096589035e
gnu: bismark: Fix references to gunzip.
...
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to
gunzip executable.
[inputs]: Add gzip.
2018-03-19 21:06:51 +01:00
51237011bf
gnu: pigx-scrnaseq: Update to 0.0.3.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3.
[inputs]: Add coreutils and perl.
2018-03-19 21:06:50 +01:00
203631d9ad
patchelf: Use 'https' for source uri.
...
* gnu/packages/elf.scm (patchelf)[source]: Use 'https' for source uri.
2018-03-19 21:48:43 +02:00
9687d4042a
gnu: python-paramiko: Update to 2.1.5.
...
* gnu/packages/python-crypto.scm (python-paramiko, python2-paramiko):
Update to 2.1.5.
2018-03-19 14:34:55 -04:00
6969ad0edd
gnu: python-pynacl: Update to 1.2.0.
...
* gnu/packages/python-crypto.scm (python-pynacl): Update to 1.2.0.
[native-inputs]: Add python-hypothesis.
2018-03-19 12:37:51 -04:00
d8f08c85ad
gnu: pigx: Update to 0.0.2.
...
* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
2018-03-19 16:55:43 +01:00
d93a1c276b
gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1.
...
* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace
ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 16:55:43 +01:00
504be7db58
gnu: bash-completion: Update to 2.8.
...
* gnu/packages/bash.scm (bash-completion): Update to 2.8.
* gnu/packages/patches/bash-completion-directories.patch: Update context.
2018-03-19 14:44:13 +01:00
39c6af4774
gnu: hdparm: Update to 9.55.
...
* gnu/packages/linux.scm (hdparm): Update to 9.55.
2018-03-19 14:41:47 +01:00
eaa69a7996
gnu: libtirpc: Update to 1.0.3.
...
* gnu/packages/onc-rpc.scm (libtirpc): Update to 1.0.3.
[source]: Remove patch.
* gnu/packages/patches/libtirpc-missing-headers.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-03-19 13:25:27 +01:00
86ce44c503
gnu: libtirpc: Always return #t from phases.
...
* gnu/packages/onc-rpc.scm (libtirpc)[arguments]: End phase with #t.
2018-03-19 13:25:26 +01:00
12c069dbcf
gnu: perl-file-basedir: Update to 0.08.
...
* gnu/packages/freedesktop.scm (perl-file-basedir): Update to 0.08.
2018-03-19 13:25:26 +01:00
0f7514580b
gnu: enlightenment: Update to 0.22.2.
...
* gnu/packages/enlightenment.scm (enlightenment): Update to 0.22.2.
2018-03-19 13:24:28 +01:00
ad19762859
gnu: python-oslo.utils: Update to 3.36.0.
...
* gnu/packages/openstack.scm (python-oslo.utils): Update to 3.36.0.
2018-03-19 13:24:28 +01:00
207e4d2705
gnu: python-oslo.i18n: Update to 3.20.0.
...
* gnu/packages/openstack.scm (python-oslo.i18n): Update to 3.20.0.
2018-03-19 13:24:28 +01:00
bae598d6c9
gnu: r-withr: Update to 2.1.2.
...
* gnu/packages/statistics.scm (r-withr): Update to 2.1.2.
2018-03-19 13:24:27 +01:00
9760061315
gnu: tilda: Update to 1.4.1.
...
* gnu/packages/terminals.scm (tilda): Update to 1.4.1.
[arguments]: Rename 'autogen phase to 'bootstrap. Clean up 'bootstrap
phase.
2018-03-19 14:22:28 +02:00
32b7ccf9b4
gnu: pigx-chipseq: Update to 0.0.8.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8.
[inputs]: Add python-magic, python-xlrd, and trim-galore.
[arguments]: Disable tests.
2018-03-19 11:07:55 +01:00
2915221bcb
gnu: pigx-scrnaseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
9dcb4d22a4
gnu: pigx-bsseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
fd757a8f21
gnu: pigx-chipseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
1a29fc3ff9
gnu: pigx-rnaseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:54 +01:00
8c6117ee22
gnu: Add ghc-pandoc-citeproc-with-pandoc-1.
...
* gnu/packages/haskell.scm (ghc-pandoc-citeproc-with-pandoc-1): New variable.
2018-03-19 11:07:54 +01:00
be95bcf088
git-download: Fix recursive checkouts.
...
* guix/git-download.scm (git-fetch)<build>: Fix match on INPUTS, which may
contain package outputs.
2018-03-18 20:00:44 -05:00
109b2f7c93
gnu: Add r-abbyyr.
...
* gnu/packages/cran.scm (r-abbyyr): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-03-19 01:06:41 +01:00
71e08fde28
glob: Add an extra glob pattern compilation stage.
...
* guix/glob.scm (compile-glob-pattern): Rename to...
(string->sglob): ... this.
(compile-sglob, string->compiled-sglob): New procedures.
(glob-match?): Replace '?, 'range, and 'set with a single clause.
* tests/glob.scm (test-compile-glob-pattern): Rename to...
(test-string->sglob): ... this. Adjust accordingly.
(test-glob-match): Use 'string->compiled-sglob' instead of
'compile-glob-pattern'.
