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17980 Commits

Author SHA1 Message Date
Ricardo Wurmus fb1e528ef1
gnu: Add r-seqminer. 
* gnu/packages/bioinformatics.scm (r-seqminer): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus 26a281ef27
gnu: Add r-compquadform. 
* gnu/packages/statistics.scm (r-compquadform): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus 769fc6bb18
gnu: Add ribodiff. 
* gnu/packages/bioinformatics.scm (ribodiff): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus e84efc50d7
gnu: Add hisat2. 
* gnu/packages/bioinformatics.scm (hisat2): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus 5f764dd7ff
gnu: Add r-fivethirtyeight. 
* gnu/packages/statistics.scm (r-fivethirtyeight): New variable.
 2017-01-17 21:46:47 +01:00
Ricardo Wurmus 40effef7ca
gnu: powertabeditor: Update to 2.0.0-alpha9. 
* gnu/packages/music.scm (powertabeditor): Update to 2.0.0-alpha9.
[source]: Simplify snippet.
[arguments]: Adjust phases; remove unnecessary configure flag.
 2017-01-17 21:46:25 +01:00
Leo Famulari 46076d08ed
Revert "gnu: cups-filters: Disable mutool integration." 
This change would cause 594 packages to be rebuilt, so it was moved to
the staging branch.

This reverts commit 58a7bbc5fe.
 2017-01-17 15:13:54 -05:00
Leo Famulari cf3768fa06
gnu: webkitgtk: Update to 2.14.3 [security fixes]. 
Fixes CVE-2016-{7586,7589,7592,7599,7623,7632,7635,7639,7641,7645,7652,7654,7656}.

* gnu/packages/webkit.scm (webkitgtk): Update to 2.14.3.
 2017-01-17 14:56:13 -05:00
Tobias Geerinckx-Rice 58a7bbc5fe
gnu: cups-filters: Disable mutool integration. 
* gnu/packages/cups.scm (cups-filters)[arguments]: Add ‘--disable-mutool’
to #:configure-flags.
[inputs]: Remove mupdf.
 2017-01-17 18:42:37 +01:00
Tobias Geerinckx-Rice 16869cecf6
gnu: libpsl: Update to 0.17.0. 
* gnu/packages/web.scm (libpsl): Update to 0.17.0.
 2017-01-17 18:42:36 +01:00
Tobias Geerinckx-Rice cdb93e50ea
gnu: proxychains-ng: Update to 4.12. 
* gnu/packages/networking.scm (proxychains-ng): Update to 4.12.
 2017-01-17 18:42:34 +01:00
Marius Bakke 718c12786b
gnu: password-store: Install bash completions. 
* gnu/packages/password-utils.scm (password-store)[arguments]: Add
'install-shell-completions' phase.
 2017-01-17 16:18:35 +01:00
Ricardo Wurmus c554c6bab8
gnu: gnucash: Update to 2.6.15. 
* gnu/packages/gnucash.scm (gnucash): Update to 2.6.15.
 2017-01-17 15:07:08 +01:00
Björn Höfling 065d012511
gnu: Add proj.4. 
* gnu/packages/geo.scm (proj.4): New variable.
(gnome-maps): Use license: prefix.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-01-17 14:41:08 +01:00
Marius Bakke f68647299c
gnu: xscreensaver: Update to 5.36. 
* gnu/packages/xdisorg.scm (xscreensaver): Update to 5.36.
 2017-01-17 14:21:10 +01:00
Leo Famulari ae6591efa5
gnu: perl-image-exiftool: Update to 10.40. 
* gnu/packages/photo.scm (perl-image-exiftool): Update to 10.40.
[synopsis, description]: Mention more capabilities.
 2017-01-17 03:50:36 -05:00
Ricardo Wurmus 265afbdfe7
gnu: ghc-quickcheck-instances: Update to 0.3.12. 
* gnu/packages/haskell.scm (ghc-quickcheck-instances): Update to 0.3.12.
[inputs]: Add ghc-scientific and ghc-vector.
 2017-01-17 03:58:19 +01:00
Leo Famulari 19083a5eee
gnu: imagemagick: Update to 6.9.7-4 [security fixes]. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.7-4.
 2017-01-16 18:39:41 -05:00
Leo Famulari 9381a02a53
gnu: Add scrypt. 
* gnu/packages/crypto.scm (scrypt): New variable.
 2017-01-16 18:02:14 -05:00
Ricardo Wurmus ce9701fb95
gnu: Add emacs-stripe-buffer. 
* gnu/packages/emacs.scm (emacs-stripe-buffer): New variable.
 2017-01-16 23:37:43 +01:00
Ricardo Wurmus 0b35f11d76
gnu: Add emacs-git-timemachine. 
* gnu/packages/emacs.scm (emacs-git-timemachine): New variable.
 2017-01-16 23:37:43 +01:00
Ludovic Courtès ae21519f63
gnu: guile-sqlite3: Provide a new source URL. 
* gnu/packages/guile.scm (guile-sqlite3)[home-page]: Change.
 2017-01-16 23:27:23 +01:00
Ludovic Courtès 384344198d
file-systems: 'file-system-needed-for-boot?' is #t for parents of the store. 
Suggested by John Darrington <john@darrington.wattle.id.au>.

