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55401 Commits

Author SHA1 Message Date
Nicolas Goaziou
c8e03dfcd1
gnu: emacs-sparql-mode: Improve description. 
* gnu/packages/emacs-xyz.scm (emacs-sparql-mode): Improve description.
 2020-08-25 09:54:47 +02:00
Michael Rohleder
19b8056c50
gnu: emacs-sparql-mode: Update to 4.0.2. 
* gnu/packages/emacs-xyz.scm (emacs-sparql-mode): Update to 4.0.2.
[propagated-inputs]: Add emacs-company.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-08-25 09:52:20 +02:00
Michael Rohleder
ed9142a672
gnu: ruby-jekyll-paginate-v2: Update to 3.0.0. 
* gnu/packages/ruby.scm (ruby-jekyll-paginate-v2): Update to 3.0.0.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-08-25 09:45:47 +02:00
Michael Rohleder
2f25868ed5
gnu: emacs-restclient: Update to 0-3.ac8aad6. 
* gnu/packages/emacs-xyz.scm (emacs-restclient): Update to 0-3.ac8aad6.
[propagated-inputs]: Add emacs-jq-mode.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-08-25 09:41:36 +02:00
Michael Rohleder
7df90fd56b
gnu: jekyll: Use GFM parser to parse kramdown. 
* gnu/packages/ruby.scm (jekyll)[propagated-inputs]: changed kramdown
parser to ruby-kramdown-parser-gfm.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-08-25 09:30:22 +02:00
Michael Rohleder
fd69aa524f
gnu: libvterm: Update to 0.1.4. 
* gnu/packages/terminals.scm (libvterm): Update to 0.1.4.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-24 13:58:27 -04:00
Mathieu Othacehe
c88bccc14e
gnu: guix: Update to 1.1.0-19.0c50d72. 
* gnu/packages/package-management.scm (guix): Update to 1.1.0-19.0c50d72.
 2020-08-24 16:07:38 +02:00
Mathieu Othacehe
0c50d7231b
gnu: guile-lzlib: Fix cross-compilation. 
* gnu/packages/guile.scm (guile-lzlib)[native-inputs]: Add "guile" when
cross-compiling.
 2020-08-24 15:02:29 +02:00
Mathieu Othacehe
65777dce0f
gnu: guile-zlib: Fix cross-compilation. 
* gnu/packages/guile.scm (guile-zlib)[native-inputs]: Add "guile" when
cross-compiling.
 2020-08-24 15:01:38 +02:00
Mathieu Othacehe
4c0c65acfa
Use "guile-zlib" and "guile-lzlib" instead of (guix config). 
* Makefile.am (MODULES): Remove guix/zlib.scm and guix/lzlib.scm,
(SCM_TESTS): remove tests/zlib.scm, tests/lzlib.scm.
* build-aux/build-self.scm (make-config.scm): Remove unused %libz variable.
* configure.ac: Remove LIBZ and LIBLZ variables and check instead for
Guile-zlib and Guile-lzlib.
* doc/guix.texi ("Requirements"): Remove zlib requirement and add Guile-zlib
and Guile-lzlib instead.
* gnu/packages/package-management.scm (guix)[native-inputs]: Add "guile-zlib"
and "guile-lzlib",
[inputs]: remove "zlib" and "lzlib",
[propagated-inputs]: ditto,
[arguments]: add "guile-zlib" and "guile-lzlib" to Guile load path.
* guix/config.scm.in (%libz, %liblz): Remove them.
* guix/lzlib.scm: Remove it.
* guix/man-db.scm: Use (zlib) instead of (guix zlib).
* guix/profiles.scm (manual-database): Do not stub (guix config) in imported
modules list, instead add "guile-zlib" to the extension list.
* guix/scripts/publish.scm: Use (zlib) instead of (guix zlib) and (lzlib)
instead of (guix lzlib),
(string->compression-type, effective-compression): do not check for zlib and
lzlib availability.
* guix/scripts/substitute.scm (%compression-methods): Do not check for lzlib
availability.
* guix/self.scm (specification->package): Add "guile-zlib" and "guile-lzlib"
and remove "zlib" and "lzlib",
(compiled-guix): remove "zlib" and "lzlib" arguments and add guile-zlib and
guile-lzlib to the dependencies, also do not pass "zlib" and "lzlib" to
"make-config.scm" procedure,
(make-config.scm): remove "zlib" and "lzlib" arguments as well as %libz and
%liblz variables.
* guix/utils.scm (lzip-port): Use (lzlib) instead of (guix lzlib) and do not
check for lzlib availability.
* guix/zlib.scm: Remove it.
* m4/guix.m4 (GUIX_LIBZ_LIBDIR, GUIX_LIBLZ_FILE_NAME): Remove them.
