nixo
/
guix-devel
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity
29,964 Commits 1 Branch 0 Tags 104 MiB
Commit Graph

23427 Commits

Author SHA1 Message Date
Oleg Pykhalov bba66e7a60
gnu: streamlink: Update to 0.11.0. 
* gnu/packages/video.scm (streamlink): Update to 0.11.0.
[native-inputs]: Add python-urllib3.
 2018-03-24 09:30:02 +03:00
Chris Marusich 272c070962
tests: Add tests for "guix pack". 
* guix/scripts/pack.scm (bootstrap-xz): New variable.
  (%options) <--bootstrap>: New option.
  (show-help): Document the new --bootstrap option.
  (guix-pack): When --bootstrap is specified, use the bootstrap Guile,
  tar, and xz to build the pack, and do not use any profile hooks or
  locales.
* doc/guix.texi (Invoking guix pull): Document the new --bootstrap
  option.
* tests/guix-pack.sh: New file.
* Makefile.am (SH_TESTS): Add guix-pack.sh.
* gnu/packages/package-management.scm (guix) <inputs>: Add util-linux.
 2018-03-24 03:04:07 +01:00
Sahithi Yarlagadda 24fa6bcac6
gnu: Add r-catdap. 
* gnu/packages/cran.scm (r-catdap): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-03-23 21:56:39 +01:00
Leo Famulari 116c12a122
gnu: Keep Krita 3 along with Krita 4. 
* gnu/packages/kde.scm (krita-3): New variable.
 2018-03-23 15:42:01 -04:00
Gábor Boskovits 2cac889151
gnu: java-aqute-bnd-annotation: Update to 3.5.0. 
* gnu/packages/java.scm (java-aqute-bnd-annotation): Update to 3.5.0.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2018-03-23 20:21:37 +01:00
Tobias Geerinckx-Rice 7aff5d025d
gnu: git: Update to 2.16.3. 
* gnu/packages/version-control.scm (git): Update to 2.16.3.
 2018-03-23 14:03:52 +01:00
Tobias Geerinckx-Rice b1be07cf04
gnu: libgee: Update to 0.20.1. 
* gnu/packages/gnome.scm (libgee): Update to 0.20.1.
 2018-03-23 11:32:16 +01:00
Tobias Geerinckx-Rice cd4c6039ea
gnu: fribidi: Update to 1.0.2. 
* gnu/packages/fribidi.scm (fribidi): Update to 1.0.2.
[arguments]: Disable building documentation for now.
 2018-03-23 11:32:16 +01:00
Tobias Geerinckx-Rice ee789a411c
gnu: parallel: Update to 20180322. 
* gnu/packages/parallel.scm (parallel): Update to 20180322.
 2018-03-23 11:32:15 +01:00
Tobias Geerinckx-Rice dd8237b6c3
gnu: coq-flocq: Use predictable source URI. 
* gnu/packages/ocaml.scm (coq-flocq)[source]: Use predictable URI.
 2018-03-23 11:32:15 +01:00
Mark H Weaver 77f2ced1a6
gnu: linux-libre@4.9: Update to 4.9.89. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.89.
 2018-03-23 04:50:01 -04:00
Mark H Weaver b06e94d310
gnu: linux-libre@4.4: Update to 4.4.123. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.123.
 2018-03-23 04:49:59 -04:00
Danny Milosavljevic ec40a0501f
gnu: Add lyx. 
* gnu/packages/patches/lyx-2.2.3-fix-test.patch: New file.
* gnu/local.mk: Add it.
* gnu/packages/tex.scm (lyx): New variable.
 2018-03-22 23:11:17 +01:00
Jelle Licht 282e48eae9
gnu: node: Update to 9.9.0. 
* gnu/packages/node.scm (node): Update to 9.9.0.
 2018-03-22 19:15:24 +01:00
Leo Famulari 5e56dfadba
gnu: krita: Update to 4.0.0. 
* gnu/packages/kde.scm (krita): Update to 4.0.0.