* gnu/system/file-systems.scm (%not-slash): New variable.
(file-prefix?): New procedure.
(file-system-needed-for-boot?): Use it to check whether FS holds the
store.
* tests/file-systems.scm ("file-system-needed-for-boot?"): New test.
* gnu/tests/install.scm (%separate-store-os)[file-systems]: Remove
'needed-for-boot?' field for "/gnu".
 2017-01-16 23:27:23 +01:00
Ricardo Wurmus b91cfa22e1
gnu: Add r-centipede. 
* gnu/packages/bioinformatics.scm (r-centipede): New variable.
 2017-01-16 23:18:27 +01:00
Julien Lepiller 1fdfbadff0
gnu: Add ocaml-lwt. 
* gnu/packages/ocaml.scm (ocaml-lwt): New variable.
 2017-01-16 22:34:53 +01:00
Julien Lepiller 37f17e2a1e
gnu: Add ocaml-ssl. 
* gnu/packages/ocaml.scm (ocaml-ssl): New variable.
 2017-01-16 22:34:51 +01:00
Julien Lepiller 1342fce102
gnu: Add ocaml-react. 
* gnu/packages/ocaml.scm (ocaml-react): New variable.
 2017-01-16 22:34:48 +01:00
Julien Lepiller 0a7b43a818
gnu: Add ocaml-ppx-tools. 
* gnu/packages/ocaml.scm (ocaml-ppx-tools): New variable.
 2017-01-16 22:34:45 +01:00
Julien Lepiller 69705efe94
gnu: Add ocaml-alcotest. 
* gnu/packages/ocaml.scm (ocaml-alcotest): New variable.
 2017-01-16 22:34:42 +01:00
Julien Lepiller f46bceb670
gnu: Add ocaml-astring. 
* gnu/packages/ocaml.scm (ocaml-astring): New variable.
 2017-01-16 22:34:39 +01:00
Julien Lepiller beeb2d419b
gnu: Add ocaml-fmt. 
* gnu/packages/ocaml.scm (ocaml-fmt): New variable.
 2017-01-16 22:34:36 +01:00
Julien Lepiller 8fe6b9327d
gnu: camlzip: Install both modules. 
* gnu/packages/ocaml.scm (camlzip) [arguments]: Install both zip and camlzip
modules.
 2017-01-16 22:34:30 +01:00
Thomas Danckaert 138adbbe05
gnu: Add python-autopep8. 
* gnu/packages/python.scm (python-autopep8, python2-autopep8): New variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-01-16 22:13:21 +01:00
Thomas Danckaert 2f4d08ee7f
gnu: kdevelop: Set more paths in wrapper script. 
* gnu/packages/kde.scm (kdevelop)[arguments]: Add more paths in
 wrap-executable: add "/share" output of kdevplatform and kcmutils to
 $XDG_DATA_DIRS; add "lib/plugins" from user profile to $QT_PLUGIN_PATH.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-01-16 22:13:21 +01:00
Thomas Danckaert fc11b0d3b2
gnu: kdevelop: Update to 5.0.3. 
* gnu/packages/kde.scm (kdevelop, kdevplatform): Update to 5.0.3.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-01-16 22:13:21 +01:00
Ludovic Courtès 0aeed5e310
grafts: Preserve the cache across recursive calls. 
Before this commit, we'd lose the cache across recursive calls to
'cumulative-grafts', which isn't great performance-wise.