* tests/lzlib.scm: Use (zlib) instead of (guix zlib) and (lzlib)
instead of (guix lzlib), and do not check for zlib and lzlib availability.
* tests/publish.scm: Ditto.
* tests/substitute.scm: Do not check for lzlib availability.
* tests/utils.scm: Ditto.
* tests/zlib.scm: Remove it.
 2020-08-24 13:35:24 +02:00
Tobias Geerinckx-Rice
5abbf435fc
gnu: nano: Update to 5.2. 
* gnu/packages/nano.scm (nano): Update to 5.2.
 2020-08-24 13:28:22 +02:00
Vinicius Monego
cb4ebb7f04
gnu: python-trytond-party: Update to 5.6.0. 
* gnu/packages/tryton.scm (python-trytond-party): Update to 5.6.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2020-08-24 13:24:08 +02:00
Vinicius Monego
106dd72bc5
gnu: python-trytond-country: Update to 5.6.0. 
* gnu/packages/tryton.scm (python-trytond-country): Update to 5.6.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2020-08-24 13:23:53 +02:00
Vinicius Monego
a5bdb72d69
gnu: python-proteus: Update to 5.6.0. 
* gnu/packages/tryton.scm (python-proteus): Update to 5.6.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2020-08-24 13:22:57 +02:00
Vinicius Monego
d649704ebc
gnu: python-trytond: Update to 5.6.5. 
* gnu/packages/tryton.scm (python-trytond): Update to 5.6.5.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2020-08-24 13:22:57 +02:00
Vinicius Monego
6de7e59f8b
gnu: tryton: Update to 5.6.3. 
* gnu/packages/tryton.scm (tryton): Update to 5.6.3.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2020-08-24 13:22:55 +02:00
Michael Rohleder
cafde61d81
gnu: Add emacs-jq-mode. 
* gnu/packages/emacs-xyz.scm (emacs-jq-mode): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-08-24 12:42:35 +02:00
Michael Rohleder
e1cab74a0b
gnu: Add ruby-kramdown-parser-gfm. 
* gnu/packages/ruby.scm (ruby-kramdown-parser-gfm): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-08-24 12:38:48 +02:00
Mathieu Othacehe
2f2dbde921
gnu: Remove duplicated linux-libre-arm64-generic-5.8. 
This fixes a test failure in "fold-available-packages with/without cache".

* gnu/packages/linux.scm (linux-libre-arm64-generic-5.8): Remove it as it
duplicates linux-libre-arm64-generic.
 2020-08-24 11:54:30 +02:00
Efraim Flashner
7bcc8004b1
gnu: scroll: Fix build. 
* gnu/packages/haskell-apps.scm (scroll)[arguments]: Add custom phase to
add a place-holder file to the static output.
 2020-08-24 12:03:29 +03:00
Tobias Geerinckx-Rice
c6872990b5
gnu: dovecot: Enable FTS stemming. 
* gnu/packages/mail.scm (dovecot)[inputs]: Add libstemmer.
 2020-08-24 04:36:52 +02:00
Tobias Geerinckx-Rice
cc82816416
gnu: python-parted: Update to 3.11.6. 
* gnu/packages/disk.scm (python-parted): Update to 3.11.6.
(python2-parted): Drop unsupported Python 2 variant.
 2020-08-24 04:36:52 +02:00
Tobias Geerinckx-Rice
56b4a1d53f
gnu: bind: Note that isc-dhcp bundles a BIND. 
This follows up on commit dad963a439.

* gnu/packages/admin.scm (isc-bind): Comment.
 2020-08-24 04:36:52 +02:00
Tobias Geerinckx-Rice
e5d9a7d405
gnu: xterm: Update to 359. 
* gnu/packages/xorg.scm (xterm): Update to 359.
 2020-08-24 04:36:52 +02:00
Tobias Geerinckx-Rice
747873e81b
gnu: evisum: Update to 0.5.3. 
* gnu/packages/enlightenment.scm (evisum): Update to 0.5.3.
 2020-08-24 04:36:51 +02:00
Tobias Geerinckx-Rice
5e9e232c84
gnu: xapian: Update to 1.4.17. 
* gnu/packages/search.scm (xapian, python-xapian-bindings): Update to
1.4.17.
 2020-08-24 04:36:51 +02:00
Tobias Geerinckx-Rice
a2765029c2
gnu: electrum: Fix share/ location. 
* gnu/packages/finance.scm (electrum)[arguments]: Rename the ‘patch-home’
phase to ‘fix-prefix’.  Do so.
 2020-08-24 04:36:51 +02:00
Tobias Geerinckx-Rice
44da87334d
gnu: electron-cash: Fix share/ location. 
