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Author SHA1 Message Date
David Thompson 52b617ffeb
gnu: Update awscli to 1.11.185. 
* gnu/packages/python-web.scm (awscli): Update to 1.11.185.
 2017-11-14 14:20:42 -05:00
Kei Kebreau 31d9e454ad
gnu: gnome-calculator: Update to 3.26.0. 
* gnu/packages/gnome.scm (gnome-calculator): Update to 3.26.0.
 2017-11-14 14:12:42 -05:00
Kei Kebreau a5a22d7b14
gnu: gnome-system-monitor: Update to 3.26.0. 
* gnu/packages/gnome.scm (gnome-system-monitor): Update to 3.26.0.
 2017-11-14 13:47:03 -05:00
Tobias Geerinckx-Rice 85a9ffcbf4
gnu: exim: Use HTTPS for home page. 
* gnu/packages/mail.scm (exim)[home-page]: Use HTTPS.
 2017-11-14 04:06:53 +01:00
Tobias Geerinckx-Rice 58b8d1b39f
gnu: iproute2: Update to 4.14.0. 
* gnu/packages/linux.scm (iproute): Update to 4.14.0.
 2017-11-14 04:06:53 +01:00
Ludovic Courtès 1b2f753d9c
gnu: Move web packages from python to python-web. 
This is in part to address <https://bugs.gnu.org/27284>.

* gnu/packages/python.scm (python-httplib2, python2-httplib2)
(python-sockjs-tornado, python2-sockjs-tornado)
(python-flask-babel, python2-flask-babel)
(python-html5lib, python2-html5lib)
(python-html5lib-0.9, python2-html5lib-0.9)
(python-html5-parser, python2-html5-parser)
(python-webencodings, python2-webencodings)
(python-openid, python2-openid, python-cssutils, python2-cssutils)
(python-cssselect, python2-cssutils)
(python-openid-cla, python2-openid-cla)
(python-openid-teams, python2-openid-teams)
(python-tornado, python2-tornado)
(python-tornado-http-auth, python-terminado, python2-terminado)
(python-webob, python2-webob, python-zope-event, python2-zope-event)
(python-zope-interface, python2-zope-interface)
(python-zope-exceptions, python2-zope-exceptions)
(python-zope-testing, python2-zope-testing)
(python-zope-testrunner, python2-zope-testrunner)
(python-zope-i18nmessageid, python2-zope-i18nmessageid)
(python-zope-schema, python2-zope-schema)
(python-zope-configuration, python2-zope-configuration)
(python-zope-proxy, python2-zope-proxy)
(python-zope-location, python2-zope-location)
(python-zope-security, python2-zope-security)
(python-zope-component, python2-zope-component)
(python-ndg-httpsclient, python2-ndg-httpsclient)
(python-websocket-client, python2-websocket-client)
(python-requests-toolbelt, python2-requests-toolbelt)
(python-rauth, python2-rauth, python-urllib3, python2-urllib3)
(awscli, python-wsgiproxy2, python2-wsgiproxy2)
(python-pastedeploy, python2-pastedeploy)
(python-webtest, python2-webtest, python-flask, python2-flask)
(python-flast-wtf, python2-flask-wtf)
(python-flask-multistatic, python2-flask-multistatic)
(python-cookies, python2-cookies)
(python-responses, python2-responses)
(python-geventhttpclient, python2-geventhttpclient)
(python-requests-oauthlib, python2-requests-oauthlib)
(python-url, python2-url, python-cachecontrol, python2-cachecontrol)
(python-betamax, python2-betamax)
(python-betamax-matchers, python2-betamax-matchers)
(python-s3transfer, python2-s3transfer)
(python-flask-restful, python-flask-basicauth)
(python-flask-sqlalchemy, python-flask-restplus)
(python-flask-restful-swagger, python-htmlmin, python2-htmlmin)
(python-flask-htmlmin, python2-flask-htmlmin)
(python-flask-login, python2-flask-login)
(python-oauth2client, python-flask-oidc)
(python-webassets, python-cssmin, python2-cssmin)
(python-elasticsearch, python2-elasticsearch)
(python-flask-script, python2-flask-script)
(python-flask-migrate, python2-flask-migrate)
(python-genshi, python2-genshi)
(python-flask-principal, python2-flask-principal)
(python-flask-httpauth, python2-flask-httpauth)
(python-uritemplate, python2-uritemplate): Move to...
* gnu/packages/python-web.scm: ... here.  New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/admin.scm, gnu/packages/backup.scm,
gnu/packages/dav.scm, gnu/packages/django.scm,
gnu/packages/docker.scm, gnu/packages/ebook.scm,
gnu/packages/logging.scm, gnu/packages/mail.scm,
gnu/packages/music.scm, gnu/packages/openstack.scm,
gnu/packages/package-management.scm, gnu/packages/rdf.scm,
gnu/packages/tls.scm, gnu/packages/tor.scm,
gnu/packages/tryton.scm, gnu/packages/version-control.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm: Adjust accordingly.
 2017-11-13 23:41:01 +01:00
Ben Woodcroft a68e586097
gnu: diamond: Update to 0.9.13. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.13.
 2017-11-14 08:25:43 +10:00
Ricardo Wurmus 5ccde2079e
gnu: Move test packages from perl to perl-check. 