 2018-03-22 13:37:25 -04:00
Leo Famulari 10e2ee7887
gnu: darktable: Update to 2.4.2. 
* gnu/packages/photo.scm (darktable): Update to 2.4.2.
 2018-03-22 12:10:55 -04:00
Ricardo Wurmus 618050a126
gnu: r-bookdown: Do not propagate ghc-pandoc. 
This package propagates r-rmarkdown, which propagates its own variant of
Pandoc.

* gnu/packages/bioinformatics.scm (r-bookdown)[propagated-inputs]: Remove
ghc-pandoc.
 2018-03-22 17:07:15 +01:00
Marius Bakke 63c295d2f5
gnu: nginx: Update to 1.13.10. 
* gnu/packages/web.scm (nginx): Update to 1.13.10.
[arguments]: Update kernel version to match glibc minimum requirement.
 2018-03-22 14:40:40 +01:00
Marius Bakke 069d0b7f91
gnu: nmap: Update to 7.70. 
* gnu/packages/admin.scm (nmap): Update to 7.70.
[source](snippet): End on #t.
[inputs]: Add ZLIB.
 2018-03-22 14:40:40 +01:00
Marius Bakke 0e4d067f9e
gnu: talloc: Update to 2.1.12. 
* gnu/packages/samba.scm (talloc): Update to 2.1.12.
 2018-03-22 14:16:36 +01:00
Marius Bakke cbcbb10a63
gnu: certbot: Update to 0.22.2. 
* gnu/packages/tls.scm (python-acme, certbot): Update to 0.22.2.
 2018-03-22 14:14:09 +01:00
Marius Bakke 5da2a934b4
gnu: python-cryptography: Update to 2.2.1. 
* gnu/packages/python-crypto.scm (python-cryptography-vectors,
python-cryptography): Update to 2.2.1.
 2018-03-22 14:02:11 +01:00
Maxim Cournoyer 247384d069
gnu: Add supercollider. 
* gnu/packages/audio.scm (supercollider): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-22 12:31:00 +01:00
Maxim Cournoyer 6f976d2880
gnu: yaml-cpp: Update to 0.6.1. 
* gnu/packages/serialization.scm (yaml-cpp): Update to 0.6.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-22 12:30:46 +01:00
Maxim Cournoyer 7624300c84
gnu: Add boost-sync. 
* gnu/packages/boost.scm (boost-sync): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-22 12:30:39 +01:00
Ludovic Courtès ca5b73114f
gnu: shepherd: Update to 0.4.0. 
* gnu/packages/admin.scm (shepherd): Update to 0.4.0.  Remove patches.
* gnu/packages/patches/shepherd-close-fds.patch,
gnu/packages/patches/shepherd-herd-status-sorted.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Remove them.
* gnu/services/admin.scm (%default-rotations): Remove
/var/log/shepherd.log.
 2018-03-22 11:43:30 +01:00
Mark H Weaver 4d7c5f6d7e
gnu: linux-libre: Update to 4.15.12. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.12.
(%linux-libre-hash): Update hash.
 2018-03-21 20:48:49 -04:00
Mark H Weaver 8ec89c358f
gnu: linux-libre@4.14: Update to 4.14.29. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.29.
(%linux-libre-4.14-hash): Update hash.
 2018-03-21 20:47:53 -04:00
Vasile Dumitrascu 4dd0f8c0c1
gnu: emacs-deferred: Update to 0.5.1. 
* gnu/packages/emacs.scm (emacs-deferred): Update to 0.5.1.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-03-22 00:09:55 +01:00
Vasile Dumitrascu 2fa6f63b16
gnu: emacs-clojure-mode: Update to 5.6.1. 
* gnu/packages/emacs.scm (emacs-clojure-mode): Update to 5.6.1.
 2018-03-22 00:08:15 +01:00
Leo Famulari b87c76dcaa
Fix copyright notice for Nils Gillmann. 