* gnu/packages/finance.scm (electron-cash)[arguments]: Drop bogus
‘local/share’ subdirectory: rename ‘patch-home’ to
‘create-output-directories’ and adjust body to match.
 2020-08-24 04:36:51 +02:00
Tobias Geerinckx-Rice
110888f85f
gnu: electron-cash: Return #t from phases. 
* gnu/packages/finance.scm (electron-cash)[arguments]: Return truth from
all phases.
 2020-08-24 04:36:51 +02:00
Tobias Geerinckx-Rice
8ee3e4d9e9
gnu: electrum: Return #t from phases. 
* gnu/packages/finance.scm (electrum)[arguments]: Return truth from
‘patch-home’.
 2020-08-24 04:36:51 +02:00
Tobias Geerinckx-Rice
598afe95c3
gnu: wireguard-tools: Cross-compile. 
* gnu/packages/vpn.scm (wireguard-tools)[arguments]: Use CC-FOR-TARGET.
 2020-08-24 04:32:48 +02:00
Tobias Geerinckx-Rice
f4ba46a2df
gnu: wireguard-tools: Update to 1.0.20200820. 
* gnu/packages/vpn.scm (wireguard-tools): Update to 1.0.20200820.
 2020-08-24 04:32:48 +02:00
Brendan Tildesley
29f61501f3
gnu: ebook.scm: Remove duplicate module import. 
Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-23 21:00:23 -04:00
Martin Becze
7afbaefea0
gnu: Added guile-srfi-145. 
* gnu/packages/guile-xyz.scm (guile-srfi-145): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-23 17:36:06 -04:00
Alexey Abramov
9e2a49db8c
gnu: dovecot: Add lucene library to support fts indexing. 
* gnu/packages/mail.scm (dovecot)[inputs]: Add ice4c, clucene.
[arguments]: Add --with-lucene configuration switch.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2020-08-24 00:19:27 +03:00
Martin Becze
e343816dcb
gnu: Add akku. 
* gnu/packages/package-management.scm (akku): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-23 17:17:11 -04:00
Oleg Pykhalov
a8c8f6fe91
gnu: emacs-bash-completion: Update to 3.1.0. 
* gnu/packages/emacs-xyz.scm (emacs-bash-completion): Update to 3.1.0.
 2020-08-23 19:36:58 +03:00
Tobias Geerinckx-Rice
509906c201
gnu: sane-backends-minimal: Update to 1.0.31. 
* gnu/packages/scanner.scm (sane-backends-minimal): Update to 1.0.31.
[inputs]: Add libxml2.
 2020-08-23 18:19:59 +02:00
Tobias Geerinckx-Rice
7e33054be8
gnu: parallel: Update to 20200822. 
* gnu/packages/parallel.scm (parallel): Update to 20200822.
 2020-08-23 18:19:57 +02:00
Oleg Pykhalov
045fb51efe
gnu: emacs-find-file-in-project: Update to 5.7.10. 
* gnu/packages/emacs-xyz.scm (emacs-find-file-in-project): Update to 5.7.10.
 2020-08-23 18:54:01 +03:00
Oleg Pykhalov
77a0bcacce
gnu: emacs-ghub: Update to 3.4.1. 
* gnu/packages/emacs-xyz.scm (emacs-ghub): Update to 3.4.1.
 2020-08-23 14:23:20 +03:00
Oleg Pykhalov
825b2d95f4
gnu: emacs-lsp-ui: Update to 7.0.1. 
* gnu/packages/emacs-xyz.scm (emacs-lsp-ui): Update to 7.0.1.
 2020-08-23 13:49:24 +03:00
Oleg Pykhalov
3f2d2236cf
gnu: emacs-org-re-reveal: Update to 3.1.0. 
* gnu/packages/emacs-xyz.scm (emacs-org-re-reveal): Update to 3.1.0.
 2020-08-23 13:49:24 +03:00
Efraim Flashner
24cc25be89
gnu: python-rpy2: Update to 3.3.5. 
* gnu/packages/statistics.scm (python-rpy2): Update to 3.3.5.
[source]: Add patches to fix test failures.
[arguments]: Adjust custom 'check phase.
 2020-08-23 11:13:16 +03:00
Tobias Geerinckx-Rice
dc12a37a0d
gnu: net-snmp: Update to 5.9 [fixes CVE-2019-20892]. 
* gnu/packages/networking.scm (net-snmp): Update to 5.9.
[inputs]: Add ncurses.
[native-inputs]: Add pkg-config.
 2020-08-23 06:15:20 +02:00
Jakub Kądziołka
c9f01b73cb
gnu: sameboy: Update to 0.13.6. 
* gnu/packages/emulators.scm (sameboy): Update to 0.13.6.
 2020-08-22 23:47:18 +02:00
Michael Rohleder
5a4990b982
gnu: lesspipe: Patch paths to inputs. 
