41f17554d8
import: cran: Update to Bioconductor 3.7.
...
* guix/import/cran.scm (%bioconductor-version): Update to 3.7.
2018-06-02 13:39:13 +02:00
4a78fd4617
Correct name and Email for ng0.
...
* .mailmap: Correct name and Email for ng0.
* Makefile.am, doc/guix.texi, etc/completion/fish/guix.fish
gnu/packages/accessibility.scm, gnu/packages/admin.scm,
gnu/packages/audio.scm, gnu/packages/autotools.scm,
gnu/packages/cdrom.scm, gnu/packages/check.scm,
gnu/packages/cinnamon.scm, gnu/packages/compression.scm,
gnu/packages/crypto.scm, gnu/packages/databases.scm,
gnu/packages/django.scm, gnu/packages/dns.scm,
gnu/packages/emacs.scm, gnu/packages/enlightenment.scm,
gnu/packages/fonts.scm, gnu/packages/fontutils.scm,
gnu/packages/forth.scm, gnu/packages/fvwm.scm,
gnu/packages/games.scm, gnu/packages/gl.scm,
gnu/packages/gnome.scm, gnu/packages/gnunet.scm,
gnu/packages/gnupg.scm, gnu/packages/gnuzilla.scm,
gnu/packages/gtk.scm, gnu/packages/guile-wm.scm,
gnu/packages/guile.scm, gnu/packages/haskell-check.scm,
gnu/packages/haskell-crypto.scm, gnu/packages/haskell.scm,
gnu/packages/image-viewers.scm, gnu/packages/image.scm,
gnu/packages/irc.scm, gnu/packages/language.scm,
gnu/packages/libcanberra.scm, gnu/packages/linux.scm,
gnu/packages/lisp.scm, gnu/packages/lolcode.scm,
gnu/packages/lxde.scm, gnu/packages/lxqt.scm,
gnu/packages/mail.scm, gnu/packages/markup.scm,
gnu/packages/mate.scm, gnu/packages/maths.scm,
gnu/packages/mc.scm, gnu/packages/messaging.scm,
gnu/packages/music.scm, gnu/packages/ncurses.scm,
gnu/packages/networking.scm, gnu/packages/nickle.scm,
gnu/packages/openbox.scm, gnu/packages/pdf.scm,
gnu/packages/perl-check.scm, gnu/packages/perl.scm,
gnu/packages/python-crypto.scm, gnu/packages/python-web.scm,
gnu/packages/python.scm, gnu/packages/qt.scm,
gnu/packages/ruby.scm, gnu/packages/rust.scm,
gnu/packages/scheme.scm, gnu/packages/serialization.scm,
gnu/packages/shells.scm, gnu/packages/ssh.scm,
gnu/packages/suckless.scm, gnu/packages/tbb.scm,
gnu/packages/telephony.scm, gnu/packages/text-editors.scm,
gnu/packages/textutils.scm, gnu/packages/time.scm,
gnu/packages/tls.scm, gnu/packages/tor.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vim.scm, gnu/packages/web.scm,
gnu/packages/wm.scm, gnu/packages/xdisorg.scm,
gnu/packages/xfce.scm, gnu/packages/xml.scm,
gnu/packages/xorg.scm, gnu/services/certbot.scm,
gnu/services/desktop.scm, gnu/services/version-control.scm,
gnu/services/web.scm, guix/import/hackage.scm,
guix/licenses.scm: Likewise.
Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2018-03-20 17:17:58 +01:00
9bb1838c3f
import: elpa: Return 'license:gpl3+ for ELPA only.
...
Fixes <https://bugs.gnu.org/30836 >.
Reported by Konrad Hinsen <konrad.hinsen@fastmail.net>.
* guix/import/elpa.scm (elpa-package->sexp): Add LICENSE parameter and
honor it.
(elpa->guix-package): Pass 'license:gpl3+ only when REPO is 'gnu.
2018-03-18 22:26:34 +01:00
07d2fed2f6
import: elpa: Fix typos in documentation strings
...
