' from (srfi srfi-1).
* guix/git.scm: Select 'mkdir-p' from (guix build utils).
2017-11-07 00:12:10 +01:00
6692d8454a
guix: records: Add match-record.
...
* guix/records.scm: New syntax-rule.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-05 15:21:53 +01:00
63ae4800de
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.
2017-11-01 01:02:03 +01:00
b5c7574b2f
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.
2017-10-30 17:20:42 +01:00
29f7bf59d5
import: cpan: Use HTTPS for home pages.
...
* guix/import/cpan.scm (cpan-home): Use HTTPS.
* tests/cpan.scm ("cpan->guix-package"): Expect it.
2017-10-29 17:32:35 +01:00
6d176ad379
import: cpan: Actually use CPAN-HOME.
...
* guix/import/cpan.scm (cpan-module->sexp): Use the CPAN-HOME procedure.
2017-10-29 17:32:35 +01:00
73f33b9379
import: cpan: Add trailing "/" to CPAN-HOME.
...
Prevent regression after commit e4bc172730
2017-10-29 17:32:12 +01:00
e4bc172730
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.
2017-10-28 18:20:59 -05:00
23055424f2
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.
2017-10-28 18:20:58 -05:00
34b1f339cd
graph: Remove mention of Graphviz from the summary line.
...
* guix/scripts/graph.scm (show-help): Remove mention of Graphviz from
the summary line.
2017-10-28 09:45:54 +02:00
0a2ce1ea0a
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.
2017-10-28 09:45:54 +02:00
90297811a9
import: github: Gracefully handle multiple-URL origins.
...
* guix/import/github.scm (latest-release)[origin-github-uri]: New
procedure. Use it.
2017-10-28 09:45:54 +02:00
6d6d193221
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'.
2017-10-28 09:45:54 +02:00
4b879e0acf
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'.
2017-10-28 09:45:54 +02:00
a1ff7e1d8d
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.
2017-10-28 09:45:53 +02:00
efff3dd4c9
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.
2017-10-27 13:11:26 -07:00
552ee77250
build-system/go: Fix installation path of executable files.
...
* guix/build/go-build-system.scm (setup-environment): Set GOBIN correctly.
2017-10-26 12:14:33 -04:00
bf7dfb1f07
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.
2017-10-25 22:25:19 -07:00
d213cc8c7f
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.
2017-10-25 22:25:19 -07:00
44c6a87f53
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'.
2017-10-25 22:25:19 -07:00
c10851cf91
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.
2017-10-24 13:10:34 -04:00
1c37f839fb
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.
2017-10-24 13:10:34 -04:00
2900665888
pull: Hide compilation warnings.
...
* guix/build/pull.scm (build-guix): Bind 'current-warning-port' to a
void port.
2017-10-23 17:08:51 -07:00
ce33c3af76
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'.
2017-10-23 17:08:50 -07:00
d298c815e6
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.
2017-10-22 22:09:00 -07:00
dedb512f8f
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.
2017-10-22 22:09:00 -07:00
7a51c78c6e
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).
2017-10-22 22:09:00 -07:00
2890ad332f
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.
2017-10-22 22:09:00 -07:00
5713bbf157
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.
2017-10-21 17:43:40 +02:00
37ce440dcf
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.
2017-10-19 23:21:49 +02:00
8c3488259e
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
798648515b
2017-10-19 23:21:49 +02:00
Ludovic Courtès