* gnu/packages/less.scm (lesspipe)[arguments]: Add phase to patch
paths to tput and file.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-22 17:45:42 -04:00
Danny Milosavljevic
1bb4fd64b7
gnu: fc-host-tools: Update to 13. 
* gnu/packages/embedded.scm (fc-host-tools): Update to 13.
[description]: Modify.
 2020-08-22 20:37:41 +02:00
Adam Kandur
ca7eada918
gnu: Add sbcl-livesupport. 
* gnu/packages/lisp-xyz.scm (sbcl-livesupport, cl-livesupport, ecl-livesupport):
New variables.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-22 14:21:58 -04:00
Timotej Lazar
e5391dcc6b
gnu: lxqt: Enable keyboard shortcuts. 
* gnu/packages/lxqt.scm (lxqt)[propagated-inputs]: Add lxqt-globalkeys.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-22 14:11:35 -04:00
Brendan Tildesley
d8e83969a9
gnu: piper: Update to 0.5.1. Disable broken tests. 
* gnu/packages/gnome.scm (piper): Update to 0.5.1. Disable tests.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-22 14:06:07 -04:00
Brendan Tildesley
3403679276
gnu: libratbag: Update to 0.14. 
* gnu/packages/gnome.scm (libratbag): Update to 0.14.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-22 14:06:07 -04:00
Paul Garlick
40fc8992db
gnu: Add fullswof-2d. 
* gnu/packages/simulation.scm (fullswof-2d): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-22 13:57:35 -04:00
Vinicius Monego
b6568c3526
gnu: Add rtaudio. 
* gnu/packages/audio.scm (rtaudio): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-22 13:39:28 -04:00
Hendursaga
2183887ba9
gnu: Add dosage. 
* gnu/packages/python-xyz.scm (dosage): New variable.
 2020-08-22 13:13:59 -04:00
Martin Becze
7a3af1ae88
gnu: Add nicotine. 
* gnu/packages/nicotine.scm (nicotine): New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-08-22 12:50:55 -04:00
Oleg Pykhalov
4536c5a0a3
gnu: emacs-epkg: Update to 3.2.2. 
* gnu/packages/emacs-xyz.scm (emacs-epkg): Update to 3.2.2.
 2020-08-22 15:52:49 +03:00
Michael Rohleder
b7e76699d2
gnu: jekyll: Loosen the requirement for kramdown. 
* gnu/packages/ruby.scm (jekyll): Loosen the requirement for kramdown.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-08-22 13:22:16 +02:00
Mark H Weaver
dad963a439
gnu: isc-dhcp: Update bundled BIND to 9.11.22 [security fixes]. 
Includes fixes for CVE-2020-8617, CVE-2020-8619, CVE-2020-8622,
CVE-2020-8623, and CVE-2020-8624.

* gnu/packages/admin.scm (isc-dhcp): Update bundled BIND to 9.11.22.
 2020-08-21 21:55:24 -04:00
Mark H Weaver
1bdc6f127f
gnu: linux-libre@4.9: Update to 4.9.233. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.233.
(linux-libre-4.9-pristine-source): Update hash.
(deblob-scripts-4.9): Update to 4.9.232.
 2020-08-21 21:45:50 -04:00
Mark H Weaver
1413074d94
gnu: linux-libre@4.4: Update to 4.4.233. 
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.233.
(linux-libre-4.4-pristine-source): Update hash.
(deblob-scripts-4.4): Update to 4.4.232.
 2020-08-21 21:44:24 -04:00
Mark H Weaver
e292224da6
gnu: linux-libre: Update to 5.8.3. 
* gnu/packages/linux.scm (linux-libre-5.8-version): Update to 5.8.3.
(linux-libre-5.8-pristine-source): Update hash.
 2020-08-21 21:01:17 -04:00
Mark H Weaver
f54f3a8c24
gnu: linux-libre@5.7: Update to 5.7.17. 
* gnu/packages/linux.scm (linux-libre-5.7-version): Update to 5.7.17.
(linux-libre-5.7-pristine-source): Update hash.
 2020-08-21 21:00:39 -04:00
Mark H Weaver
518d06d132
gnu: linux-libre@5.4: Update to 5.4.60. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.60.
(linux-libre-5.4-pristine-source): Update hash.
 2020-08-21 20:59:52 -04:00
Mark H Weaver
10df5c487b
gnu: linux-libre@4.19: Update to 4.19.141. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.141.
(linux-libre-4.19-pristine-source): Update hash.
 2020-08-21 20:58:49 -04:00
Mark H Weaver
c6f92ba5e0
gnu: linux-libre@4.14: Update to 4.14.194. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.194.
(linux-libre-4.14-pristine-source): Update hash.
