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26107 Commits

Author SHA1 Message Date
Tobias Geerinckx-Rice f4548394d4
gnu: java: Fix several synopses & descriptions. 
* gnu/packages/java.scm (java-plexus-classworlds)[description]: Fix typo and
use @code.
(java-plexus-container-default-bootstrap)[synopsis]: Hyphenate for clarity,
as done in the description.
[description]: Fix typo and use @dfn.
(java-jmh)[description]: Fix typo.
(java-xerial-core)[synopsis, description]: Fix typos.
 2017-12-01 16:08:57 +01:00
Ludovic Courtès c7ffbfe9f9
gnu: guile: Add version 2.2.3. 
* gnu/packages/guile.scm (guile-2.2.3): New variable.
 2017-12-01 16:00:15 +01:00
Ludovic Courtès 8ad4f0aa31
gnu: gnome-default-applications: Add Evince for PDF and PS. 
* gnu/packages/gnome.scm (gnome-default-applications)[propagated-inputs]:
Add EVINCE.
[arguments]: Associate Evince with application/pdf and
application/postscript.
 2017-12-01 16:00:14 +01:00
Ludovic Courtès 4afc903a8c
services: xorg: Add 'font-misc-misc' to the default font set. 
Fixes <https://bugs.gnu.org/24279>.
Reported by John Darrington <john@darrington.wattle.id.au>.

* gnu/services/xorg.scm (%default-xorg-fonts): Add FONT-MISC-MISC.
 2017-12-01 16:00:14 +01:00
Ludovic Courtès e261e27676
guix system: 'init' displays a progress bar while copying. 
Until now it would print the name of each store item being copied, which
was verbose and unhelpful.

* guix/scripts/system.scm (copy-closure): Use 'progress-reporter/bar'
and 'call-with-progress-reporter'.
(guix-system): Parameterize 'current-terminal-columns'.
 2017-12-01 16:00:14 +01:00
Ludovic Courtès e4ecd51e23
guix system: Simplify closure copy. 
* guix/scripts/system.scm (copy-item): Add 'references' argument and
remove 'references*' call.  Turn into a non-monadic procedure.
(copy-closure): Remove initial call to 'references*'.  Only pass ITEM to
'topologically-sorted*' since that's equivalent.  Compute the list of
references corresponding to TO-COPY and pass it to 'copy-item'.
 2017-12-01 16:00:14 +01:00
Ludovic Courtès 1fafa2f587
weather: Use (guix progress) for progress report. 
* guix/progress.scm (start-progress-reporter!, stop-progress-reporter!)
(progress-reporter-report!): New procedures.
* guix/scripts/weather.scm (call-with-progress-reporter): New procedure.
(package-outputs)[update-progress!]: Remove.
Use 'call-with-progress-reporter' instead.
(guix-weather): Parameterize 'current-terminal-columns'.
 2017-12-01 16:00:14 +01:00
Ludovic Courtès 4cdb27af48
progress: Add 'progress-reporter/bar'. 
* guix/progress.scm (progress-reporter/bar): New procedure.
 2017-12-01 16:00:14 +01:00
Ludovic Courtès 5ed534ccc3
progress: 'progress-bar' accounts for brackets. 
* guix/progress.scm (progress-bar): Subtract 2 to BAR-WIDTH to account
for brackets.
 2017-12-01 16:00:14 +01:00
Ludovic Courtès 1252dd325b
progress: Factorize erase-in-line. 
* guix/progress.scm (erase-in-line): New procedure.
(progress-reporter/file): Use it.
 2017-12-01 16:00:14 +01:00
Tobias Geerinckx-Rice e695d79dc6
gnu: ghc-edisoncore: Fix typo in synopsis. 
* gnu/packages/haskell.scm (ghc-edisoncore)[synopsis]: Fix typo.
 2017-12-01 15:03:13 +01:00
Tobias Geerinckx-Rice fb5569b0c8
gnu: man-pages: Update to 4.14. 
* gnu/packages/man.scm (man-pages): Update to 4.14.
 2017-12-01 15:03:12 +01:00
Mathieu Othacehe 00e39b2ea4
system: vm: Do not add EFI partition on ARM system. 
* gnu/system/vm.scm (qemu-img): Do not add EFI partition if we are targetting
  ARM.

