b1d096f869
Revert "gnu: patchelf: Update argument phase."
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It causes too many rebuilds this late in the 'staging' cycle.
This reverts commit c1d1cd817c
2018-03-20 00:06:34 +01:00
d41ad1d553
gnu: uwsgi: Update to 2.0.17 [fixes CVE-2018-7490].
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* gnu/packages/web.scm (uwsgi): Update to 2.0.17.
[source]: Use HTTPS URL.
2018-03-19 18:56:26 -04:00
cfbf6de18c
gnu: mcron: Update to 1.1 and deprecate "mcron2".
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* gnu/packages/guile.scm (mcron): Update to 1.1.
[native-inputs]: Add TZDATA-FOR-TESTS.
[arguments]: New field.
(mcron2): Define using 'deprecated-package'.
* gnu/services/mcron.scm: Replace 'mcron2' with 'mcron'.
* doc/guix.texi (Scheduled Job Execution): Likewise.
* gnu/tests/base.scm (%mcron-os): Remove comment about mcron2.
2018-03-19 23:19:49 +01:00
f88028c432
gnu: linux-libre: Update to 4.15.11.
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* gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.11.
(%linux-libre-hash): Update hash.
2018-03-19 18:02:29 -04:00
dd07a549d0
gnu: linux-libre@4.14: Update to 4.14.28.
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* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.28.
(%linux-libre-4.14-hash): Update hash.
2018-03-19 18:01:49 -04:00
cc367c7c7a
gnu: linux-libre@4.9: Update to 4.9.88.
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* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.88.
2018-03-19 18:01:12 -04:00
75abeb73e3
gnu: linux-libre@4.4: Update to 4.4.122.
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* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.122.
2018-03-19 18:00:37 -04:00
9010123565
gnu: weechat: Update to 2.1.
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* gnu/packages/irc.scm (weechat): Update to 2.1.
2018-03-19 22:26:41 +01:00
1d9b041c2e
gnu: perl-xml-compile-soap: Update to 3.24.
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* gnu/packages/xml.scm (perl-xml-compile-soap): Update to 3.24.
2018-03-19 22:26:41 +01:00
fa3fff430b
gnu: perl-xml-simple: Update to 2.25.
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* gnu/packages/xml.scm (perl-xml-simple): Update to 2.25.
2018-03-19 22:26:40 +01:00
8d0d14479d
gnu: perl-math-random-secure: Fix typo.
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* gnu/packages/crypto.scm (perl-math-random-secure)[description]: Fix
the spelling of ‘millennia’.
2018-03-19 22:26:30 +01:00
24a2e9172a
build-system/meson: Use 'target-arm32?' for armhf-linux case.
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* guix/build-system/meson.scm (lower, meson-build): Replace armhf-linux
detection with 'target-arm32?' macro.
2018-03-19 22:07:37 +02:00
9dbdc830f6
gnu: pigx-bsseq: Update to 0.0.7.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7.
[inputs]: Add coreutils, sed, and grep.
2018-03-19 21:06:51 +01:00
096589035e
gnu: bismark: Fix references to gunzip.
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* 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.
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* 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.
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* gnu/packages/elf.scm (patchelf)[source]: Use 'https' for source uri.
2018-03-19 21:48:43 +02:00
05666fb8db
patchelf: Use 'https' for source uri.
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* gnu/packages/elf.scm (patchelf)[source]: Use 'https' for source uri.
2018-03-19 21:48:06 +02:00
c1d1cd817c
gnu: patchelf: Update argument phase.
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* gnu/packages/elf.scm (patchelf)[arguments]: Use 'modify-phases'
syntax. Replace 'system*' with 'invoke'.
2018-03-19 21:48:06 +02:00
c24f1f1614
gnu: patchelf: Use 'target-arm32?' for armhf-linux case.
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* gnu/packages/elf.scm (patchelf)[inputs]: Replace armhf-linux detection
logic with 'target-arm32?' macro.
[arguments]: Same.
2018-03-19 21:48:03 +02:00
9687d4042a
gnu: python-paramiko: Update to 2.1.5.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/haskell.scm (ghc-pandoc-citeproc-with-pandoc-1): New variable.
2018-03-19 11:07:54 +01:00
4eade64706
Merge branch 'master' into staging
2018-03-19 03:50:39 +01:00
be95bcf088
git-download: Fix recursive checkouts.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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'.
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* 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.
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* 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.
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* 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.
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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.
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This is a followup to 44dd3d579d
2018-03-18 22:25:54 +01:00
Marius Bakke