This is a followup to commit af23710ff5.

* gnu/packages/linux.scm: Fix name and email address for Nils Gillmann.
 2018-03-21 18:26:25 -04:00
Leo Famulari 4102588f85
gnu: mpd: Update to 0.20.18. 
* gnu/packages/mpd.scm (mpd): Update to 0.20.18.
 2018-03-21 18:26:25 -04:00
Tobias Geerinckx-Rice e2f9847be0
gnu: Add tinyscheme. 
* gnu/packages/scheme.scm (tinyscheme): New public variable.
 2018-03-21 18:38:23 +01:00
Tobias Geerinckx-Rice 0d73f1481b
gnu: libosinfo: Update usb.ids. 
This follows up commit 0def912088, which
tried to use the CVS ID as the SVN revision, which unfortunately doesn't
work.

* gnu/packages/virtualization.scm (libosinfo)[native-inputs]: Update
revision and hash for ‘usb.ids’.
 2018-03-21 17:00:11 +01:00
Leo Famulari ab68cbf2ee
gnu: rawtherapee: Update to 5.4. 
* gnu/packages/photo.scm (rawtherapee): Update to 5.4.
 2018-03-21 11:43:16 -04:00
Ricardo Wurmus 363ee7a3f4
gnu: pigx-chipseq: Update to 0.0.10. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.10.
[inputs]: Remove r-rcas and duplicate of snakemake; add r-biocparallel,
r-biostrings, r-dplyr, r-genomicalignments, rsamtools, r-s4vectors, r-tibble,
r-tidyr, r-htmlwidgets, and r-rmarkdown.
 2018-03-21 11:52:56 +01:00
Danny Milosavljevic 0def912088
gnu: libosinfo: Fix URL for usb.ids. 
Fixes <http://bugs.gnu.org/30890>.

* gnu/packages/virtualization.scm (libosinfo)[native-inputs]: Fix URL of
"usb.ids".
 2018-03-21 08:23:15 +01:00
Danny Milosavljevic db6609bd10
gnu: texlive-fonts-amsfonts: Make build reproducible. 
* gnu/packages/tex.scm (texlive-fonts-amsfonts)[arguments]<#:phases>[build]:
Make build reproducible.
 2018-03-21 01:36:50 +01:00
Leo Famulari af23710ff5
gnu: util-linux: Fix CVE-2018-7738 without grafting. 
* gnu/packages/linux.scm (util-linux)[replacement]: Remove field.
(util-linux-2.31.1): New variable.
* gnu/system.scm (%base-packages): Use util-linux-2.31.1.
 2018-03-20 17:14:22 -04:00
Tobias Geerinckx-Rice 8023f0fd03
gnu: gparted: Update to 0.31.0. 
* gnu/packages/disk.scm (gparted): Update to 0.31.0.
 2018-03-20 19:49:47 +01:00
Tobias Geerinckx-Rice 8abbe5dc82
gnu: coq-flocq: Update phase style. 
* gnu/packages/ocaml.scm (coq-flocq)[arguments]: Substitute INVOKE for
SYSTEM* and end all phases with an explicit #t.
 2018-03-20 19:49:47 +01:00
Tobias Geerinckx-Rice 324f192700
gnu: leocad: Use HTTPS home page. 
* gnu/packages/lego.scm (leocad)[home-page]: Use HTTPS.
 2018-03-20 19:49:47 +01:00
Tobias Geerinckx-Rice 84775d65a8
gnu: leocad: Update phase style. 
* gnu/packages/lego.scm (leocad)[arguments]: Substitute INVOKE for
SYSTEM* and end all phases with an explicit #t.
 2018-03-20 19:49:47 +01:00
Tobias Geerinckx-Rice b5df3e266b
gnu: leocad: Update to 18.02. 
* gnu/packages/lego.scm (leocad): Update to 18.02.
 2018-03-20 19:49:46 +01:00
Tobias Geerinckx-Rice 7d15cf175e
gnu: gmp-ecm: Update to 7.0.4. 
