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Author SHA1 Message Date
Josh Holland 4506018e28
gnu: Mercurial: Update to 5.0 
* gnu/packages/version-control.scm (mercurial): Update to 5.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-09 12:11:37 +02:00
Ludovic Courtès e6b1a2248f
services: Log-in services now require "pam_loginuid". 
Fixes <https://bugs.gnu.org/35553>.
Reported by Bruno Haible <bruno@clisp.org>.

* gnu/services/base.scm (login-pam-service): Pass #:login-uid? #t to
'unix-pam-service'.
* gnu/services/ssh.scm (lsh-pam-services, openssh-pam-services):
Likewise.
* gnu/services/xorg.scm (slim-pam-service): Likewise.
(gdm-pam-service): Likewise for "gdm-autologin" and "gdm-password".
* gnu/tests/base.scm (run-basic-test)["getlogin on tty1"]: New test.
* gnu/tests/ssh.scm (run-ssh-test): Add #:test-getlogin? parameter.
["getlogin"]: New test.
(%test-dropbear): Pass #:test-getlogin? #f.
 2019-05-09 12:11:36 +02:00
Ludovic Courtès af55ca481d
system: pam: Add #:login-uid? parameter to 'unix-pam-service'. 
* gnu/system/pam.scm (unix-pam-service): Add #:login-uid? parameter.  In
then 'session' field, add "pam_loginuid.so" as required when LOGIN-UID?
is true.
 2019-05-09 12:11:36 +02:00
Ludovic Courtès 56038bac60
gnu: Add hostapd. 
* gnu/packages/admin.scm (hostapd): New variable.
 2019-05-09 12:11:36 +02:00
Ludovic Courtès 6ad799d7c5
services: slim: Provide the 'xorg-server' Shepherd service. 
This is a followup to 61569171d0.

* gnu/services/xorg.scm (slim-shepherd-service): Add 'xorg-server' to
'provision' when VT is "vt7".
 2019-05-09 12:11:36 +02:00
Ludovic Courtès cae0725b80
bootloader: grub: Remove unneeded 'terminal_output'. 
Fixes <https://bugs.gnu.org/35585>.
Reported by Florian Pelz <pelzflorian@pelzflorian.de>.

This statement was added in 8d058e7b1b but
turned out to be unnecessary.