UEFI support on u-boot is still experimental, so do not add EFI partition on
ARM for now.
 2017-12-01 13:55:49 +01:00
Mathieu Othacehe e45b573c2d
utils: Add target-arm32? procedure. 
* guix/utils.scm (target-arm32?): New exported procedure.
 2017-12-01 13:55:45 +01:00
Dave Love f1de0e37d5
gnu: openfoam: Clean up to reduce closure. 
This saves ~1GB.

* gnu/packages/simulation.scm (openfoam)[outputs]: Add debug.
[arguments]: Clean up .o and src after build.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-12-01 11:28:48 +01:00
ng0 6101cad4d1
gnu: Add geomyidae. 
* gnu/packages/web.scm (geomyidae): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-12-01 11:28:48 +01:00
Mike Gerwitz 491cbd3553
gnu: Add emacs-evil-matchit. 
* gnu/packages/emacs.scm (emacs-evil-matchit): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-12-01 11:28:48 +01:00
Ludovic Courtès c03ba83c17
gnu: git: Run tests sequentially. 
Fixes <https://bugs.gnu.org/29512>.
Reported by George myglc2 Clemmer <myglc2@gmail.com>.

* gnu/packages/version-control.scm (git)[arguments]: Add
 #:parallel-tests?.
 2017-12-01 11:28:48 +01:00
Ludovic Courtès f8446df663
gnu: elogind: Remove "uaccess" tag usage in "seat-late" rules. 
* gnu/packages/freedesktop.scm (elogind)[arguments]: Add
'remove-uaccess-tag' phase.
 2017-12-01 11:28:48 +01:00
Mark H Weaver 1776d5cd18
gnu: linux-libre: Update to 4.14.3. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.14.3.
(%linux-libre-hash): Update hash.
 2017-12-01 01:37:08 -05:00
Mark H Weaver 6850c9ced5
gnu: linux-libre@4.9: Update to 4.9.66. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.66.
 2017-12-01 01:36:21 -05:00
Mark H Weaver 8b8600022c
gnu: linux-libre@4.4: Update to 4.4.103. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.103.
 2017-12-01 01:35:44 -05:00
Kei Kebreau 9ce07f2dba
doc: Update the example VCS snapshot package definition. 
In commit ee17a9e06e, the helpers git-version
and git-file-name removed the need to build version and file name strings
manually for packages that use VCS snapshots.

doc/guix.texi (Version Numbers): Use git-version and git-file-name.
 2017-11-30 12:19:29 -05:00
Rutger Helling 34a28c13f5
gnu: qemu: Enable seccomp support. 
* gnu/packages/virtualization.scm (qemu)[inputs]: Add libseccomp.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-30 18:14:57 +01:00
ng0 e33904336f
gnu: fish-guix: Update to 0.1.2.1. 
* gnu/packages/shells.scm (fish-guix): Update to 0.1.2.1.
(license): Switch to bsd-3.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-30 18:14:57 +01:00
Ludovic Courtès f00515b483
vm: Filter out file systems that refer to UUIDs or labels. 
* gnu/system/vm.scm (virtualized-operating-system)[user-file-systems]:
Filter out things that refer to file system UUIDs or labels.
 2017-11-30 18:14:57 +01:00
Vasile Dumitrascu 1d0865c19a
gnu: monero-core: Fix missing dependency. 
* gnu/packages/finance.scm (monero-core)[inputs]: Add readline.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-30 18:14:57 +01:00
Mike Gerwitz 1d752e4345
gnu: Add xautolock. 
* gnu/packages/xdisorg.scm (xautolock): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-30 18:14:56 +01:00
Ludovic Courtès e42f026eb5
ui: Present 'use-modules' hints with a question mark. 
Suggested by myglc2 <myglc2@gmail.com>.