* gnu/packages/algebra.scm (gmp-ecm): Update to 7.0.4.
[source]: Use predictable URI.
 2018-03-20 19:49:46 +01:00
Tobias Geerinckx-Rice ef8b9a771c
gnu: r-spams: Use predictable source URI. 
* gnu/packages/statistics.scm (r-spams)[source]: Use predictable
URI.
 2018-03-20 19:49:46 +01:00
Ricardo Wurmus d7a11f1a8d
gnu: pigx-chipseq: Update to 0.0.9. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.9.
[inputs]: Add coreutils and grep.
 2018-03-20 19:47:37 +01:00
Vijayalakshmi 385e8614ef
gnu: Add python-logwrap. 
* gnu/packages/python.scm (python-logwrap): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2018-03-20 19:47:37 +01:00
Oleg Pykhalov 8c4bd04c86
gnu: python-ptyprocess: Update source URL. 
* gnu/packages/python.scm (python-ptyprocess)[origin](source): Update URL.
 2018-03-20 21:43:42 +03:00
Marius Bakke 576e0ae495
gnu: rofi: Update source hash. 
The tarball was updated in-place with a bugfix; see
<https://github.com/DaveDavenport/rofi/issues/782>.

* gnu/packages/xdisorg.scm (rofi)[source](sha256): Adjust hash.
[arguments]: Remove phase 'add-missing-configuration-files'.
 2018-03-20 19:23:34 +01:00
ng0 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
Kei Kebreau f812145e3e
gnu: ruby-sanitize: Update to 4.6.3. 
This fixes CVE-2018-3740.

* gnu/packages/ruby.scm (ruby-sanitize): Update to 4.6.3.
 2018-03-20 11:20:33 -04:00
宋文武 32745b71e1
gnu: cdogs-sdl: Update to commit bab20313. 
Fixes <https://bugs.gnu.org/30623>.

* gnu/packages/games.scm (cdogs-sdl): Update to commit
bab2031369b9ea2dbeb7eedbde10a43dd8ca83db.
[source]: Use git-fetch.
 2018-03-20 22:33:18 +08:00
Sahithi Yarlagadda c56739df6b
gnu: Add r-dyn. 
* gnu/packages/cran.scm (r-dyn): New variable.
 2018-03-20 15:00:52 +01:00
Ricardo Wurmus 4f1e4f33a0
gnu: pigx-bsseq: Update to 0.0.8. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
 2018-03-20 14:56:44 +01:00
Marius Bakke dc7e07c9b9
Merge branch 'staging' 2018-03-20 14:13:05 +01:00
Ricardo Wurmus 616446ffbf
gnu: pigx-rnaseq: Update to 0.0.3. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3.
[inputs]: Add gzip.
 2018-03-20 12:20:51 +01:00
Tobias Geerinckx-Rice c657716ede
gnu: dnsmasq: Fix description typos. 
* gnu/packages/dns.scm (dnsmasq)[description]: Fix some typos.
 2018-03-20 02:03:52 +01:00
Tobias Geerinckx-Rice 4e6c51d4eb
gnu: dnsmasq: Update to 2.79. 
* gnu/packages/dns.scm (dnsmasq): Update to 2.79.
 2018-03-20 02:03:52 +01:00
Marius Bakke a3e2b72ca9
gnu: certbot: Update to 0.22.1. 
* gnu/packages/tls.scm (python-acme, certbot): Update to 0.22.1.
 2018-03-20 01:40:07 +01:00
Marius Bakke 818e6d9704
gnu: python-cryptography: Update to 2.2. 
* gnu/packages/python-crypto.scm (python-cryptography-vectors,
python-cryptography): Update to 2.2.
 2018-03-20 01:25:10 +01:00
Marius Bakke c9838530d3
gnu: imlib2: Update to 1.5.1. 
* gnu/packages/image.scm (imlib2): Update to 1.5.1.