* gnu/packages/perl.scm (perl-test2-bundle-extended,
perl-test2-plugin-nowarnings, perl-test-base, perl-test-class,
perl-test-class-most, perl-test-cleannamespaces, perl-test-command,
perl-test-cpan-meta, perl-test-cpan-meta-json, perl-test-deep,
perl-test-differences, perl-test-directory, perl-test-eol,
perl-test-exception, perl-test-fatal, perl-test-file-sharedir-dist,
perl-test-files, perl-test-harness, perl-test-leaktrace,
perl-test-longstring, perl-test-manifest, perl-test-memory-cycle,
perl-test-mockobject, perl-test-mocktime, perl-test-most, perl-test-needs,
perl-test-notabs, perl-test-nowarnings, perl-test-number-delta,
perl-test-output, perl-test-pod, perl-test-pod-coverage, perl-test-requires,
perl-test-script, perl-test-sharedfork, perl-test-simple, perl-test-taint,
perl-test-tester, perl-test-trap, perl-test-utf8, perl-test-warn,
perl-test-warnings, perl-test-without-module, perl-test-writevariants,
perl-test-yaml, perl-test-trailingspace): Move variables to ...
* gnu/packages/perl-check.scm: ... this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/admin.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/crypto.scm,
gnu/packages/databases.scm,
gnu/packages/glib.scm,
gnu/packages/gnupg.scm,
gnu/packages/image-viewers.scm,
gnu/packages/language.scm,
gnu/packages/networking.scm,
gnu/packages/package-management.scm,
gnu/packages/perl.scm,
gnu/packages/terminals.scm,
gnu/packages/tex.scm,
gnu/packages/version-control.scm,
gnu/packages/web.scm,
gnu/packages/xml.scm,
gnu/packages/xorg.scm: Use perl-check module.
 2017-11-13 23:03:01 +01:00
Ricardo Wurmus 587d175266
gnu: ghc-tls: Move to (gnu packages tls). 
* gnu/packages/haskell.scm (ghc-tls): Move from here...
* gnu/packages/tls.scm (ghc-tls): ...to here.
* gnu/packages/haskell-web.scm: Use (gnu packages tls).
 2017-11-13 18:40:55 +01:00
Ricardo Wurmus f24eba89f4
gnu: Move crypto packages from haskell to haskell-crypto. 
* gnu/packages/haskell.scm (ghc-asn1-types, ghc-asn1-encoding, ghc-asn1-parse,
ghc-crypto-api, ghc-crypto-api-tests, ghc-cryptohash, ghc-cryptohash-md5,
ghc-cryptohash-sha1, ghc-cryptonite, ghc-digest, ghc-entropy, ghc-pem,
ghc-puremd5, ghc-sha, ghc-x509, ghc-x509-store, ghc-x509-validation,
ghc-x509-system): Move variables to ...
* gnu/packages/haskell-crypto.scm: ... this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/haskell.scm,
gnu/packages/haskell-web.scm,
gnu/packages/version-control.scm: Include haskell-crypto module.
 2017-11-13 18:36:51 +01:00
Ricardo Wurmus 44b7374a22
gnu: Move web packages from haskell to haskell-web. 
* gnu/packages/haskell.scm (ghc-tagsoup, ghc-cookie, ghc-http-types, ghc-http,
ghc-http-client, ghc-http-client-tls, ghc-http-date, ghc-http2,
ghc-http-conduit, ghc-wai, ghc-wai-logger, ghc-wai-extra, ghc-wai-conduit,
ghc-warp, ghc-warp-tls, ghc-xss-sanitize, ghc-css-text, ghc-mime-types,
ghc-html, ghc-xhtml, ghc-blaze-html, ghc-aeson, ghc-aeson-pretty,
ghc-aeson-qq, ghc-multipart): Move variables to ...
* gnu/packages/haskell-web.scm: ... this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/haskell.scm,
gnu/packages/idris.scm,
gnu/packages/version-control.scm,
gnu/packages/wm.scm: Include haskell-web module.
 2017-11-13 18:12:37 +01:00
Ricardo Wurmus a06b9b5007
gnu: Move testing packages from haskell to haskell-check. 
* gnu/packages/haskell.scm (ghc-clock-bootstrap, ghc-tasty-ant-xml,
ghc-tasty-smallcheck, ghc-tasty-quickcheck, ghc-tasty-golden, ghc-tasty,
ghc-tasty-hunit, ghc-tasty-kat, ghc-tasty-th, ghc-tasty-rerun,
ghc-quickcheck-instances, ghc-quickcheck-unicode, ghc-quickcheck-io,
ghc-quickcheck, ghc-test-framework, ghc-test-framework-hunit,
ghc-test-framework-quickcheck2, ghc-test-framework-th, ghc-hunit,
hspec-discover, ghc-hspec-core, ghc-hspec-meta, ghc-hspec, ghc-hspec-contrib,
ghc-hspec-expectations): Move variables to ...
* gnu/packages/haskell-check.scm: ... this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/haskell.scm,
gnu/packages/idris.scm,
gnu/packages/version-control.scm,
gnu/packages/wm.scm: Include haskell-check module.
 2017-11-13 18:12:27 +01:00
Ricardo Wurmus d4735e8c65
gnu: cd-hit: Update source tarball hash. 
* gnu/packages/bioinformatics.scm (cd-hit)[source]: Update hash.
 2017-11-13 16:02:35 +01:00
Kei Kebreau 62f0806f4c
Revert "gnu: totem: Enable parallel build." 
This reverts commit e5f748a6c0.
 2017-11-13 07:47:23 -05:00
Ludovic Courtès b918473189
gnu: guix: Update snapshot. 
* gnu/packages/package-management.scm (guix): Update to ff23b47.
 2017-11-13 11:31:27 +01:00
Efraim Flashner 6b7490b340
gnu: ibus: Update to 1.5.17. 
* gnu/packages/ibus.scm (ibus): Update to 1.5.17.
 2017-11-13 10:19:26 +02:00
Efraim Flashner ce12b31157
gnu: ibus: Enable wayland support. 
* gnu/packages/ibus.scm (ibus)[arguments]: Add configure flag to enable
wayland support.
[inputs]: Add wayland.
 2017-11-13 10:19:26 +02:00
Kei Kebreau f35bb0711c
gnu: libsoup: Update to 2.60.2. 
* gnu/packages/gnome.scm (libsoup): Update to 2.60.2.