* gnu/bootloader/grub.scm (grub-configuration-file): Remove
'terminal_output' statement.
 2019-05-09 12:11:36 +02:00
Ludovic Courtès fb98e430d4
installer: Add missing 'G_' call. 
* gnu/installer/newt/user.scm (run-user-page): Add 'G_' call for "User
creation".
 2019-05-09 12:11:36 +02:00
Maxim Cournoyer 063edf928a
gnu: Add python-pylibmc. 
* gnu/packages/databases.scm (python-pylibmc, python2-pylibmc): New variables.
 2019-05-09 00:22:38 -04:00
Maxim Cournoyer da6026792b
gnu: Add libmemcached. 
* gnu/packages/databases.scm (libmemcached): New variable.
 2019-05-09 00:22:37 -04:00
Mark H Weaver c526b3176f
gnu: linux-libre: Update to 5.0.14. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 5.0.14.
(%linux-libre-hash): Update hash.
 2019-05-08 22:51:27 -04:00
Mark H Weaver 013130cf0b
gnu: linux-libre@4.19: Update to 4.19.41. 
* gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.41.
(%linux-libre-4.19-hash): Update hash.
 2019-05-08 22:19:29 -04:00
Mark H Weaver f9ab5c47bd
gnu: linux-libre@4.14: Update to 4.14.117. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.117.
(%linux-libre-4.14-hash): Update hash.
 2019-05-08 22:18:13 -04:00
Mark H Weaver 9902e3dfd8
gnu: linux-libre@4.9: Update to 4.9.174. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.174.
 2019-05-08 22:17:31 -04:00
Tobias Geerinckx-Rice 429a38a009
gnu: usbutils: Add ‘python’ output. 
* gnu/packages/linux.scm (usbutils)[outputs]: Add ‘python’.
[arguments]: Add ‘separate-python-output’ phase.
 2019-05-09 01:14:55 +02:00
Tobias Geerinckx-Rice a6592732cf
gnu: usbutils: Fix broken lsusb.py. 
* gnu/packages/linux.scm (usbutils)[inputs]: Add python.
 2019-05-09 01:14:55 +02:00
Tobias Geerinckx-Rice 5b26635893
gnu: usbutils: Update to 012. 
* gnu/packages/linux.scm (usbutils): Update to 012.
[arguments]: Add ‘patch-bootstrap-scripts’ phase.
[native-inputs]: Add autoconf, automake, and libtool.
 2019-05-09 01:14:55 +02:00
Tobias Geerinckx-Rice 26fad5b7df
gnu: mbpfan: Update to 2.1.1. 
* gnu/packages/linux.scm (mbpfan): Update to 2.1.1.
 2019-05-08 23:21:34 +02:00
Tobias Geerinckx-Rice b786ae69aa
gnu: dovecot: Update to 2.3.6. 
* gnu/packages/mail.scm (dovecot): Update to 2.3.6.
 2019-05-08 23:21:34 +02:00
Tobias Geerinckx-Rice 05ee17872c
gnu: mpop: Update to 1.4.4. 
* gnu/packages/mail.scm (mpop): Update to 1.4.4.
 2019-05-08 23:21:34 +02:00
Tobias Geerinckx-Rice 3f45c6cfcb
gnu: gmime: Update to 3.2.3. 
* gnu/packages/mail.scm (gmime): Update to 3.2.3.
 2019-05-08 23:21:34 +02:00
Tobias Geerinckx-Rice 9f53d58ae1
gnu: opari2: Use HTTPS home page. 
* gnu/packages/profiling.scm (opari2)[home-page]: Use HTTPS.
 2019-05-08 23:21:34 +02:00
Tobias Geerinckx-Rice 2cea4ac780
gnu: opari2: Update to 2.0.4. 
* gnu/packages/profiling.scm (opari2): Update to 2.0.4.
 2019-05-08 23:21:34 +02:00
Tobias Geerinckx-Rice d21649440b
gnu: fasm: Update to 1.73.11. 
* gnu/packages/assembly.scm (fasm): Update to 1.73.11.
 2019-05-08 23:21:34 +02:00
Leo Famulari 5c89429586
gnu: Syncthing: Update to 1.1.2. 
*  gnu/packages/syncthing.scm (syncthing): Update to 1.1.2.
 2019-05-08 14:57:11 -04:00
Efraim Flashner e54a6543a0
gnu: python-efl: Update to 1.22.0. 
* gnu/packages/enlightenment.scm (python-efl): Update to 1.22.0.
[source]: Use https.  Add snippet to remove files generated by cython.
 2019-05-08 19:55:13 +03:00
Efraim Flashner 944bdb2afe
gnu: terminology: Update build. 
* gnu/packages/enlightenment.scm (terminology)[arguments]: Add to
configure-flags.  Add custom 'set-home-directory phase.
 2019-05-08 19:55:13 +03:00
Efraim Flashner 3ec29587b5
gnu: efl: Update to 1.22.2. 
* gnu/packages/enlightenment.scm (efl): Update to 1.22.2.
[propagated-inputs]: Move libsndfile, pulseaudio ...
[inputs]: ... to here.
[source]: Remove patch.
* gnu/packages/patches/efl-mesa-compat.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2019-05-08 19:55:12 +03:00
Tobias Geerinckx-Rice 515a92cf20
gnu: liburcu: Update to 0.11.0. 
* gnu/packages/datastructures.scm (liburcu): Update to 0.11.0.
 2019-05-08 16:41:55 +02:00
Nicolas Goaziou 1a6482d43c
gnu: Add copyright header. 
* gnu/packages/fonts.scm: Add copyright header.
 2019-05-08 15:20:08 +02:00
Nicolas Goaziou 4b360985eb
gnu: Add font-sil-andika. 
* gnu/packages/fonts.scm (font-sil-andika): New variable.
 2019-05-08 15:18:55 +02:00
Rutger Helling aa986c9cd6
gnu: retroarch: Update to 1.7.7. 
* gnu/packages/emulators.scm (retroarch): Update to 1.7.7.
 2019-05-08 08:15:46 +02:00
Oleg Pykhalov 56aee1968f
gnu: emacs-irfc: Update to 20130824.507-1. 
This commits changes package's source hash, because 'irfc.el' file was
modified. New file contains HTTPS instead of HTTP URLs.