* guix/import/elpa.scm: Fix typos in docstrings.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-03-18 00:02:05 +01:00
44dd3d579d
import: elpa: use https in download URLs
...
* guix/import/elpa.scm (elpa-url): Use HTTPS.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-03-18 00:02:05 +01:00
b402f4ee34
import: cpan: Drop "v" prefix from version strings.
...
Fixes <https://bugs.gnu.org/30641 >.
Reported by Oleg Pykhalov <go.wigust@gmail.com>.
* guix/import/cpan.scm (cpan-version): Drop the "v" prefix when it is
there.
2018-03-01 14:54:55 +01:00
5e2495d09e
import: utils: 'alist->package' allows false license.
...
Reported by <pkill9@runbox.com>.
Fixes <https://bugs.gnu.org/30470 >.
* guix/import/utils.scm (alist->package): Check whether 'license' is
false and set the 'license' field to #f in this case.
* tests/import-utils.scm ("alist->package with false license"): New
test.
2018-02-16 11:10:12 +01:00
8286215326
gnu: Use one spelling for ‘copyright’.
...
* gnu/packages/gtk.scm: Standardise on ‘copyright’ spelling in
file headers.
* gnu/packages/pdf.scm: Likewise.
* gnu/packages/perl-check.scm: Likewise.
* gnu/packages/perl.scm: Likewise.
* guix/import/gem.scm: Likewise.
* guix/import/hackage.scm: Likewise.
2018-01-10 18:21:20 +01:00
1e63ecee0b
import: crate: Gracefully deal with missing license info.
...
Reported by Fis Trivial <ybbs.daans@hotmail.com>.
Fixes <https://bugs.gnu.org/28987 >.
* guix/import/crate.scm (crate-fetch): Check whether the "license" info
is present.
2018-01-08 11:45:35 +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
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
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
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
90eaa9419a
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'.
2017-10-10 23:12:04 +02:00
b719ddbbbb
import: pypi: Remove unneeded import.
...
* guix/import/pypi.scm: Remove unneeded import.
2017-10-10 23:12:03 +02:00
5e892bc365
import: Add generic data to package converter.
...
* 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.
2017-09-28 13:10:11 +02:00
68a91a183b
import: Add package->code.
...
* guix/import/print.scm: New file.
* tests/print.scm: New file.
* Makefile.am (SCM_TESTS): Add new test file.
(MODULES): Add print.scm.
2017-09-28 13:10:10 +02:00
c1d8b3b3b5
upstream: Add new GNOME updater.
...
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.
2017-09-26 00:35:06 +02:00
01ef804d69
import: cpan: Replace '(package-license perl) with 'perl-license.
...
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.
2017-09-12 23:15:36 +01:00
e956ae16a4
import: cpan: Updater returns a list of URLs.
...
* guix/import/cpan.scm (latest-release): Return a list in the 'urls'
field of 'upstream-source'.
2017-07-24 17:35:26 +02:00
94a400beba
import cran: Generate a valid 'license' field for "GPL".
...
Fixes <http://bugs.gnu.org/27294 >.
Reported by Joshua Sierles <joshua@joshua.si>.
* guix/import/cran.scm (string->license) <"GPL">: Return a quoted list.
2017-06-26 22:52:06 +02:00
afbc94194e
guix: Add texlive importer.
...
* guix/import/texlive.scm: New file.
* guix/scripts/import/texlive.scm: New file.
* Makefile.am (MODULES): Add them.
* tests/texlive.scm: New file.
* Makefile.am (SCM_TESTS): Add it.
* guix/scripts/import.scm (importers): Add texlive importer.
* doc/guix.texi (Invoking guix import): Document it.
2017-06-15 17:03:19 +02:00
d1e7ca2df8
import: pypi: Always use pypi.io URL with downcased package name.
...
* guix/import/pypi.scm (make-pypi-sexp): Always use pypi.io URL with
downcased package name.