 2017-11-12 21:20:24 -05:00
Leo Famulari c0d1fa64d0
gnu: imagemagick: Update to 6.9.9-23. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-23.
 2017-11-12 17:50:01 -05:00
Leo Famulari 2560aa7adb
gnu: Remove unrar. 
This package is abandoned upstream and contains serious bugs:

http://seclists.org/oss-sec/2017/q3/329
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-14120
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-14121
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-14122

* gnu/packages/compression.scm (unrar): Remove variable.
 2017-11-12 16:17:08 -05:00
Rutger Helling 8420c7a356
gnu: linux-libre: Change URL to HTTPS. 
* gnu/packages/linux.scm (linux-libre): Change URL to HTTPS.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-11-12 15:46:44 -05:00
Efraim Flashner 1650cf9284
gnu: mupdf: Unbundle mujs. 
* gnu/packages/pdf.scm (mupdf)[source]: Remove bundled mujs.
[inputs]: Add mujs.
 2017-11-12 19:39:21 +02:00
Efraim Flashner 89ba894eb3
gnu: Add mujs. 
* gnu/packages/javascript.scm (mujs): New variable.
 2017-11-12 19:39:20 +02:00
Efraim Flashner 76379dcace
gnu: mupdf: Use https. 
* gnu/packages/pdf.scm (mupdf)[source]: Use https.
[home-page]: Same.
 2017-11-12 19:39:20 +02:00
Efraim Flashner 31f248fa2c
gnu: pdf.scm: Arrange modules alphabetically. 
* gnu/packages/pdf.scm: Arrange modules alphabetically.
 2017-11-12 19:39:17 +02:00
Efraim Flashner b07bfd06ee
gnu: lash: Don't build static libraries. 
* gnu/packages/audio.scm (lash)[arguments]: Add configure-flag to
disable static libraries.
 2017-11-12 12:04:49 +02:00
Efraim Flashner 44df780768
gnu: lash: Don't build lashd. 
This fixes bug#28174.

* gnu/packages/audio.scm (lash)[arguments]: Add phase to skip building lashd.
 2017-11-12 12:04:46 +02:00
Kei Kebreau c7b433de47
gnu: glib-networking: Update to 2.54.1. 
* gnu/packages/gnome.scm (glib-networking): Update to 2.54.1.
 2017-11-12 01:17:10 -05:00
Efraim Flashner 1e2a36e1b0
gnu: ffmpeg: Reduce the size of the closure. 
* gnu/packages/video.scm (ffmpeg)[arguments]: Add new configure flags to
disable the html man pages and the static libraries.
 2017-11-12 07:11:29 +02:00
Efraim Flashner 7e0d513fb9
gnu: mupdf: Use Texinfo for the description. 
* gnu/packages/pdf.scm (mupdf)[description]: Use Texinfo to mark up the
description.
 2017-11-12 07:11:25 +02:00
Leo Famulari b7ca42aa99
gnu: w3m: Find an editor in the environment. 
* gnu/packages/w3m.scm (w3m)[arguments]: Pass an empty value for --with-editor
in #:configure-flags.
[source]: Use git-file-name.
 2017-11-11 23:04:39 -05:00
Leo Famulari 882d921344
gnu: mupdf: Actually fix CVE-2017-15587. 
The original fix could be removed by an optimizing compiler.

* gnu/packages/patches/mupdf-CVE-2017-15587.patch: Revise patch.
 2017-11-11 22:34:24 -05:00
Tobias Geerinckx-Rice 07cc9245e6
gnu: libusb-compat: Use the same home page as libusb. 
* gnu/packages/libusb.scm (libusb-compat)[home-page]: Update.
 2017-11-12 03:25:49 +01:00
Tobias Geerinckx-Rice 5ade9bc769
gnu: fcgi: Fix typo in description. 
* gnu/packages/web.scm (fcgi)[description]: Fix typo.
 2017-11-12 03:25:48 +01:00
Tobias Geerinckx-Rice d1b5043947
gnu: fcgi: Use archived home page fork. 
* gnu/packages/web.scm (fcgi)[home-page]: Use archived version.
 2017-11-12 03:25:48 +01:00
Tobias Geerinckx-Rice 9c2917f9e7
gnu: lynx: Use new home page. 
* gnu/packages/web-browsers.scm (lynx)[home-page]: Update.
 2017-11-12 03:25:47 +01:00
Tobias Geerinckx-Rice 6862e4bfe7
gnu: perl-mime-types: Update to 2.14. 
* gnu/packages/perl.scm (perl-mime-types): Update to 2.14.
 2017-11-12 03:25:47 +01:00
Ludovic Courtès f9035ef213
gnu: mailutils: Update to 3.4. 
* gnu/packages/mail.scm (mailutils): Update to 3.4.
 2017-11-11 23:21:54 +01:00
Ludovic Courtès cda2e2c719
gnu: emacs-emms: Update to 4.4. 
* gnu/packages/emacs.scm (emms): Update to 4.4.
 2017-11-11 23:21:54 +01:00
Jan Nieuwenhuizen 327df26fbf
gnu: nyacc: Update to 0.82.4. 
* gnu/packages/mes.scm (nyacc): Update to 0.82.4.
 2017-11-11 23:11:04 +01:00
Leo Famulari 4564782c3d
gnu: nvi: Build with support for Unicode text. 
* gnu/packages/nvi.scm (nvi)[arguments]: Pass '--enable-widechar'
to #:configure-flags.
 2017-11-11 12:00:37 -05:00
Marius Bakke 56f35d92f5
gnu: lvm2: Update to 2.02.176. 
* gnu/packages/linux.scm (lvm2): Update to 2.02.176.
 2017-11-11 07:40:55 +01:00
Marius Bakke ec03062171
gnu: libstaroffice: Update to 0.0.5. 