 2018-03-20 01:24:48 +01:00
Marius Bakke 264cb77646
gnu: imagemagick: Update to 6.9.9-39. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-39.
 2018-03-20 01:09:16 +01:00
Marius Bakke 0d729c5b14
gnu: zziplib: Correct license. 
* gnu/packages/compression.scm (zziplib)[license]: Add MPL1.1.
 2018-03-20 01:06:43 +01:00
Marius Bakke 3f986ff657
gnu: zziplib: Update to 0.13.69. 
* gnu/packages/compression.scm (zziplib): Update to 0.13.69.
[home-page]: Use new GitHub home.
[source](uri): Adjust accordingly.
[arguments]: Remove.
 2018-03-20 00:56:04 +01:00
Marius Bakke 712be306a8
gnu: rofi: Update to 1.5.1. 
* gnu/packages/xdisorg.scm (rofi): Update to 1.5.1.
 2018-03-20 00:34:00 +01:00
Marius Bakke dbc75dadb5
Revert "Revert "gnu: patchelf: Update argument phase."" 
This change only affects armhf, which doesn't use PatchELF.  My bad!

This reverts commit b1d096f869.
 2018-03-20 00:20:59 +01:00
Marius Bakke b1d096f869
Revert "gnu: patchelf: Update argument phase." 
It causes too many rebuilds this late in the 'staging' cycle.

This reverts commit c1d1cd817c.
 2018-03-20 00:06:34 +01:00
Leo Famulari d41ad1d553
gnu: uwsgi: Update to 2.0.17 [fixes CVE-2018-7490]. 
* gnu/packages/web.scm (uwsgi): Update to 2.0.17.
[source]: Use HTTPS URL.
 2018-03-19 18:56:26 -04:00
Ludovic Courtès cfbf6de18c
gnu: mcron: Update to 1.1 and deprecate "mcron2". 
* 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
Mark H Weaver f88028c432
gnu: linux-libre: Update to 4.15.11. 
* 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
Mark H Weaver dd07a549d0
gnu: linux-libre@4.14: Update to 4.14.28. 
* 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
Mark H Weaver cc367c7c7a
gnu: linux-libre@4.9: Update to 4.9.88. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.88.
 2018-03-19 18:01:12 -04:00
Mark H Weaver 75abeb73e3
gnu: linux-libre@4.4: Update to 4.4.122. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.122.
 2018-03-19 18:00:37 -04:00
Tobias Geerinckx-Rice 9010123565
gnu: weechat: Update to 2.1. 
* gnu/packages/irc.scm (weechat): Update to 2.1.
 2018-03-19 22:26:41 +01:00
Tobias Geerinckx-Rice 1d9b041c2e
gnu: perl-xml-compile-soap: Update to 3.24. 
* gnu/packages/xml.scm (perl-xml-compile-soap): Update to 3.24.
 2018-03-19 22:26:41 +01:00
Tobias Geerinckx-Rice fa3fff430b
gnu: perl-xml-simple: Update to 2.25. 
* gnu/packages/xml.scm (perl-xml-simple): Update to 2.25.
 2018-03-19 22:26:40 +01:00
Tobias Geerinckx-Rice 8d0d14479d
gnu: perl-math-random-secure: Fix typo. 
* gnu/packages/crypto.scm (perl-math-random-secure)[description]: Fix
the spelling of ‘millennia’.
 2018-03-19 22:26:30 +01:00
Ricardo Wurmus 9dbdc830f6
gnu: pigx-bsseq: Update to 0.0.7. 
* 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Efraim Flashner 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
Efraim Flashner 05666fb8db
patchelf: Use 'https' for source uri. 
* gnu/packages/elf.scm (patchelf)[source]: Use 'https' for source uri.
 2018-03-19 21:48:06 +02:00
Efraim Flashner c1d1cd817c
gnu: patchelf: Update argument phase. 
* gnu/packages/elf.scm (patchelf)[arguments]: Use 'modify-phases'
syntax.  Replace 'system*' with 'invoke'.