 2020-08-21 20:56:13 -04:00
Leo Famulari
7bb0527cef
gnu: linux-libre: Update to 5.8.2. 
* gnu/packages/aux-files/linux-libre/5.8-arm.conf,
gnu/packages/aux-files/linux-libre/5.8-arm64.conf,
gnu/packages/aux-files/linux-libre/5.8-i686.conf,
gnu/packages/aux-files/linux-libre/5.8-x86_64.conf: New files.
* Makefile.am (AUX_FILES): Add them.
* gnu/packages/linux.scm (linux-libre-5.8): New variable.
(linux-libre-version, linux-libre-pristine-source, linux-libre-source,
linux-libre): Point to linux-libre-5.8*.
 2020-08-21 17:59:42 -04:00
Leo Famulari
1bc275034f
gnu: Use a descriptive file-name for linux-libre deblobbing scripts. 
Fixes <https://bugs.gnu.org/42789>.

* gnu/packages/linux.scm (linux-libre-deblob-scripts): Set the file-name of the
deblob and deblob-check scripts.
 2020-08-21 17:59:38 -04:00
Prafulla Giri
c02398edf4
gnu: Add ronn-ng 
* gnu/packages/groff.scm (ronn-ng): New public variable.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2020-08-21 14:33:17 +02:00
Tobias Geerinckx-Rice
cc16c576a5
gnu: dovecot: Support zstd compression. 
* gnu/packages/mail.scm (dovecot)[inputs]: Add zstd:lib.
 2020-08-21 05:17:22 +02:00
Jakub Kądziołka
19ab580074
gnu: vim: Update to 8.2.1500. 
* gnu/packages/vim.scm (vim): Update to 8.2.1500.
 2020-08-21 02:25:05 +02:00
Jakub Kądziołka
3e09a2be74
gnu: vim: Install man pages. 2020-08-21 02:25:04 +02:00
Julien Lepiller
c5b20437ed
gnu: enchant: Depend on hunspell. 
* gnu/packages/enchant.scm (enchant): Add hunspell as an input.
 2020-08-21 01:42:43 +02:00
Julien Lepiller
2a29f4767f
gnu: hunspell-dict-en: Install all affix files. 
* gnu/packages/aspell.scm (aspell-word-list): Install affix files
corresponding to installed dictionary files.
 2020-08-21 01:41:58 +02:00
Eric Bavier
1cc75fef12
gnu: libmhash: Fix use-after-free in tests. 
* gnu/packages/patches/libmhash-hmac-fix-uaf.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/mcrypt.scm (libmhash)[source]: Use it.
 2020-08-20 15:28:13 -05:00
Ricardo Wurmus
c6443c2c8f
gnu: r-fourcseq: Update to 1.22.1. 
* gnu/packages/cran.scm (r-fourcseq): Update to 1.22.1.
 2020-08-20 21:25:34 +02:00
Ricardo Wurmus
4e0acfe5e7
gnu: r-complexheatmap: Update to 2.4.3. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.3.
 2020-08-20 21:25:34 +02:00
Ricardo Wurmus
e9d2cab0bf
gnu: r-gage: Update to 2.38.3. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.38.3.
[propagated-inputs]: Add r-go-db.
 2020-08-20 21:25:34 +02:00
Ricardo Wurmus
9da4a25b33
gnu: r-annotationhub: Update to 2.20.2. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.2.
 2020-08-20 21:25:34 +02:00
Ricardo Wurmus
67f8477fb5
gnu: r-delayedarray: Update to 0.14.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.1.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
b414add3d1
gnu: r-annotationdbi: Update to 1.50.3. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.3.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
e9128480d4
gnu: r-biocviews: Update to 1.56.2. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.2.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
b828c3ea90
gnu: r-biocset: Update to 1.2.2. 
* gnu/packages/bioconductor.scm (r-biocset): Update to 1.2.2.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
a27a402eba
gnu: r-experimenthub: Update to 1.14.2. 
* gnu/packages/bioconductor.scm (r-experimenthub): Update to 1.14.2.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
1bdc770dc6
gnu: r-variancepartition: Update to 1.18.3. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.18.3.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
1bf630660b
gnu: r-rsubread: Update to 2.2.6. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.2.6.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
a20538ab7e
gnu: r-rbowtie: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.28.1.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
4a504b80c2
gnu: r-biocfilecache: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 1.12.1.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
82cb9a99f8
gnu: r-rbowtie2: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-rbowtie2): Update to 1.10.1.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
a8840a04d7
gnu: r-motifstack: Update to 1.32.1. 
* gnu/packages/bioconductor.scm (r-motifstack): Update to 1.32.1.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
69f3b27822
gnu: r-clusterprofiler: Update to 3.16.1. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.16.1.