* gnu/packages/libreoffice.scm (libstaroffice): Update to 0.0.5.
 2017-11-11 07:18:34 +01:00
Marius Bakke 45d5c80253
gnu: libvisio: Update to 0.1.6. 
* gnu/packages/libreoffice.scm (libvisio): Update to 0.1.6.
[source](patches): Remove.
* gnu/packages/patches/libvisio-fix-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-11-11 07:15:39 +01:00
Marius Bakke 7a9283a619
gnu: libetonyek: Update to 0.1.7. 
* gnu/packages/libreoffice.scm (libetonyek): Update to 0.1.7.
[source](patches): Remove.
[arguments]<#:phases>: Remove.
[native-inputs]: Remove AUTOCONF and AUTOMAKE.
* gnu/packages/patches/libetonyek-build-with-mdds-1.2.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-11-11 07:13:01 +01:00
Rutger Helling 074ff555ab
gnu: libreoffice: Update to 5.3.7.2 and enable GTK3. 
* gnu/packages/libreoffice.scm (libreoffice): Update to 5.3.7.2
[source]: Change URL to HTTPS.
[inputs]: Add gtk+.
[configure-flags]: Remove "--disable-gtk3".

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-11 07:03:06 +01:00
Alex Vong ce1ac8eea6
gnu: python2-rpython: Update to 0.2.1. 
* gnu/packages/python.scm (python2-rpython): Update to 0.2.1.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-11 07:00:22 +01:00
Alex Vong e65acb3124
gnu: python-sympy: Update to 1.1.1. 
* gnu/packages/python.scm (python-sympy, python2-sympy): Update to 1.1.1.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-11 06:57:00 +01:00
Marius Bakke e077e7da7f
gnu: python-sqlparse: Fix syntax error. 
This is a follow-up to commit 8d688cd27f.

* gnu/packages/python.scm (python-sqlparse)[arguments]: Add missing lambda.
 2017-11-11 06:40:50 +01:00
Tobias Geerinckx-Rice 8d688cd27f
gnu: python-sqlparse: Update to 0.2.4. 
* gnu/packages/python.scm (python-sqlparse, python2-sqlparse): Update to
0.2.4.
[arguments]: Don't invoke ‘2to3’.
 2017-11-11 05:17:59 +01:00
Tobias Geerinckx-Rice 9629c6b4b2
gnu: cyrus-sasl: Use new home page. 
* gnu/packages/cyrus-sasl.scm (cyrus-sasl)[home-page]: Update.
 2017-11-11 05:17:58 +01:00
Tobias Geerinckx-Rice 11ed4108fb
gnu: methylkit: Use new home page. 
* gnu/packages/bioinformatics.scm (methylkit)[home-page]: Update.
 2017-11-11 05:17:58 +01:00
Ben Woodcroft 7c087150ec
gnu: vsearch: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.6.0.
 2017-11-11 09:33:16 +10:00
Leo Famulari 74c0aeb027
gnu: webkitgtk: Update to 2.18.3 [fixes CVE-2017-{13788,13798,13803}]. 
* gnu/packages/webkit.scm (webkitgtk): Update to 2.18.3.
 2017-11-10 12:48:15 -05:00
Leo Famulari adf7e69cab
gnu: qemu: Fix CVE-2017-{15038,15268,15289}. 
* gnu/packages/patches/qemu-CVE-2017-15038.patch,
gnu/packages/patches/qemu-CVE-2017-15268.patch,
gnu/packages/patches/qemu-CVE-2017-15289.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/virtualization.scm (qemu)[source]: Use them.
 2017-11-10 12:16:31 -05:00
Kei Kebreau d4d7d70912
gnu: Fix hunspell-dict-en-* dictionary installation. 
* gnu/packages/aspell.scm (aspell-word-list)[arguments]: Install the .dic file
for all hunspell dictionaries.
 2017-11-10 11:59:09 -05:00
Ricardo Wurmus 0af4df7e61
gnu: cutadapt: Update to 1.14. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.14.
 2017-11-10 15:32:42 +01:00
Ricardo Wurmus ae451b9dc2
gnu: synergy: Fix minor problems with the package definitions. 
* gnu/packages/synergy.scm (synergy)[source]: Return #t in the snippet.
[arguments]: Let build phases return #t; fix typo in comment.
[home-page]: Change to redirection target.
[description]: Fix typo.
 2017-11-10 15:19:06 +01:00
Jelle Licht 177475cfb5
gnu: password-store: Install passmenu script. 
* gnu/packages/password-utils (password-store)
  [inputs]: Add dmenu and xdotool.
  [arguments]<#:phases>['patch-passmenu-path']: New phase.
  [arguments]<#:phases>['install-passmenu']: New phase.
 2017-11-10 14:22:28 +01:00
Diego Nicola Barbato 011f57695a
gnu: Add Epson escpr printer driver. 
* gnu/packages/cups.scm (escpr): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-10 13:07:54 +01:00
Efraim Flashner 179b7ac66d
gnu: postgresql@9.6: Update to 9.6.6 [security fixes]. 
This fixes CVE-2017-12172, CVE-2017-15098, CVE-2017-15099.

* gnu/packages/databases.scm (postgresql@9.6): Update to 9.6.6.
 2017-11-10 10:24:13 +02:00
Mark H Weaver 74bea6a036
gnu: linux-libre: Update to 4.13.12. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.13.12.
(%linux-libre-hash): Update hash.
 2017-11-09 21:11:00 -05:00
Mark H Weaver 4cacbf33a6
gnu: linux-libre@4.9: Update to 4.9.61. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.61.
 2017-11-09 21:10:14 -05:00
Mark H Weaver 3a79bd03ff
gnu: linux-libre@4.4: Update to 4.4.97. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.97.
 2017-11-09 21:09:34 -05:00
Mark H Weaver f8071bea91
gnu: linux-libre@4.1: Update to 4.1.46. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.46.