* gnu/packages/emacs-xyz.scm (emacs-irfc): Update to 20130824.507-1.
 2019-05-08 02:06:51 +03:00
Nicolas Goaziou 5d51a9771d
gnu: tlp: Update to 1.2.2. 
* gnu/packages/linux.scm (tlp): Update to 1.2.2.
 2019-05-07 23:41:00 +02:00
Christopher Baines 5b3d3cf71c
services: dovecot: Rename auth-verbose-passwords?. 
* gnu/services/mail.scm (dovecot-configuration)[auth-verbose-passwords?]:
Rename to auth-verbose-passwords, and change the type to a string, as this
parameter can take one of three string values.
* doc/guix.texi (Dovecot service): Update the corresponding documentation.
 2019-05-07 20:52:02 +01:00
Pierre Neidhardt 338defe0cb
gnu: sbcl-next: Update to 1.2.1. 
* gnu/packages/web-browsers.scm (sbcl-next): Update to 1.2.1.
 2019-05-07 19:18:37 +02:00
Pierre Neidhardt cbbdc5c795
gnu: next-gtk-webkit: Update to 1.2.1. 
* gnu/packages/web-browsers.scm (next-gtk-webkit): Update to 1.2.1.
 2019-05-07 19:18:28 +02:00
Diego Nicola Barbato 61569171d0
services: slim: Allow SLiM to be started on multiple ttys. 
This change makes it possible to add multiple SLiM services to an operating
system configuration by setting the new 'display' and 'vt' fields in their
configurations to different values.  Each SLiM service will get its own
authfile, logfile, lockfile, and shepherd service, which will start SLiM on a
different tty.

* gnu/services/xorg.scm: Export slim-configuration-display and
  slim-configuration-vt.
  (<slim-configuration>)[display, vt]: New fields.
  (slim-shepherd-service): Refactor let.
  [slim.cfg]: Use new fields for setting display_name, xserver_arguments,
  authfile, lockfile, and logfile.
  [shepherd-service][provision]: Name the shepherd service according to the
  value of 'vt'.
  [shepherd-service][start]: Delete the right lockfile.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-07 15:46:54 +02:00
Diego Nicola Barbato 6426a8fb6c
gnu: slim: Allow customisation of Xorg display. 
Previously SLiM could only start on display :0.0.  This change makes it
possible to run multiple instances of SLiM at the same time.

* gnu/packages/patches/slim-display.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/display-managers.scm (slim): Use it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-07 15:46:54 +02:00
Ludovic Courtès 341225ac6c
gnu: gnome-control-center: Patch file name of 'nm-connection-editor'. 
* gnu/packages/gnome.scm (gnome-control-center)[argument]: In
'patch-paths' phase, provide absolute file name to
'nm-connection-editor' in panels/network/*.c
 2019-05-07 15:46:53 +02:00
Ludovic Courtès 1df38cfcc7
gnu: gnome-control-center: Patch file name of 'gkbd-keyboard-display'. 
Fixes <https://bugs.gnu.org/35605>.
Reported by sirgazil <sirgazil@zoho.com>.