 2018-03-19 21:48:06 +02:00
Efraim Flashner c24f1f1614
gnu: patchelf: Use 'target-arm32?' for armhf-linux case. 
* 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
Leo Famulari 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
Leo Famulari 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 39c6af4774
gnu: hdparm: Update to 9.55. 
* gnu/packages/linux.scm (hdparm): Update to 9.55.
 2018-03-19 14:41:47 +01:00
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Efraim Flashner 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Marius Bakke 4eade64706
Merge branch 'master' into staging 2018-03-19 03:50:39 +01:00
Vijayalakshmi Vedantham 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
Sohom Bhattacharjee 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
Christopher Baines 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
Ben Woodcroft e218b0c8b3
gnu: Add ruby-ruby-engine. 
* gnu/packages/ruby.scm (ruby-ruby-engine): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft 670ee20a57
gnu: Add ruby-rake. 
* gnu/packages/ruby.scm (ruby-rake): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft d64ebebd8e
gnu: Add ruby-erubis. 
* gnu/packages/ruby.scm (ruby-erubis): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft 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
Ben Woodcroft c4550f7568
gnu: Add ruby-creole. 
* gnu/packages/ruby.scm (ruby-creole): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft 6ef8525607
gnu: Add ruby-contest. 
* gnu/packages/ruby.scm (ruby-contest): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft a0a7e6903a
gnu: Add ruby-rack-protection. 
* gnu/packages/ruby.scm (ruby-rack-protection): New variable.
 2018-03-18 10:23:52 +00:00
Ben Woodcroft 20a0f80414
gnu: Add ruby-rack-test. 
* gnu/packages/ruby.scm (ruby-rack-test): New variable.
 2018-03-18 10:23:51 +00:00
Ben Woodcroft 34138e42ba
gnu: Add ruby-asciidoctor. 
* gnu/packages/ruby.scm (ruby-asciidoctor): New variable.
 2018-03-18 10:23:51 +00:00
Ben Woodcroft 63e07468b3
gnu: Add ruby-asciimath. 
* gnu/packages/maths.scm (ruby-asciimath): New variable.
 2018-03-18 10:23:49 +00:00
Mark H Weaver 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
Marius Bakke 7ace97395f
Merge branch 'master' into staging 2018-03-18 01:09:25 +01:00
Christopher Baines 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
Christopher Baines 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
Christopher Baines 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
Ludovic Courtès 44efe67ed0
gnu: guile-git: Update to 2bb9fbb. 
* gnu/packages/guile.scm (guile-git): Update to 2bb9fbb.
 2018-03-18 00:02:06 +01:00
Ludovic Courtès b34ac82482
gnu: nss-mdns: Adjust Avahi socket file name. 
Fixes <https://bugs.gnu.org/30613>.
Regression introduced in 550f4509ac.
Reported by George myglc2 Clemmer <myglc2@gmail.com>.

* gnu/packages/avahi.scm (nss-mdns)[arguments]: Remove
 #:configure-flags.  Add #:phases.
 2018-03-18 00:02:06 +01:00
Ludovic Courtès 80f565d313
gnu: datamash: Update to 1.3. 
* gnu/packages/datamash.scm (datamash): Update to 1.3.
 2018-03-18 00:02:06 +01:00
ng0 c217df913e
gnu: fvwm: Add '.desktop' file. 
* gnu/packages/fvwm.scm (fvwm)[arguments]: Add new phase to create '.desktop' file.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-18 00:02:05 +01:00
Gábor Boskovits 3c27414968
gnu: java-simple-xml: Fix java8 test failures. 
* gnu/packages/patches/javas-simple-xml-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/java.scm (java-simple-xml)[source](patches): Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-03-18 00:02:05 +01:00
Efraim Flashner 5983b78368
gnu: shaderc: Clean up package arguments. 
* gnu/packages/vulkan.scm (shaderc)[version]: Remove extra '-'.