 2017-11-09 21:08:51 -05:00
Tobias Geerinckx-Rice 3c3d20c8f3
gnu: libpsl: Update to 0.19.1. 
* gnu/packages/web.scm (libpsl): Update to 0.19.1.
 2017-11-10 02:37:15 +01:00
Rutger Helling 1d8e73ba67
gnu: postgresql: Update to 10.1 [security fixes]. 
Fixes CVE-2017-12172, CVE-2017-15098 and CVE-2017-15099.

* gnu/packages/databases.scm (postgresql): Update to 10.1.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-10 01:22:53 +01:00
Kyle Meyer e99f045cc8
gnu: Add r-directlabels. 
* gnu/packages/statistics.scm (r-directlabels): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-09 23:54:48 +01:00
Alex Vong d3150731a8
gnu: emacs-ahungry-theme: Update to 1.8.0. 
* gnu/packages/emacs.scm (emacs-ahungry-theme): Update to 1.8.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-09 23:54:48 +01:00
Marek Benc f021382be4
gnu: Add nxbelld. 
* gnu/packages/xdisorg.scm (nxbelld): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-09 23:54:48 +01:00
Efraim Flashner d8f075c3a3
gnu: %intel-compatible-systems: Re-add variable. 
This is a follow-up to cfbe7b7f4c.

* gnu/packages/linux.scm (%intel-compatible-systems): New variable.
 2017-11-09 22:25:48 +02:00
Mathieu Othacehe cfbe7b7f4c
gnu: linux: Add linux-libre arm kernel. 
* Makefile.am (AUX_FILES): Add arm config file.
* gnu/packages/aux-files/linux-libre/4.13-arm.conf: New file.
* gnu/packages/linux.scm (%intel-compatible-systems): Rename to
  %linux-compatible-systems and add "armhf-linux".
  (linux-libre): Adapt consequently.

The config file for arm is taken from debian armmp kernel. It's a generic
firmware for ARMv7 multiplatform compatible SoCs.
 2017-11-09 20:35:11 +01:00
Leo Famulari 3694a9b33b
gnu: chromaprint: Update to 1.4.2. 
* gnu/packages/mp3.scm (chromaprint): Update to 1.4.2.
 2017-11-09 13:23:39 -05:00
Kei Kebreau ad9b8987f3
gnu: libwnck: Update to 3.24.1. 
* gnu/packages/gnome.scm (libwnck): Update to 3.24.1.
 2017-11-09 12:17:37 -05:00
Ben Woodcroft da4a707c88
gnu: roary: Update to 3.11.0. 
* gnu/packages/bioinformatics.scm (roary): Update to 3.11.0.
[inputs]: Add perl-digest-md5-file.
 2017-11-09 18:12:32 +10:00
Kei Kebreau e5f748a6c0
gnu: totem: Enable parallel build. 
* gnu/packages/gnome.scm (totem)[arguments]: Set #:parallel-build? to #t
implicitly.
 2017-11-08 20:43:40 -05:00
Leo Famulari 8f220b7b41
gnu: tremc: Update to 0.9.0-1.9755b50. 
* gnu/packages/bittorrent.scm (tremc): Update to 0.9.0-1.9755b50.
[version]: Use git-version.
[source]: Use git-file-name.
 2017-11-08 19:32:32 -05:00
Leo Famulari ea1f073d73
gnu: slurm: Update to 16.05.11 [fixes CVE-2017-15566]. 
* gnu/packages/parallel.scm (slurm): Update to 16.05.11.
[source]: Use the recommended download URL.
 2017-11-08 19:32:31 -05:00
Leo Famulari a3dd13ae0e
gnu: rpm: Update to 4.13.0.2 [fixes CVE-2017-{7500,7501}]. 
* gnu/packages/package-management.scm (rpm): Update to 4.13.0.2.
 2017-11-08 19:00:07 -05:00
Leo Famulari 7df4194b16
gnu: python-icalendar: Update to 4.0.0. 
* gnu/packages/python.scm (python-icalendar): Update to 4.0.0.
 2017-11-08 18:36:29 -05:00
Leo Famulari 03b154f800
gnu: syncthing: Update to 0.14.40. 
* gnu/packages/syncthing.scm (syncthing): Update to 0.14.40.
[inputs]: Add go-github-com-zillode-notify.
 2017-11-08 17:24:02 -05:00
Leo Famulari 52ff28e4aa
gnu: Add go-github-com-zillode-notify. 
* gnu/packages/syncthing.scm (go-github-com-zillode-notify): New variable.
 2017-11-08 17:24:01 -05:00
Leo Famulari 4cf6827de3
gnu: go-github-com-audriusbutkevicius-kcp-go: Update to 0.0.0-1.8ae5f52. 
* gnu/packages/syncthing.scm (go-github-com-audriusbutkevicius-kcp-go):
Update to 0.0.0-1.8ae5f52.
[propagated-inputs]: Add go-github-com-tjfoc-gmsm-sm4.
 2017-11-08 17:24:01 -05:00
Leo Famulari f44169c2a7
gnu: Add go-github-com-tjfoc-gmsm-sm4. 
* gnu/packages/syncthing.scm (go-github-com-tjfoc-gmsm-sm4): New variable.
 2017-11-08 17:24:01 -05:00
Ricardo Wurmus 34260a10d7
gnu: miso: Use pypi-uri. 
* gnu/packages/bioinformatics.scm (miso)[source]: Use pypi-uri.
 2017-11-08 17:41:08 +01:00
Ricardo Wurmus e5c17b8d9d
gnu: Add r-vcd. 
* gnu/packages/cran.scm (r-vcd): New variable.
 2017-11-08 17:34:35 +01:00
Ricardo Wurmus 018cf270a3
gnu: Add r-laeken. 
* gnu/packages/cran.scm (r-laeken): New variable.