* guix/ui.scm (report-load-error): Write "Did you forget" rather than
"Try adding."
 2017-11-30 18:14:56 +01:00
Ricardo Wurmus 117d8cc40e
gnu: jellyfish: Update to 2.2.7. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.7.
[native-inputs]: Add pkg-config.
[inputs]: Add htslib.
 2017-11-30 17:38:36 +01:00
Ricardo Wurmus f1b90a2b58
gnu: r-bigmemory: Update to 4.5.31. 
* gnu/packages/statistics.scm (r-bigmemory): Update to 4.5.31.
[propagated-inputs]: Remove r-r-utils.
 2017-11-30 17:28:27 +01:00
Ricardo Wurmus b50a4b1391
gnu: r-cowplot: Update to 0.9.1. 
* gnu/packages/statistics.scm (r-cowplot): Update to 0.9.1.
[propagated-inputs]: Add r-scales.
 2017-11-30 17:28:27 +01:00
Ricardo Wurmus a3ae2fa537
gnu: r-rcppprogress: Update to 0.4. 
* gnu/packages/statistics.scm (r-rcppprogress): Update to 0.4.
[propagated-inputs]: Add r-devtools.
 2017-11-30 17:28:26 +01:00
Ricardo Wurmus 0382d37734
gnu: r-rmarkdown: Update to 1.8. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.8.
[propagated-inputs]: Remove r-catools; add r-mime and r-stringr.
 2017-11-30 17:28:26 +01:00
Ricardo Wurmus e35cac9581
gnu: r-batchjobs: Update to 1.7. 
* gnu/packages/statistics.scm (r-batchjobs): Update to 1.7.
[propagated-inputs]: Add r-backports, r-data-table, and r-stringi; remove
r-fail and r-stringr.
 2017-11-30 17:28:25 +01:00
Ricardo Wurmus 05fd8e6b46
gnu: r-pracma: Update to 2.1.1. 
* gnu/packages/maths.scm (r-pracma): Update to 2.1.1.
 2017-11-30 17:28:24 +01:00
Ricardo Wurmus 9b8d02011f
gnu: r-annotationhub: Update to 2.10.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.1.
 2017-11-30 17:28:24 +01:00
Ricardo Wurmus 87e91a9fff
gnu: r-msnid: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.12.1.
 2017-11-30 17:28:23 +01:00
Ricardo Wurmus 439492654b
gnu: r-maldiquant: Update to 1.17. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.17.
 2017-11-30 17:28:23 +01:00
Ricardo Wurmus 06e8e0fc6c
gnu: r-genomicalignments: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.1.
 2017-11-30 17:28:22 +01:00
Ricardo Wurmus 1ce5d32b49
gnu: r-limma: Update to 3.34.2. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.2.
 2017-11-30 17:28:22 +01:00
Ricardo Wurmus 8131cf4162
gnu: r-variantannotation: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.2.
 2017-11-30 17:28:21 +01:00
Ricardo Wurmus d2081a17ed
gnu: r-getopt: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.1.
 2017-11-30 17:28:20 +01:00
Ricardo Wurmus 4220ab0c81
gnu: r-gseabase: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.1.
 2017-11-30 17:28:20 +01:00
Ricardo Wurmus d259932ca8
gnu: r-dexseq: Update to 1.24.1. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.1.
 2017-11-30 17:28:19 +01:00
Ricardo Wurmus 058644c0f2
gnu: r-deseq2: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.1.
 2017-11-30 17:28:18 +01:00
Ricardo Wurmus 654c29aceb
gnu: r-annotate: Update to 1.56.1. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.1.
 2017-11-30 17:28:18 +01:00
Ricardo Wurmus 814fd32670
gnu: r-circlize: Update to 0.4.2. 
* gnu/packages/cran.scm (r-circlize): Update to 0.4.2.
 2017-11-30 17:28:17 +01:00
Ricardo Wurmus d76f987c42
gnu: r-rcpp: Update to 0.12.14. 
* gnu/packages/cran.scm (r-rcpp): Update to 0.12.14.
 2017-11-30 17:28:17 +01:00
Ricardo Wurmus 26007cd5ee
gnu: r-timedate: Update to 3042.101. 
* gnu/packages/cran.scm (r-timedate): Update to 3042.101.
 2017-11-30 17:28:16 +01:00