nixo
/
guix-devel
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity
34,799 Commits
1 Branch
0 Tags
104 MiB
Commit Graph

34799 Commits (910a20e2b8ac6d1c331ff79535831cce6222b3a3)

Author SHA1 Message Date
Ricardo Wurmus eb251fe524
gnu: r-igraph: Update to 1.2.2. 
* gnu/packages/graph.scm (r-igraph): Update to 1.2.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus c273bcdfce
gnu: r-diffusionmap: Update to 1.1-0.1. 
* gnu/packages/graph.scm (r-diffusionmap): Update to 1.1-0.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 6f6aef80e3
gnu: r-seurat: Update to 2.3.4. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4.
[source]: Remove snippet.
[arguments]: Remove.
[native-inputs]: Remove.
[propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger,
r-stringr, r-tclust, and rvgam; add r-httr.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 07bd90ce90
gnu: r-msnbase: Update to 2.6.3. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 4ee8c37cca
gnu: r-maldiquant: Update to 1.18. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 48b21f8b6b
gnu: r-seqminer: Update to 6.1. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus ad2ed8d01f
gnu: r-genomicfeatures: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus f2e79823c6
gnu: r-rtracklayer: Update to 1.40.6. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus aea1b6fb8a
gnu: r-delayedarray: Update to 0.6.5. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 3e61c2a8b1
gnu: r-rsamtools: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus a02340058c
gnu: r-biocparallel: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 1d56c79f86
gnu: r-genomicranges: Update to 1.32.6. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 688cb08527
gnu: r-limma: Update to 3.36.3. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 33a103a543
gnu: r-variantannotation: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 1adf4596a6
gnu: r-edger: Update to 3.22.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 5728d9c6c0
gnu: r-iranges: Update to 2.14.11. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 3c04375614
gnu: r-biocviews: Update to 1.48.3. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus ce0e762bf9
gnu: r-annotationforge: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 65050163e0
gnu: r-chippeakanno: Update to 3.14.1. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.1.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 88e4ed55d6
gnu: Add r-clipr. 
* gnu/packages/cran.scm (r-clipr): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 6a8469755c
gnu: Add r-rdpack. 
* gnu/packages/cran.scm (r-rdpack): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus dd954dd743
gnu: Add r-gbrd. 
* gnu/packages/cran.scm (r-gbrd): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 53718658d2
gnu: Add r-polynom. 
* gnu/packages/cran.scm (r-polynom): New variable.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 356230da4a
gnu: Add r-fansi. 
* gnu/packages/cran.scm (r-fansi): New variable.
 2018-09-05 20:03:03 +02:00
Ludovic Courtès 3b0153bd82
gnu: guix-daemon: Add dependency on Guile-Gcrypt. 
This is a followup to 53166aec98, which
made Guile-Gcrypt a hard dependency.

* gnu/packages/package-management.scm (guix-daemon)[inputs]: Add
GUILE-GCRYPT.
 2018-09-05 15:48:04 +02:00
Ludovic Courtès 7903f00a74
gnu: cuirass: Add dependency on Guile-Gcrypt. 
This is a followup to 53166aec98, which
added a hard dependency of Guix on Guile-Gcrypt.