[propagated-inputs]: Add r-rlang.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
fc1c3c6f9f
gnu: r-gosemsim: Update to 2.14.1. 
* gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.14.1.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
0827e0be36
gnu: r-oligo: Update to 1.52.1. 
* gnu/packages/bioconductor.scm (r-oligo): Update to 1.52.1.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
1c43c6fa6b
gnu: r-oligoclasses: Update to 1.50.4. 
* gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.50.4.
 2020-08-20 21:25:29 +02:00
Tobias Geerinckx-Rice
15593de33c
gnu: bind: Update to 9.16.6 [multiple CVE fixes]. 
Fixes CVE-2020-8620, CVE-2020-8621, CVE-2020-8622, CVE-2020-8623, and
CVE-2020-8624.

* gnu/packages/dns.scm (isc-bind): Update to 9.16.6.
 2020-08-20 21:17:06 +02:00
Tobias Geerinckx-Rice
3f28ebd0ff
gnu: perl-catalyst-plugin-configloader: Update to 0.35. 
* gnu/packages/web.scm (perl-catalyst-plugin-configloader): Update to 0.35.
 2020-08-20 21:17:05 +02:00
Tobias Geerinckx-Rice
a7841fc486
gnu: perl-catalyst-devel: Update to 1.41. 
* gnu/packages/web.scm (perl-catalyst-devel): Update to 1.41.
 2020-08-20 21:17:04 +02:00
Tobias Geerinckx-Rice
a5526c75b8
gnu: ne: Update to 3.3.0. 
* gnu/packages/text-editors.scm (ne): Update to 3.3.0.
 2020-08-20 21:17:04 +02:00
Tobias Geerinckx-Rice
149d91814c
gnu: p11-kit: Update to 0.23.21. 
* gnu/packages/tls.scm (p11-kit): Update to 0.23.21.
 2020-08-20 21:17:03 +02:00
Ricardo Wurmus
d7f578f8c2
gnu: r-pbapply: Update to 1.4-3. 
* gnu/packages/statistics.scm (r-pbapply): Update to 1.4-3.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
800d95fe73
gnu: r-chron: Update to 2.3-56. 
* gnu/packages/statistics.scm (r-chron): Update to 2.3-56.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
5e1c17a750
gnu: r-dplyr: Update to 1.0.2. 
* gnu/packages/statistics.scm (r-dplyr): Update to 1.0.2.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
bc438f5a8f
gnu: r-mgcv: Update to 1.8-32. 
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-32.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
5eb753a276
gnu: r-mass: Update to 7.3-52. 
* gnu/packages/statistics.scm (r-mass): Update to 7.3-52.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
4be3979e99
gnu: r-stanheaders: Update to 2.21.0-6. 
* gnu/packages/cran.scm (r-stanheaders): Update to 2.21.0-6.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
69939ce955
gnu: r-showtext: Update to 0.9. 
* gnu/packages/cran.scm (r-showtext): Update to 0.9.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
4dcbea180d
gnu: r-haplo-stats: Update to 1.8.2. 
* gnu/packages/cran.scm (r-haplo-stats): Update to 1.8.2.
[propagated-inputs]: Add r-arsenal.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
c4a48418f7
gnu: r-emmeans: Update to 1.5.0. 
* gnu/packages/cran.scm (r-emmeans): Update to 1.5.0.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
88bf81c61b
gnu: r-abjutils: Update to 0.3.1. 
* gnu/packages/cran.scm (r-abjutils): Update to 0.3.1.
[propagated-inputs]: Remove r-devtools, r-furrr, r-future, r-glue, r-httr, r-progress, r-readr, r-scales, and r-tibble.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
432c62787c
gnu: r-hdf5r: Update to 1.3.3. 
* gnu/packages/cran.scm (r-hdf5r): Update to 1.3.3.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
74b438e563
gnu: r-hardyweinberg: Update to 1.6.6. 
* gnu/packages/cran.scm (r-hardyweinberg): Update to 1.6.6.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
c764026c26
gnu: r-jomo: Update to 2.7-2. 
* gnu/packages/cran.scm (r-jomo): Update to 2.7-2.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
4e6aa9aa6f
gnu: r-ape: Update to 5.4-1. 
* gnu/packages/cran.scm (r-ape): Update to 5.4-1.
 2020-08-20 19:32:24 +02:00
Ricardo Wurmus
677e83a927
gnu: Add r-arsenal. 
* gnu/packages/cran.scm (r-arsenal): New variable.
 2020-08-20 19:32:23 +02:00
Andreas Enge
280455809d
gnu: python-fpylll: Update to 0.5.2. 
* gnu/packages/algebra.scm (python-fpylll): Update to 0.5.2.
 2020-08-20 19:27:10 +02:00
Andreas Enge
b9ef00258c
gnu: fplll: Update to 5.3.2. 