 2017-11-08 17:34:11 +01:00
Ricardo Wurmus 697e341e74
gnu: fastcap: Use texlive-tiny. 
* gnu/packages/engineering.scm (fastcap)[native-inputs]: Replace texlive with
texlive-tiny.
[arguments]: Fix indentation; set HOME in "make-pdf" phase to avoid font
errors with texlive-tiny.
 2017-11-08 17:15:24 +01:00
Ricardo Wurmus 7e3aca2b78
gnu: librecad: Fix build. 
* gnu/packages/engineering.scm (librecad)[arguments]: Add phase
"patch-boost-error".
 2017-11-08 16:21:54 +01:00
Ricardo Wurmus b72b42cf02
gnu: Add r-performanceanalytics. 
* gnu/packages/cran.scm (r-performanceanalytics): New variable.
 2017-11-08 16:21:54 +01:00
Ricardo Wurmus 3699383e6f
gnu: Add r-xts. 
* gnu/packages/cran.scm (r-xts): New variable.
 2017-11-08 16:21:53 +01:00
Ricardo Wurmus 5a80c15c14
gnu: Remove "open source" from descriptions. 
All software in Guix is Free Software.

* gnu/packages/aidc.scm (libdmtx)[description]: Remove "open source" string.
* gnu/packages/firmware.scm (seabios)[description]: Likewise.
* gnu/packages/libupnp.scm (libupnp)[description]: Likewise.
* gnu/packages/maths.scm (cubicle)[description]: Likewise.
* gnu/packages/mingw.scm (mingw-w64)[description]: Likewise.
* gnu/packages/game-development.scm (openmw)[description]: Likewise.
[synopsis]: Remove "Free software".
 2017-11-08 16:21:53 +01:00
Ricardo Wurmus 88fb156288
gnu: pcb: Update to 4.0.2. 
* gnu/packages/engineering.scm (pcb): Update to 4.0.2.
[arguments]: Add build phase "fix-check-for-display".
 2017-11-08 16:21:53 +01:00
Efraim Flashner c8b38f8ea6
gnu: time: Update license. 
* gnu/packages/time.scm (time)[license]: Change to gpl3+.
 2017-11-08 10:52:09 +02:00
Efraim Flashner dd00e0919f
gnu: time: Update to 1.8. 
* gnu/packages/time.scm (time): Update to 1.8.
[arguments]: Remove custom 'configure phase.
 2017-11-08 10:49:19 +02:00
Ricardo Wurmus 12a24ee878
gnu: Add glusterfs. 
* gnu/packages/file-systems.scm (glusterfs): New variable.
 2017-11-07 23:32:46 +01:00
Ricardo Wurmus 2e648d2bc4
gnu: r-prabclus: Update description. 
* gnu/packages/statistics.scm (r-prabclus)[description]: Fix grammar errors.
 2017-11-07 23:32:46 +01:00
Ricardo Wurmus 14e5f6b20a
gnu: r-fdrtool: Update description. 
* gnu/packages/statistics.scm (r-fdrtool)[description]: Use "@dfn" syntax.
 2017-11-07 23:32:46 +01:00
Ricardo Wurmus 738dda8330
gnu: Add r-bbmle. 
* gnu/packages/cran.scm (r-bbmle): New variable.
 2017-11-07 23:32:46 +01:00
Ricardo Wurmus 7b0569c0a9
gnu: Add r-rsofia. 
* gnu/packages/cran.scm (r-rsofia): New variable.
 2017-11-07 23:32:46 +01:00
Ricardo Wurmus c49102ecca
gnu: Add r-hitc. 
* gnu/packages/bioinformatics.scm (r-hitc): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus 30eb4e37c8
gnu: Add r-fithic. 
* gnu/packages/bioinformatics.scm (r-fithic): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus fbf5440637
gnu: Add r-sushi. 
* gnu/packages/bioinformatics.scm (r-sushi): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus 9232cac410
gnu: Add r-vioplot. 
* gnu/packages/cran.scm (r-vioplot): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus 3a22732cd8
gnu: Add r-sm. 
* gnu/packages/cran.scm (r-sm): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus 2e4ce60e7c
gnu: Add r-gwascat. 
* gnu/packages/bioinformatics.scm (r-gwascat): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus 4272000661
gnu: Add r-gviz. 
* gnu/packages/bioinformatics.scm (r-gviz): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus 794ff347a9
gnu: Add r-gqtlstats. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus 7fd5f60b8f
gnu: Add r-hardyweinberg. 
* gnu/packages/cran.scm (r-hardyweinberg): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus 10e16fa93d
gnu: Add r-mice. 
* gnu/packages/cran.scm (r-mice): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus 66c39102e5
gnu: Add r-ldblock. 
* gnu/packages/bioinformatics.scm (r-ldblock): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus 15f98b0d23
gnu: Add r-erma. 
* gnu/packages/bioinformatics.scm (r-erma): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus 421c68e3f7
gnu: Add r-homo-sapiens. 
* gnu/packages/bioinformatics.scm (r-homo-sapiens): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus b52a866d14
gnu: Add r-org-hs-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus dd5fc8b78e
gnu: Add r-snpstats. 
* gnu/packages/bioinformatics.scm (r-snpstats): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus e2b927993e
gnu: Add r-gqtlbase. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus 96a392a0b2
gnu: Add r-gprofiler. 
* gnu/packages/bioinformatics.scm (r-gprofiler): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus 60faf94597
gnu: Add r-ggbio. 
* gnu/packages/bioinformatics.scm (r-ggbio): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus 7af1f40373
gnu: Add r-biovizbase. 
* gnu/packages/bioinformatics.scm (r-biovizbase): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus 2f6f61fd8e
gnu: Add r-organismdbi. 
* gnu/packages/bioinformatics.scm (r-organismdbi): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus aa30ab5aee
gnu: Add r-ensembldb. 
* gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus 763e98103a
gnu: Add r-annotationfilter. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus 04e2a2e969
gnu: Add r-dirichletmultinomial. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): New variable.
 2017-11-07 23:32:41 +01:00
Ricardo Wurmus 3af149f524
gnu: Add r-complexheatmap. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): New variable.
 2017-11-07 23:32:41 +01:00
Ricardo Wurmus 902fb15d92
gnu: Add r-genomicfiles. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): New variable.
 2017-11-07 23:32:41 +01:00
Marius Bakke cd215877a0
gnu: bdftopcf: Update to 1.1. 
* gnu/packages/xorg.scm (bdftopcf): Update to 1.1.
[native-inputs]: Change from LIBXFONT to LIBXFONT2.
 2017-11-07 23:29:23 +01:00
Marius Bakke d469bc09bd
gnu: feh: Update to 2.22.2. 
* gnu/packages/image-viewers.scm (feh): Update to 2.22.2.
 2017-11-07 22:16:27 +01:00
Jan Nieuwenhuizen 625492ee1a
gnu: gcc-4.7: Resurrect building with gcc-5.4.0. 
* gnu/packages/patches/gcc-4-compile-with-gcc-5.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gcc.scm (gcc-4.7): Use it.
 2017-11-07 22:03:51 +01:00
Rutger Helling a67f094671
gnu: Add websockify. 
* gnu/packages/web.scm (websockify): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-07 21:56:42 +01:00
Gábor Boskovits 75d342ffa9
gnu: Add python-networkx2. 
* gnu/packages/python.scm (python-networkx2, python2-networkx2): New variables.
* gnu/local.mk (dist_patch_DATA): Register 'python-networkx2-reproducible-build.patch'.
* gnu/packages/patches/python-networkx2-reproducible-build.patch: New file.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-07 21:17:20 +01:00
Gábor Boskovits 2b295f5a2f
gnu: Add python-pydot. 
* gnu/packages/graphviz.scm (python-pydot, python2-pydot): New variables.

Modified-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-07 21:03:15 +01:00
Marius Bakke 38ad27da80
gnu: mercurial: Update to 4.4.1. 
* gnu/packages/version-control.scm (mercurial): Update to 4.4.1.
 2017-11-07 20:23:29 +01:00
Marius Bakke 4a30c1c0e2
gnu: vim: Update to 8.0.1274 [fixes CVE-2017-1000382]. 
* gnu/packages/vim.scm (vim): Update to 8.0.1274.
 2017-11-07 20:21:46 +01:00
Marius Bakke 31a963fe80
gnu: notmuch: Update to 0.25.2. 
* gnu/packages/mail.scm (notmuch): Update to 0.25.2.
 2017-11-07 20:01:03 +01:00
Efraim Flashner 9129804230
gnu: psm: Only use as an input on supported-systems. 
Syntax help supplied by bavier@member.fsf.org

* gnu/packages/linux.scm (libfabric)[inputs]: Only use psm as an input
on systems where psm is supported.
* gnu/packages/mpi.scm (openmpi)[inputs]: Same.
 2017-11-07 20:41:08 +02:00
Efraim Flashner b516b78002
gnu: psm: Limit supported systems. 
* gnu/packages/linux.scm (psm)[supported-systems]: New field, limit to
i686-linux and x86_64-linux.
 2017-11-07 20:41:05 +02:00
Efraim Flashner 174807b9a4
gnu: gnupg: Update to 2.2.2. 
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.2.
 2017-11-07 19:34:29 +02:00
Efraim Flashner 2f17187ff3
gnu: mediainfo: Change order of custom phases. 
* gnu/packages/video.scm (mediainfo)[arguments]: Change to the build
directory before executing the autogen script.
 2017-11-07 19:34:25 +02:00
Mathieu Othacehe 6541673354
gnu: linux: Fix kconfig selection. 
* gnu/packages/linux.scm (make-linux-libre): When cross-compiling,
  "kconfig" field is in native-inputs variable. So config is always #f
  when cross-compiling linux.
 2017-11-07 18:16:02 +01:00
Dave Love f4433d09a1
gnu: openmpi: Add dependency on PSM. 
* gnu/packages/mpi.scm (openmpi)[inputs]: Add PSM.
 2017-11-07 18:09:13 +01:00
Dave Love 7bc05ef0ac
gnu: libfabric: Add dependency on PSM. 
* gnu/packages/linux.scm (libfabric)[inputs]: Add PSM.
 2017-11-07 18:09:13 +01:00
Dave Love fd23d259cd
gnu: Add PSM. 
* gnu/packages/linux.scm (psm): New variable.
* gnu/packages/patches/psm-arch.patch,
gnu/packages/patches/psm-ldflags.patch,
gnu/packages/patches/psm-repro.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
 2017-11-07 18:09:13 +01:00
Gábor Boskovits 63b7fbe1bb
gnu: diffoscope: Update to 88. 
* gnu/packages/package-management.scm (diffoscope): Update to 88.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
ng0 db0164b21f
gnu: awesome: Update to 4.2. 
* gnu/packages/wm.scm (awesome): Update to 4.2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
Timothy Sample 51bc8357e8
gnu: gdm: Add configure flags for better defaults. 
* gnu/packages/gnome.scm (gdm)[arguments]<#:configure-flags>: Add
--with-initial-vt=7 and --enable-gdm-xsession.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
Timothy Sample 950d8e5d8c
gnu: gdm: Fix config file path. 
* gnu/packages/gnome.scm (gdm)[arguments]<#:phases>: Fix the
'pre-configure phase so that GDM finds its config file.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
Oleg Pykhalov ad54924285
gnu: expect: Change home-page to http://expect.sourceforge.net/. 
* gnu/packages/tcl.scm (expect): Change home-page to
  http://expect.sourceforge.net/.