[arguments]: Remove extra 'mkdir-p' calls and refer to inputs directly.
 2018-03-17 23:15:34 +02:00
Rutger Helling 308b17f676
Revert "gnu: shaderc: Use more standard keys." 
This reverts commit 9bc0591bc1.
This commit broke 'shaderc'.
 2018-03-17 21:59:27 +01:00
Christopher Baines fb6f35ba1d
gnu: Add python-prometheus-client. 
* gnu/packages/monitoring.scm (python-prometheus-client,
python2-prometheus-client): New variables.
 2018-03-17 20:44:50 +00:00
Tobias Geerinckx-Rice 3def739da1
gnu: Use the CMake build system's #:build-type key. 
* gnu/packages/code.scm (rtags)[arguments]: Move the CMAKE_BUILD_TYPE
from #:configure-flags to #:build-type.
* gnu/packages/databases.scm (apache-arrow)[arguments]: Likewise
* gnu/packages/engineering.scm (kicad)[arguments]: Likewise
* gnu/packages/flashing-tools.scm (heimdall)[arguments]: Likewise
* gnu/packages/graphics.scm (openscenegraph)[arguments]: Likewise
* gnu/packages/linux.scm (rdma-core)[arguments]: Likewise
* gnu/packages/music.scm (portmidi)[arguments]: Likewise
* gnu/packages/photo.scm (rawtherapee)[arguments]: Likewise
* gnu/packages/rdesktop.scm (freerdp)[arguments]: Likewise
* gnu/packages/serialization.scm (flatbuffers)[arguments]: Likewise
* gnu/packages/web.scm (tidy-html)[arguments]: Likewise
 2018-03-17 16:37:28 +01:00
Tobias Geerinckx-Rice c695fb769c
gnu: Fix common unquote typos. 
It's easy to mistype ‘("foo" foo)’ as ‘("foo", foo)’ (which also works).
Fix such typos for the proper edification of our young.

* gnu/packages/android.scm: Move unquotes to their operands.
* gnu/packages/bootloaders.scm: Likewise.
* gnu/packages/build-tools.scm: Likewise.
* gnu/packages/chemistry.scm: Likewise.
* gnu/packages/compression.scm: Likewise.
* gnu/packages/connman.scm: Likewise.
* gnu/packages/django.scm: Likewise.
* gnu/packages/emulators.scm: Likewise.
* gnu/packages/engineering.scm: Likewise.
* gnu/packages/file-systems.scm: Likewise.
* gnu/packages/freedesktop.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gimp.scm: Likewise.
* gnu/packages/gl.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/graphics.scm: Likewise.
* gnu/packages/haskell.scm: Likewise.
* gnu/packages/irc.scm: Likewise.
* gnu/packages/julia.scm: Likewise.
* gnu/packages/kde-frameworks.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/lua.scm: Likewise.
* gnu/packages/mail.scm: Likewise.
* gnu/packages/make-bootstrap.scm: Likewise.
* gnu/packages/messaging.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/networking.scm: Likewise.
* gnu/packages/ocaml.scm: Likewise.
* gnu/packages/perl.scm: Likewise.
* gnu/packages/python.scm: Likewise.
* gnu/packages/python-web.scm: Likewise.
* gnu/packages/qt.scm: Likewise.
* gnu/packages/ratpoison.scm: Likewise.
* gnu/packages/sdl.scm: Likewise.
* gnu/packages/sml.scm: Likewise.
* gnu/packages/terminals.scm: Likewise.
* gnu/packages/text-editors.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/virtualization.scm: Likewise.
* gnu/packages/vulkan.scm: Likewise.
* gnu/packages/wget.scm: Likewise.
* gnu/packages/wine.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xml.scm: Likewise.
* gnu/packages/xorg.scm: Likewise.
 2018-03-17 16:37:27 +01:00
Tobias Geerinckx-Rice 9bc0591bc1
gnu: shaderc: Use more standard keys. 