* gnu/packages/algebra.scm (fplll): Update to 5.3.2.
 2020-08-20 19:23:03 +02:00
Tobias Geerinckx-Rice
d9461f688c
gnu: python-libtmux: Update to 0.8.3. 
* gnu/packages/tmux.scm (python-libtmux): Update to 0.8.3.
 2020-08-20 18:40:45 +02:00
Tobias Geerinckx-Rice
37e64053b3
gnu: vis: Run most tests. 
* gnu/packages/text-editors.scm (vis)[arguments]: Add ‘unpack-test-suite’
and ‘set-up-tests’ phase.  Run the tests after wrapping vis.
[native-inputs]: Add vis-test origin.
 2020-08-20 18:40:44 +02:00
Tobias Geerinckx-Rice
d198eca0b3
gnu: vis: Fetch sources from git. 
* gnu/packages/text-editors.scm (vis)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
 2020-08-20 18:40:43 +02:00
Tobias Geerinckx-Rice
c82cf31def
gnu: vis: Update to 0.6. 
* gnu/packages/text-editors.scm (vis): Update to 0.6.
 2020-08-20 18:40:43 +02:00
Michael Rohleder
25a6846462
gnu: emacs-browse-at-remote: Update to 0.14.0. 
* gnu/packages/emacs-xyz.scm (emacs-browse-at-remote): Update to 0.14.0.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2020-08-20 19:27:32 +03:00
Michael Rohleder
dfe4d0134b
gnu: emacs-perspective: Update to 2.10. 
* gnu/packages/emacs-xyz.scm (emacs-perspective): Update to 2.10.
(arguments): Run tests suite.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2020-08-20 19:27:32 +03:00
Michael Rohleder
c00ebfd6d7
gnu: emacs-ob-restclient: Update to 0.02-2.f7449b2. 
* gnu/packages/emacs-xyz.scm (emacs-ob-restclient): Update to 0.02-2.f7449b2.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2020-08-20 19:26:08 +03:00
Michael Rohleder
fba499cb07
gnu: emacs-visual-regexp: Update to 1.1.2. 
* gnu/packages/emacs-xyz.scm (emacs-visual-regexp): Update to 1.1.2.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
 2020-08-20 19:09:54 +03:00
Nicolas Goaziou
e6e5b797f3
gnu: keepassxc: Update to 2.6.1. 
* gnu/packages/password-utils.scm (keepassxc): Update to 2.6.1.
 2020-08-20 16:07:51 +02:00
Nicolas Goaziou
19da905921
gnu: emacs-org-superstar: Update to 1.4.0. 
* gnu/packages/emacs-xyz.scm (emacs-org-superstar): Update to 1.4.0.
 2020-08-20 14:08:32 +02:00
Jakub Kądziołka
a9e961b0c3
gnu: ccextractor: Fix build. 
* gnu/packages/gstreamer.scm (ccextractor): Add LEPTONICA to inputs.
 2020-08-20 13:53:01 +02:00
Tobias Geerinckx-Rice
2ca5b4858f
gnu: chrony: Update to 3.5.1 [fixes CVE-2020-14367]. 
* gnu/packages/ntp.scm (chrony): Update to 3.5.1.
 2020-08-20 12:53:06 +02:00
Nicolas Goaziou
3c8ab1f3bf
gnu: grammalecte: Update to 1.12.0. 
* gnu/packages/dictionaries.scm (grammalecte): Update to 1.12.0.
 2020-08-20 12:52:04 +02:00
Morgan Smith
8aa31b9305
gnu: emacs-doom-modeline: Update to 3.0.0. 
* gnu/packages/emacs-xyz.scm (emacs-doom-modeline): Update to 3.0.0.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-08-20 09:19:49 +02:00
Tobias Geerinckx-Rice
cdbb0e55c1
gnu: blender: Add colour management support. 
* gnu/packages/graphics.scm (blender)[inputs]: Add opencolorio.
 2020-08-20 06:20:11 +02:00
Tobias Geerinckx-Rice
2283cf4c1d
gnu: Add opencolorio. 
* gnu/packages/image-processing.scm (opencolorio): New public variable.
 2020-08-20 06:20:10 +02:00
Tobias Geerinckx-Rice
48d9c7c59a
gnu: wireshark: Update to 3.2.6. 
* gnu/packages/networking.scm (wireshark): Update to 3.2.6.
 2020-08-20 06:16:46 +02:00
Tobias Geerinckx-Rice
cecaa0b383
gnu: libostree: Update to 2020.5. 
* gnu/packages/package-management.scm (libostree): Update to 2020.5.
 2020-08-20 06:16:45 +02:00
Tobias Geerinckx-Rice
b14a139c96
gnu: iperf: Update to 3.9. 