This bug was already present before
d38bc9a9f6.

* guix/grafts.scm (with-cache): In the miss case, call 'current-state'
after EXP has been evaluated.
 2017-01-16 22:13:21 +01:00
Ludovic Courtès 90ad5c8836
grafts: Actually cache grafts during the derivation DAG traversal. 
This fixes a regression introduced in
d38bc9a9f6 whereby the cache was
effectively disabled.

Reported by Thomas Danckaert <thomas.danckaert@gmail.com>.

* guix/grafts.scm (with-cache): In the cache miss case, wrap body in
'mbegin'.
 2017-01-16 22:13:21 +01:00
Mark H Weaver b09903619f
gnu: linux-libre: Update to 4.9.4. 
* gnu/packages/linux.scm (%linux-libre-version, %linux-libre-hash)
(linux-libre): Update to 4.9.4.
 2017-01-16 05:26:33 -05:00
Mark H Weaver 8220c963e1
gnu: linux-libre@4.4: Update to 4.4.43. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.43.
 2017-01-16 05:23:04 -05:00
ng0 ad1c349db0
gnu: dwm: Add '.desktop' file. 
Fixes <https://bugs.gnu.org/25438>.

* gnu/packages/suckless.scm (dwm)[arguments]: Add
'install-xsession' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-01-16 11:03:46 +01:00
ng0 0d2c8f3420
gnu: dwm: Use modify-phases. 
* gnu/packages/suckless.scm (dwm): Use modify-phases.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-01-16 11:03:46 +01:00
Christopher Baines 849a1b8133
profiles: Export 'ca-certificate-bundle'. 
* guix/profiles.scm: Export ca-certificate-bundle, such that it can be used in
other G-expressions.  This is useful where these G-expressions run programs
that require a ca-certificate-bundle, e.g. git.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-01-16 11:03:42 +01:00
Christopher Baines 7d8b59139a
services: Export 'service-extension' procedures. 
* gnu/services.scm: Export service-extension-target and
service-extension-compute.  This allows for greater extensiblity of services
by enabling service extensions to be wrapped.  For example, the parameters
passed to the compute function can be modified, or the return value of the
compute function can be modified.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-01-16 11:03:26 +01:00
Marius Bakke 4ec840917c
gnu: zathura-pdf-poppler: Update to 0.2.7. 
* gnu/packages/pdf.scm (zathura-pdf-poppler): Update to 0.2.7.
 2017-01-16 10:21:46 +01:00
Marius Bakke 16a9f83fe0
gnu: zathura-djvu: Update to 0.2.6. 
* gnu/packages/pdf.scm (zathura-djvu): Update to 0.2.6.
 2017-01-16 10:20:15 +01:00
Marius Bakke fe5fe355fd
gnu: zathura-ps: Update to 0.2.4. 
* gnu/packages/pdf.scm (zathura-ps): Update to 0.2.4.
 2017-01-16 10:18:47 +01:00
Marius Bakke 4df3dc419d
gnu: zathura-cb: Update to 0.1.6. 
* gnu/packages/pdf.scm (zathura-cb): Update to 0.1.6.
 2017-01-16 10:16:59 +01:00
Marius Bakke 623feb452a
gnu: zathura: Update to 0.3.7. 
* gnu/packages/pdf.scm (zathura): Update to 0.3.7.
 2017-01-16 10:15:00 +01:00
Marius Bakke 24bbd9e149
gnu: girara: Update to 0.2.7. 
* gnu/packages/gtk.scm (girara): Update to 0.2.7.
 2017-01-16 10:14:00 +01:00
Marius Bakke 017ecf72ca
gnu: vim: Update to 8.0.0194. 
* gnu/packages/vim.scm (vim, vim-full): Update to 8.0.0194.
 2017-01-16 10:09:19 +01:00