 2017-11-07 18:50:46 +03:00
Ricardo Wurmus e160aa1f81
gnu: Add r-gage. 
* gnu/packages/bioinformatics.scm (r-gage): New variable.
 2017-11-07 12:39:51 +01:00
Ricardo Wurmus 3121814ef1
gnu: Add r-keggrest. 
* gnu/packages/bioinformatics.scm (r-keggrest): New variable.
 2017-11-07 12:39:51 +01:00
Ricardo Wurmus a9540107c6
gnu: antlr3-3.3: Prettify build phases. 
* gnu/packages/java.scm (antlr3-3.3)[arguments]: Prettify build phases
"bin-install" and "generate-grammar".
 2017-11-07 12:39:50 +01:00
Ricardo Wurmus 9ecc4c69eb
gnu: r-servr: Update to 0.8. 
* gnu/packages/web.scm (r-servr): Update to 0.8.
 2017-11-07 08:15:45 +01:00
Ricardo Wurmus 60ec9da3aa
gnu: r-tidyselect: Update to 0.2.3. 
* gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.3.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus baa00ee90d
gnu: r-msnbase: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.0.
[propagated-inputs]: Add r-lattice; remove r-reshape2.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus 39d9098def
gnu: r-mutationalpatterns: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.0.
[propagated-inputs]: Add r-cowplot, r-ggdendro, and r-s4vectors.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus 14b3c71911
gnu: r-annotationhub: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0.
[propagated-inputs]: Add r-curl.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus 15ca195979
gnu: r-mzr: Remove bundled copy of boost. 
* gnu/packages/bioinformatics.scm (r-mzr)[source]: Remove boost source.
[arguments]: Add build phase "use-system-boost" to link with our boost
package and avoid building the bundled sources.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus 34b9675449
gnu: r-mzr: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus b500dbcdef
gnu: r-mzid: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus eeaa6967f9
gnu: r-chipseq: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.28.0.
[propagated-inputs]: Add r-lattice.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus 158b6743dc
gnu: r-genomicfeatures: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.0.
[propagated-inputs]: Add r-rmysql.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus 74248d22a0
gnu: Add r-rmysql. 
* gnu/packages/databases.scm (r-rmysql): New variable.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus 4dd469ef6d
gnu: r-rtracklayer: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.0.
[arguments]: Adjust patch to use system zlib.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus a044c7f4c4
gnu: r-biocparallel: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.12.0.
[propagated-inputs]: Add r-bh.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus 42e11d3301
gnu: r-biomart: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.0.
[propagated-inputs]: Add r-progress and r-stringr.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus 010ab2ffd2
gnu: r-edger: Update to 3.20.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.1.
[propagated-inputs]: Add r-rcpp.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus eb3f5cc76a
gnu: r-gostats: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.44.0.
[propagated-inputs]: Add r-rgraphviz.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus 2404cc4283
gnu: r-category: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.44.0.
[propagated-inputs]: Remove r-rsqlite; add r-dbi.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus 65a8cd6676
gnu: r-lubridate: Update to 1.7.1. 
* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.1.
[propagated-inputs]: Add r-rcpp.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus 689edf1153
gnu: r-preprocesscore: Update to 1.40.0. 
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.40.0.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus e7f680f071
gnu: r-r-utils: Update to 2.6.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.6.0.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus ecfe98a17a
gnu: r-openssl: Update to 0.9.8. 
* gnu/packages/statistics.scm (r-openssl): Update to 0.9.8.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus aced057fbc
gnu: r-rlang: Update to 0.1.4. 
* gnu/packages/statistics.scm (r-rlang): Update to 0.1.4.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus 1be0f53664
gnu: r-vsn: Update to 3.46.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.46.0.
[propagated-inputs]: Remove r-hexbin.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus 007424b5a5
gnu: r-motifrg: Rename input label. 
* gnu/packages/bioinformatics.scm (r-motifrg)[propagated-inputs]:
Rename label of r-bsgenome-hsapiens-ucsc-hg19.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus ce59d62519
gnu: r-motifrg: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.22.0.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus 98791c25c8
gnu: r-qvalue: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.10.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus 87fa5aface
gnu: r-fastseq: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-fastseq): Update to 1.24.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus 1567c8d91b
gnu: r-interactivedisplaybase: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to
1.16.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus 0096127974
gnu: r-edaseq: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.12.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus 22752bef3b
gnu: r-msnid: Update to 1.11.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.11.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus 8140f680ad
gnu: r-deseq: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.30.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus 531e80903f
gnu: r-aroma-light: Update to 3.8.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.8.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus a998c9a464
gnu: r-pcamethods: Update to 1.70.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.70.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus 8a8138d248
gnu: r-affyio: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.48.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus dad5f83817
gnu: r-affy: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.56.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus 9a665dfb6f
gnu: r-protgenerics: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.10.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus 617700895b
gnu: r-seqlogo: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.44.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus e127c918f8
gnu: r-genomation: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.10.0.
[propagated-inputs]: Remove r-rhtslib.
[inputs]: Remove zlib.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus e6ce4bf00d
gnu: r-impute: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.52.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus 0f948b116b
gnu: r-seqpattern: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.10.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus e67850b40d
gnu: r-bsgenome: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.46.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus d13a3fea7e
gnu: r-topgo: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus aeb73879f6
gnu: r-graph: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.56.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus 96fb465174
gnu: r-genomicalignments: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus 6fcbed7329
gnu: r-summarizedexperiment: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus cb0a9a7493
gnu: r-delayedarray: Update to 0.4.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.4.1.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus f8068419a6
gnu: r-rsamtools: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.30.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus b719435ebb
gnu: r-biostrings: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.46.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus 0f8d98f294
gnu: r-annotationdbi: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.40.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus ca52123611
gnu: r-biobase: Update to 2.38.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.38.0.
 2017-11-07 08:15:34 +01:00