2017-06-15 09:49:13 +02:00
4679dd6967
import: cpan: Update CPAN importer to use MetaCPAN v1 API.
...
* guix/import/cpan.scm (module->dist-name, cpan-fetch): Use metacpan.org
URLs.
* tests/cpan.scm ("cpan->guix-package"): Adjust accordingly.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-06-07 15:06:34 +02:00
17a69cf623
import cran: Check if pkg-config is needed.
...
* guix/import/cran.scm (needs-pkg-config?): New procedure.
(description->package): Use it.
2017-05-16 21:43:35 +02:00
a0f43208cb
import cran: Refactor "needs-zlib?".
...
* guix/import/cran.scm (tarball-files-match-pattern?): New procedure.
(needs-zlib?): Implement in terms of "tarball-files-match-pattern?".
2017-05-16 21:43:15 +02:00
ff8c179ab6
import cran: Export package predicates.
...
* guix/import/cran.scm (cran-package?, bioconductor-package?,
bioconductor-data-package?, bioconductor-experiment-package?): Export
procedures.
2017-05-16 21:42:18 +02:00
daaa270ecc
import cran: Add predicate for Bioconductor experiment packages.
...
* guix/import/cran.scm (bioconductor-experiment-package?): New variable.
2017-05-16 21:40:39 +02:00
c9ffa91fd3
import cran: Exclude experiment packages in predicate "bioconductor-package?".
...
* guix/import/cran.scm (bioconductor-package?): Exclude experiment packages,
because they cannot be updated with the default bioconductor updater.
2017-05-16 21:40:03 +02:00
7c9fcb0825
import cran: Fetch DESCRIPTION files from Github mirror.
...
* guix/import/cran.scm (%bioconductor-svn-url): Remove variable.
(bioconductor-mirror-url): New procedure.
(fetch-description): Take a REPOSITORY symbol instead of a BASE-URL string.
(cran->guix-package): Pass REPOSITORY symbol to "fetch-description".
(latest-cran-release, latest-bioconductor-release): Adjust accordingly.
(bioconductor-package?): Update comment about SVN.
2017-05-16 21:39:06 +02:00
22fc581db3
import: pypi: Robustify latest-release.
...
* guix/import/pypi.scm (latest-release): Check if pypi-fetch has
failed. If so return #f, else construct the <upstream-source>.
2017-05-13 12:40:20 +02:00
db427602d8
import: cran: Robustify cran-package?.
...
* guix/import/cran.scm (package->upstream-name): Return #f if url
start and end index could not be determined.
(cran-package?): Check if the upstream-name can be extracted from
given package.
* tests/cran.scm: Add "r-minimal is not a cran package" to make sure that
r-minimal is not detected as a cran package.
This fixes a failure of guix refresh on r-minimal because no
upsteam-name can be determined from ".../R-version.tar.gz" uri.
2017-05-13 12:40:20 +02:00
69daee23af
ui: Rename '_' to 'G_'.
...
This avoids collisions with '_' when the latter is used as a 'match'
pattern for instance. See
<https://lists.gnu.org/archive/html/guix-devel/2017-04/msg00464.html >.
* guix/ui.scm: Rename '_' to 'G_'.
* po/guix/Makevars (XGETTEXT_OPTIONS): Adjust accordingly.
* build-aux/compile-all.scm (warnings): Remove 'format'.