* gnu/packages/vulkan.scm (shaderc)[arguments]: Move cmake options from
the raw INVOKE call to #:build-type and #:configure-flags.  Adjust the
‘configure’ phase accordingly.
 2018-03-17 16:37:26 +01:00
Tobias Geerinckx-Rice 8696fbbad1
gnu: shaderc: Use standard versioning scheme. 
* gnu/packages/vulkan.scm (shaderc)[version]: Use GIT-VERSION with a
‘0.0.0’ prefix.
 2018-03-17 16:37:26 +01:00
Tobias Geerinckx-Rice 49c4c4de85
gnu: shaderc: Fix formatting. 
* gnu/packages/vulkan.scm (shaderc): Use conventional indentation.
[native-inputs]: Move unquotes to their operands.
 2018-03-17 16:37:25 +01:00
Tobias Geerinckx-Rice 36a17f056c
gnu: texlive-latex-type1cm: Fix description typo. 
* gnu/packages/tex.scm (texlive-latex-type1cm)[description]: Fix typo.
 2018-03-17 16:37:25 +01:00
Tobias Geerinckx-Rice f17f9984c3
gnu: python-pkginfo: Update to 1.4.2. 
* gnu/packages/python.scm (python-pkginfo): Update to 1.4.2.
 2018-03-17 16:37:25 +01:00
Tobias Geerinckx-Rice 4bd77a5dd0
gnu: python-nbformat: Update to 4.4.0. 
* gnu/packages/python.scm (python-nbformat): Update to 4.4.0.
 2018-03-17 16:37:24 +01:00
Tobias Geerinckx-Rice 40a1020240
gnu: python-simplejson: Update to 3.13.2. 
* gnu/packages/python.scm (python-simplejson): Update to 3.13.2.
 2018-03-17 16:37:24 +01:00
Tobias Geerinckx-Rice c8674cf5fe
gnu: python-ptyprocess: Update to 0.5.2. 
* gnu/packages/python.scm (python-ptyprocess): Update to 0.5.2.
 2018-03-17 16:37:24 +01:00
Tobias Geerinckx-Rice e83539e8cc
gnu: python-chai: Update to 1.1.2. 
* gnu/packages/python.scm (python-chai): Update to 1.1.2.
 2018-03-17 16:37:23 +01:00
Tobias Geerinckx-Rice c300630d55
gnu: python-jupyter-console: Update to 5.2.0. 
* gnu/packages/python.scm (python-jupyter-console): Update to 5.2.0.
 2018-03-17 16:37:23 +01:00
Tobias Geerinckx-Rice c7bb731af8
gnu: python-kazoo: Update to 2.4.0. 
* gnu/packages/python.scm (python-kazoo): Update to 2.4.0.
 2018-03-17 16:37:23 +01:00
Tobias Geerinckx-Rice 96de54114c
gnu: python-jupyter-core: Update to 4.4.0. 
* gnu/packages/python.scm (python-jupyter-core): Update to 4.4.0.
 2018-03-17 16:37:22 +01:00
Tobias Geerinckx-Rice 34f53e4fbf
gnu: python-phonenumbers: Update to 8.9.1. 
* gnu/packages/python.scm (python-phonenumbers): Update to 8.9.1.
 2018-03-17 16:37:22 +01:00
Tobias Geerinckx-Rice e5fa7df963
gnu: python-decorator: Update to 4.2.1. 
* gnu/packages/python.scm (python-decorator): Update to 4.2.1.
 2018-03-17 16:37:22 +01:00
Tobias Geerinckx-Rice f212a85e41
gnu: python-jsonschema: Update to 2.6.0. 
* gnu/packages/python.scm (python-jsonschema): Update to 2.6.0.
 2018-03-17 16:37:21 +01:00
Tobias Geerinckx-Rice c9ec726cd8
gnu: python-protobuf: Update to 3.5.2. 
* gnu/packages/protobuf.scm (python-protobuf): Update to 3.5.2.
 2018-03-17 16:37:21 +01:00