* gnu/packages/ci.scm (cuirass)[inputs]: Add GUILE-GCRYPT.
[arguments]: In 'wrap-program' phase, use 'string-join' to compute
'mods'.  Define 'objs' for use in GUILE_LOAD_COMPILED_PATH, and take
objects from lib/guile/X.Y/site-ccache.
 2018-09-05 15:35:54 +02:00
Ludovic Courtès 5e3082df1c
gnu: guile-fibers: Install .go files to "…/site-ccache". 
* gnu/packages/guile.scm (guile-fibers)[arguments]: New field.
 2018-09-05 15:35:54 +02:00
Eric Bavier 3f5e6ccf9b
slepc: Upgrade to 3.9.2. 
* gnu/packages/maths.scm (slepc): Upgrade to 3.9.2.
 2018-09-05 08:10:38 -05:00
Eric Bavier c15be1280e
petsc: Upgrade to 3.9.3. 
* gnu/packages/maths.scm (petsc): Upgrade to 3.9.3.
[arguments]: Remove unnecessary configure flags.
 2018-09-05 08:10:37 -05:00
Eric Bavier a3a99e27bb
petsc: Move example code to "examples" output. 
* gnu/packages/maths.scm (petsc)[arguments]: New 'move-examples' phase.
 2018-09-05 08:10:37 -05:00
Eric Bavier b26e4f26ff
gnu: Add SUNDIALS. 
* gnu/packages/maths.scm (sundials, sundials-openmpi): New variables.
 2018-09-05 08:10:31 -05:00
Alex Vong 296f091b48
gnu: packages: mp3: Use HTTPS where possible. 
* gnu/packages/mp3.scm (libmad)[home-page]: Use HTTPS.
(libid3tag)[home-page]: Likewise.
(mp3info)[source, home-page]: Likewise.
(mpg123)[source]: Likewise.
(libmpcdec)[source, home-page]: Likewise.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-05 20:56:55 +08:00
Alex Vong 998100e6e8
gnu: eyed3: Update home page. 
* gnu/packages/mp3.scm (eyed3)[home-page]: Update to redirected HTTPS URL.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2018-09-05 20:56:55 +08:00
Ludovic Courtès 53166aec98
gnu: guix: Update to 3d43017. 
* gnu/packages/package-management.scm (guix): Update to 3d43017.
 2018-09-05 14:31:48 +02:00
Ludovic Courtès 3d43017026
tests: Adjust 'add-file-tree-to-store' test for lack of /bin/sh. 
* tests/store.scm (%shell): New variable.
("add-file-tree-to-store"): Use it instead of "/bin/sh".  This fixes
builds in the chroot build environment.
 2018-09-05 13:59:10 +02:00
Ludovic Courtès 185948b8a8
gnu: xorg: Fix typo. 
* gnu/packages/xorg.scm: Fix typo in Benjamin's email address.
 2018-09-05 13:57:43 +02:00
Ludovic Courtès 030f1367f0
channels: Add 'latest-channel-derivation' convenience procedure. 
* guix/channels.scm (latest-channel-derivations): Remove.
(latest-channel-instances*, latest-channel-derivation): New procedures.
 2018-09-05 12:01:48 +02:00
Ricardo Wurmus 4fd2622df8
gnu: python-tables: Update to 3.4.4. 
* gnu/packages/python.scm (python-tables): Update to 3.4.4.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus 8afdeb8751
gnu: python-pybigwig: Update to 0.3.12. 
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12.
[propagated-inputs]: Add python-numpy.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus 0d7974c376
gnu: libbigwig: Update to 0.4.2. 
* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.2.
[source]: Fetch from git.
[arguments]: Disable tests; remove build phases "disable-curl-test" and
"create-target-dirs".
[native-inputs]: Add python-2.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus ca1dc4c76a
gnu: nss-pam-ldapd: Update to 0.9.10. 
* gnu/packages/openldap.scm (nss-pam-ldapd): Update to 0.9.10.
 2018-09-05 11:44:52 +02:00
Rutger Helling fefe17b088
gnu: dolphin-emu: Update to commit 5f0d825. 
* gnu/packages/emulators.scm (dolphin-emu): Update to commit 5f0d825.
 2018-09-05 10:23:20 +02:00
Leo Famulari fcf4841c0e
gnu: Zsh: Patch some tests that began failing in 5.6. 
* gnu/packages/shells.scm (zsh)[arguments]: Patch the tests rather than deleting
them.
 2018-09-04 18:34:01 -04:00
Leo Famulari 95681e5586
gnu: Zsh: Update to 5.6 [fixes CVE-2018-{0502,13259}]. 
* gnu/packages/shells.scm (zsh): Update to 5.6.
[arguments]: Skip some tests.
 2018-09-04 18:10:53 -04:00
Ludovic Courtès ca71942445
Switch to Guile-Gcrypt. 
This removes (guix hash) and (guix pk-crypto), which now live as part of
Guile-Gcrypt (version 0.1.0.)