* gnu/packages.scm,
gnu/services.scm,
gnu/services/shepherd.scm,
gnu/system.scm,
gnu/system/shadow.scm,
guix/gnupg.scm,
guix/http-client.scm,
guix/import/cpan.scm,
guix/import/elpa.scm,
guix/import/pypi.scm,
guix/nar.scm,
guix/scripts.scm,
guix/scripts/archive.scm,
guix/scripts/authenticate.scm,
guix/scripts/build.scm,
guix/scripts/challenge.scm,
guix/scripts/container.scm,
guix/scripts/container/exec.scm,
guix/scripts/copy.scm,
guix/scripts/download.scm,
guix/scripts/edit.scm,
guix/scripts/environment.scm,
guix/scripts/gc.scm,
guix/scripts/graph.scm,
guix/scripts/hash.scm,
guix/scripts/import.scm,
guix/scripts/import/cpan.scm,
guix/scripts/import/cran.scm,
guix/scripts/import/crate.scm,
guix/scripts/import/elpa.scm,
guix/scripts/import/gem.scm,
guix/scripts/import/gnu.scm,
guix/scripts/import/hackage.scm,
guix/scripts/import/nix.scm,
guix/scripts/import/pypi.scm,
guix/scripts/import/stackage.scm,
guix/scripts/lint.scm,
guix/scripts/offload.scm,
guix/scripts/pack.scm,
guix/scripts/package.scm,
guix/scripts/perform-download.scm,
guix/scripts/publish.scm,
guix/scripts/pull.scm,
guix/scripts/refresh.scm,
guix/scripts/size.scm,
guix/scripts/substitute.scm,
guix/scripts/system.scm,
guix/ssh.scm,
guix/upstream.scm: Use 'G_' instead of '_'. Most of this change was
obtained by running: "sed -i -e's/(_ "/(G_ "/g' `find -name \*.scm`".
2017-05-03 16:16:17 +02:00
7c3e4660a5
import: Update Bioconductor release to 3.5.
...
* guix/import/cran.scm: Change Bioconductor release to 3.5.
2017-04-28 11:02:26 +02:00
5ae63362ae
import cran: Distinguish Bioconductor data packages.
...
* guix/import/cran.scm (bioconductor-package?): Exclude Bioconductor
data packages.
(bioconductor-data-package?): New procedure.
2017-04-05 18:38:51 +02:00
e1f02f92e9
Replace (compose not PROC) with simpler idioms.
...
* gnu/packages/bioinformatics.scm (python-pysam)[arguments] <check>:
Use (negate proc) instead of (compose not proc).
* guix/import/cran.scm (recursive-import): Likewise.
* guix/import/elpa.scm (filter-dependencies): Use 'remove' instead of
'(filter (compose not proc) ...)'.
2017-03-28 22:15:44 +02:00
2dca8b2d51
import cran: Automatically add gfortran and zlib when needed.
...
* guix/import/cran.scm (needs-fortran?, needs-zlib?): New procedures.
(description->package): Use them.
2017-03-28 15:37:47 +02:00
aeb64f3cb2
gnu: r: Do not build recommended packages.
...
* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.
2017-03-17 10:14:02 +01:00
4c0c4db070
utils: Move base16 procedures to (guix base16).
...
* guix/utils.scm (bytevector->base16-string, base16-string->bytevector):
Move to...
* guix/base16.scm: ... here. New file.
* tests/utils.scm ("bytevector->base16-string->bytevector"): Move to...
* tests/base16.scm: ... here. New file.
* Makefile.am (MODULES): Add guix/base16.scm.
(SCM_TESTS): Add tests/base16.scm.
* build-aux/download.scm, guix/derivations.scm,
guix/docker.scm, guix/import/snix.scm, guix/pk-crypto.scm,
guix/scripts/authenticate.scm, guix/scripts/download.scm,
guix/scripts/hash.scm, guix/store.scm, tests/hash.scm,
tests/pk-crypto.scm: Adjust imports accordingly.
2017-03-16 22:50:14 +01:00
57075ade97
import: stackage: Avoid using (guix ui) in importer code.
...
* guix/import/stackage.scm (stackage->guix-package, stackage-lts-info-fetch):
Raise 'message' condition instead of using 'leave' from (guix ui).
* guix/scripts/import/stackage.scm (guix-import-stackage): Handle conditions.
2017-02-14 08:38:45 +01:00
a4824c60ef
import: hackage: Handle unknown packages gracefully.
...
* guix/import/hackage.scm (hackage-fetch): Add 'guard'.
2017-02-09 19:36:08 +01:00
Ricardo Wurmus