* gnu/packages/networking.scm (iperf): Update to 3.9.
 2020-08-20 06:16:45 +02:00
Tobias Geerinckx-Rice
77c96b5cb7
gnu: nng: Update to 1.3.2. 
* gnu/packages/networking.scm (nng): Update to 1.3.2.
 2020-08-20 06:16:44 +02:00
Tobias Geerinckx-Rice
ac570f00b0
gnu: mate-power-manager: Update to 1.24.2. 
* gnu/packages/mate.scm (mate-power-manager): Update to 1.24.2.
[source]: Hard-code NAME.
 2020-08-20 06:16:44 +02:00
Timothy Sample
8d06906017
gnu: agda: Adjust for using shared libraries. 
See also 9e5496e0ae.

* gnu/packages/agda.scm (agda)[arguments]: Add a phase that sets
'LD_LIBRARY_PATH'; update the 'configure' phase to match the current
Haskell build system code.
 2020-08-19 23:58:47 -04:00
Timothy Sample
856def7bb3
gnu: ganeti: Tell GHC to use shared libraries. 
Fixes <https://bugs.gnu.org/42934>.
Reported by Marius Bakke <marius@gnu.org>.

* gnu/packages/virtualization.scm (ganeti)[arguments]: Add a phase
that tells GHC to use shared libraries.
 2020-08-19 23:58:47 -04:00
Timothy Sample
991ca49961
gnu: ghc-regex-pcre: Set '#:extra-directories'. 
This is a follow-up to commit 54a5fd0791.

* gnu/packages/haskell-xyz.scm (ghc-regex-pcre)[arguments]: Set
'#:extra-directories'.
 2020-08-19 23:58:47 -04:00
Timothy Sample
a928f35b2c
gnu: ghc-pcre-light: Set '#:extra-directories'. 
This is a follow-up to commit 54a5fd0791.

* gnu/packages/haskell-xyz.scm (ghc-pcre-light)[arguments]: Set
'#:extra-directories'.
 2020-08-19 23:58:46 -04:00
Tobias Geerinckx-Rice
9c5e3fb6a5
gnu: blender: Update to 2.83.5. 
* gnu/packages/graphics.scm (blender): Update to 2.83.5.
 2020-08-20 05:14:15 +02:00
Tobias Geerinckx-Rice
9372337f62
gnu: xtl: Update to 0.6.16. 
* gnu/packages/cpp.scm (xtl): Update to 0.6.16.
 2020-08-20 05:14:15 +02:00
Tobias Geerinckx-Rice
c28f242b44
gnu: mailutils: Update to 3.10. 
* gnu/packages/mail.scm (mailutils): Update to 3.10.
[arguments]: Patch a failing moderator test.
 2020-08-20 05:14:15 +02:00
Mark H Weaver
8502974c34
gnu: linux-libre: Update to 5.7.16. 
* gnu/packages/linux.scm (linux-libre-5.7-version): Update to 5.7.16.
(linux-libre-5.7-pristine-source): Update hash.
(deblob-scripts-5.7): Update to 5.7.16.
 2020-08-19 19:35:03 -04:00
Mark H Weaver
2046529ebc
gnu: linux-libre@5.8: Update to 5.8.2. 
* gnu/packages/linux.scm (linux-libre-5.8-version): Update to 5.8.2.
(linux-libre-5.8-pristine-source): Update hash.
(deblob-scripts-5.8): Update to 5.8.2.
 2020-08-19 19:34:04 -04:00
Mark H Weaver
95ff922c3e
gnu: linux-libre@5.4: Update to 5.4.59. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.59.
(linux-libre-5.4-pristine-source): Update hash.
(deblob-scripts-5.4): Update to 5.4.59.
 2020-08-19 19:33:00 -04:00
Mark H Weaver
0c3799efde
gnu: linux-libre@4.19: Update to 4.19.140. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.140.
(linux-libre-4.19-pristine-source): Update hash.
(deblob-scripts-4.19): Update to 4.19.140.
 2020-08-19 19:30:42 -04:00
Tobias Geerinckx-Rice
4c7d16c551
gnu: unknown-horizons: Fix build with python@3.8 and python-pytest@5. 
* gnu/packages/games.scm (unknown-horizons)[source]: Add patch.
[arguments]: Add a ‘fix-tests-with-pytest>=4’ phase.
[native-inputs]: Add python-distro.
* gnu/packages/patches/unknown-horizons-python-3.8-distro.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2020-08-19 23:02:26 +02:00
Tobias Geerinckx-Rice
5c83e8ec11
gnu: unknown-horizons: Return #t from all phases. 
* gnu/packages/games.scm (unknown-horizons)[arguments]: Return #t from ‘set-HOME’.
 2020-08-19 23:02:26 +02:00