* guix/gcrypt.scm, guix/hash.scm, guix/pk-crypto.scm,
tests/hash.scm, tests/pk-crypto.scm: Remove.
* configure.ac: Test for Guile-Gcrypt.  Remove LIBGCRYPT and
LIBGCRYPT_LIBDIR assignments.
* m4/guix.m4 (GUIX_ASSERT_LIBGCRYPT_USABLE): Remove.
* README: Add Guile-Gcrypt to the dependencies; move libgcrypt as
"required unless --disable-daemon".
* doc/guix.texi (Requirements): Likewise.
* gnu/packages/bash.scm, guix/derivations.scm, guix/docker.scm,
guix/git.scm, guix/http-client.scm, guix/import/cpan.scm,
guix/import/cran.scm, guix/import/crate.scm, guix/import/elpa.scm,
guix/import/gnu.scm, guix/import/hackage.scm,
guix/import/texlive.scm, guix/import/utils.scm, guix/nar.scm,
guix/pki.scm, guix/scripts/archive.scm,
guix/scripts/authenticate.scm, guix/scripts/download.scm,
guix/scripts/hash.scm, guix/scripts/pack.scm,
guix/scripts/publish.scm, guix/scripts/refresh.scm,
guix/scripts/substitute.scm, guix/store.scm,
guix/store/deduplication.scm, guix/tests.scm, tests/base32.scm,
tests/builders.scm, tests/challenge.scm, tests/cpan.scm,
tests/crate.scm, tests/derivations.scm, tests/gem.scm,
tests/nar.scm, tests/opam.scm, tests/pki.scm,
tests/publish.scm, tests/pypi.scm, tests/store-deduplication.scm,
tests/store.scm, tests/substitute.scm: Adjust imports.
* gnu/system/vm.scm: Likewise.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this.  Add GUILE-GCRYPT.
(expression->derivation-in-linux-vm)[config]: Remove.
(iso9660-image)[config]: Remove.
(qemu-image)[config]: Remove.
(system-docker-image)[config]: Remove.
* guix/scripts/pack.scm: Adjust imports.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this.  Add GUILE-GCRYPT.
(self-contained-tarball)[build]: Call 'make-config.scm' without
 #:libgcrypt argument.
(squashfs-image)[libgcrypt]: Remove.
[build]: Call 'make-config.scm' without #:libgcrypt.
(docker-image)[config, json]: Remove.
[build]: Add GUILE-GCRYPT to the extensions  Remove (guix config) from
the imported modules.
* guix/self.scm (specification->package): Remove "libgcrypt", add
"guile-gcrypt".
(compiled-guix): Remove #:libgcrypt.
[guile-gcrypt]: New variable.
[dependencies]: Add it.
[*core-modules*]: Remove #:libgcrypt from 'make-config.scm' call.
Add #:extensions.
[*config*]: Remove #:libgcrypt from 'make-config.scm' call.
(%dependency-variables): Remove %libgcrypt.
(make-config.scm): Remove #:libgcrypt.
* build-aux/build-self.scm (guile-gcrypt): New variable.
(make-config.scm): Remove #:libgcrypt.
(build-program)[fake-gcrypt-hash]: New variable.
Add (gcrypt hash) to the imported modules.  Adjust load path
assignments.
* gnu/packages/package-management.scm (guix)[propagated-inputs]: Add
GUILE-GCRYPT.
[arguments]: In 'wrap-program' phase, add GUILE-GCRYPT to the search
path.
 2018-09-04 17:25:11 +02:00
Ludovic Courtès 7e1d229019
inferior: Add home-page and location package accessors. 
* guix/inferior.scm (inferior-package-home-page)
(inferior-package-location): New procedures.
* tests/inferior.scm ("inferior-packages"): Test them.
 2018-09-04 17:22:55 +02:00
Alex Vong 1bf758767d
gnu: Add emacs-picpocket. 
* gnu/packages/emacs.scm (emacs-picpocket): New public variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:39:43 +02:00
Paul Garlick 71ca16b58d
gnu: petsc-openmpi: Configure with support for hdf5 data format. 
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add
hdf5-parallel-openmpi.
[arguments]: Add '--with-hdf5-include' and '--with-hdf5-lib'
flags.  Add 'set-test-environment' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:22:48 +02:00
Jonathan Brielmaier b50658fe8a
gnu: kicad: Update to 5.0.0. 
* gnu/packages/engineering.scm (kicad): Update to 5.0.0.
[source]: Change from git to url-fetch.
[arguments]: Remove now unneeded build version parameter.
[inputs]: Add opencascade-oce.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-04 15:02:59 +02:00
Arun Isaac 906a396bff
gnu: ghc-zlib: Enable tests. 
* gnu/packages/haskell.scm (ghc-zlib)[arguments]: Enable tests. Allow building
with newer tasty.
[native-inputs]: Add ghc-quickcheck, ghc-tasty, ghc-tasty-hunit and
ghc-tasty-quickcheck.
 2018-09-04 17:31:09 +05:30