* gnu/build/linux-modules.scm (read-module-aliases): Use
'string->compiled-sglob' instead of 'compile-glob-pattern'.
2018-03-18 22:57:17 +01:00
e914b398af
glob: Support square brackets in patterns.
...
* guix/glob.scm (wildcard-indices): Remove.
(parse-bracket): New procedure.
(compile-glob-pattern): Rewrite. Support square brackets for sets and
ranges.
(glob-match?): Support sets and ranges.
* tests/glob.scm (test-compile-glob-pattern)
(test-glob-match): New macros.
Use them to rewrite the existing tests, and add new tests.
2018-03-18 22:35:36 +01:00
675e81a082
linux-modules: 'load-linux-module*' honors BLACK-LIST in recursive calls.
...
* gnu/build/linux-modules.scm (load-linux-module*): Pass BLACK-LIST in
recursive call.
2018-03-18 22:35:27 +01:00
a57df67b59
linux-modules: Add 'current-kernel-directory'.
...
* gnu/build/linux-modules.scm (current-kernel-directory): New procedure.
(current-alias-file): Use it.
2018-03-18 22:35:03 +01:00
248db51c7e
vm: Display a backtrace upon error by default.
...
* gnu/system/vm.scm (expression->derivation-in-linux-vm): Pass
#:on-error to 'base-initrd'.
2018-03-18 22:34:40 +01:00
17cdd3d0fe
tests: elpa: Don't actually download files.
...
* tests/elpa.scm (eval-test-with-elpa): Mock 'url-fetch'.
2018-03-18 22:33:41 +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
e5425ed950
import: elpa: Adjust test for HTTPS URLs.
...
This is a followup to 44dd3d579d
2018-03-18 22:25:54 +01:00
14f2105dc6
gnu: youtube-dl: Update to 2018.03.14.
...
* gnu/packages/video.scm (youtube-dl): Update to 2018.03.14.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-03-18 18:47:16 +01:00
72406062b9
gnu: shotwell: Update to 0.28.0.
...
* gnu/packages/gnome.scm (shotwell): Update to 0.28.0.
2018-03-18 10:35:23 +00:00
e218b0c8b3
gnu: Add ruby-ruby-engine.
...
* gnu/packages/ruby.scm (ruby-ruby-engine): New variable.
2018-03-18 10:23:52 +00:00
670ee20a57
gnu: Add ruby-rake.
...
* gnu/packages/ruby.scm (ruby-rake): New variable.
2018-03-18 10:23:52 +00:00
d64ebebd8e
gnu: Add ruby-erubis.
...
* gnu/packages/ruby.scm (ruby-erubis): New variable.
2018-03-18 10:23:52 +00:00
b88502c95c
gnu: Add ruby-sporkmonger-rack-mount.
...
* gnu/packages/ruby.scm (ruby-sporkmonger-rack-mount): New variable.
2018-03-18 10:23:52 +00:00
c4550f7568
gnu: Add ruby-creole.
...
* gnu/packages/ruby.scm (ruby-creole): New variable.
2018-03-18 10:23:52 +00:00
6ef8525607
gnu: Add ruby-contest.
...
* gnu/packages/ruby.scm (ruby-contest): New variable.
2018-03-18 10:23:52 +00:00
a0a7e6903a
gnu: Add ruby-rack-protection.
...
* gnu/packages/ruby.scm (ruby-rack-protection): New variable.
2018-03-18 10:23:52 +00:00
20a0f80414
gnu: Add ruby-rack-test.
...
* gnu/packages/ruby.scm (ruby-rack-test): New variable.
2018-03-18 10:23:51 +00:00
34138e42ba
gnu: Add ruby-asciidoctor.
...
* gnu/packages/ruby.scm (ruby-asciidoctor): New variable.
2018-03-18 10:23:51 +00:00
63e07468b3
gnu: Add ruby-asciimath.
...
* gnu/packages/maths.scm (ruby-asciimath): New variable.
2018-03-18 10:23:49 +00:00
cc4c8a576c
gnu: icecat: Fix CVE-2018-{5146,5147}, etc.
...
Includes fixes for CVE-2018-5146 and CVE-2018-5147.
* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from
the upstream mozilla-esr52 repository.
2018-03-17 21:44:23 -04:00
be5ed14213
gnu: Add terraform-docs.
...
* gnu/packages/terraform.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
2018-03-17 23:04:29 +00:00
ed0c6a768e
gnu: Add go-github-com-hashicorp-hcl.
...
* gnu/packages/golang.scm (go-github-com-hashicorp-hcl): New variable.
2018-03-17 23:04:29 +00:00
c4d2cffae7
gnu: Add go-github-com-tj-docopt.
...
* gnu/packages/golang.scm (go-github-com-tj-docopt): New variable.
2018-03-17 23:04:29 +00:00
95bd9f65a8
git: 'switch-to-ref' accepts short commit IDs.
...
Fixes <https://bugs.gnu.org/30716 >.
Reported by Björn Höfling <bjoern.hoefling@bjoernhoefling.de>.
* guix/git.scm (switch-to-ref): When REF is a commit, check the length
of COMMIT and use 'object-lookup-prefix' if available.
2018-03-18 00:02:06 +01:00
Ricardo Wurmus