* gnu/packages/gnome.scm (gnome-control-center)[arguments]: In
'patch-paths' phase, patch "cc-region-panel.cc" and provide it with the
absolute file name of 'gkbd-keyboard-display'.
 2019-05-07 15:46:53 +02:00
Pierre Neidhardt bdd30bf00b
gnu: Add sbcl-find-port, cl-find-port, and ecl-find-port. 
* gnu/packages/lisp.scm (sbcl-find-port, cl-find-port, ecl-find-port): New
variables.
 2019-05-07 12:43:31 +02:00
Ludovic Courtès 91936f153a
installer: "Exit" button in user page actually exits. 
Fixes <https://bugs.gnu.org/35607>.
Reported by Florian Pelz <pelzflorian@pelzflorian.de>.

* gnu/installer/newt/user.scm (run-user-page): Add 'cond' clause for
ARGUMENT = EXIT-BUTTON.
 2019-05-07 12:18:44 +02:00
Ludovic Courtès 6c5790a2fa
uuid: 'fat-uuid->string' preserves leading zeros. 
Fixes <https://bugs.gnu.org/35582>.
Reported by sirgazil <sirgazil@zoho.com>.

Previously, leading zeros would be removed, leading to an "invalid"
UUID:

  (uuid->string (uuid "00CA-050E" 'fat32))
  ⇒ "CA-50E"
  (string->uuid "CA-50E" 'fat32)
  ⇒ #f

* gnu/system/uuid.scm (fat-uuid->string): Pad digits with zeros.
* tests/uuid.scm ("uuid, FAT32, leading zeros preserved"): New test.
 2019-05-07 12:18:44 +02:00
Nicolas Goaziou 08c06cd8ac
gnu: grammalecte: Update to 1.0.2. 
* gnu/packages/dictionaries.scm (grammalecte): Update to 1.0.2.
 2019-05-07 10:25:19 +02:00
Mathieu Othacehe 445bd4d5e5
installer: Add password 'hide' checkbox. 
* gnu/installer/newt/page.scm (run-input-page)[input-hide-checkbox?]: New
parameter adding a checkbox to toggle password hiding. By default, the
checkbox is active and the password is hence hided.
* gnu/installer/newt/partition.scm (prompt-luks-passwords): Enable the
previous parameter on both password input pages.
* gnu/installer/newt/user.scm (run-root-password-page): Enable the previous
parameter,
(confirm-password): ditto,
(run-user-add-page): add a checkbox to toggle password hiding.
 2019-05-07 09:25:45 +02:00
Maxim Cournoyer d9ef50b3bc
gnu: tegola: Fix build. 
* gnu/packages/geo.scm (tegola)[arguments]: Adapt the "unpack-path" for the new
unpack phase.
* gnu/packages/geo.scm (tegola)[phases]{set-version}: Update the directory path.
{rename-import}: Remove phase.
 2019-05-06 23:10:36 -04:00
Maxim Cournoyer bdc0c20cab
gnu: imposm3: Fix build. 
* gnu/packages/geo.scm (imposm3)[arguments]: Adapt unpack-path for the new
unpack phase.
[phases]: Remove the "rename-import" phase, now obsolete.
 2019-05-06 23:05:05 -04:00
Maxim Cournoyer fb09818277
gnu: restic: Fix build. 
This fixes a regression introduced by commit f42e4ebb56.

* gnu/packages/backup.scm (restic)[arguments]: Remove "unpack-path" argument.
[phases]{build, check, install, install-docs}: Update the working directory to
"src/github.com/restic/restic".
 2019-05-06 22:36:43 -04:00
Maxim Cournoyer d879fd80c7
gnu: syncthing: Fix build. 
* gnu/packages/syncthing.scm (syncthing)[arguments]: Drop the unpack-path
  argument, made unnecessary by commit f42e4ebb56.
 2019-05-06 20:50:36 -04:00
Ludovic Courtès 46c102ca5e
installer: Skip network selection dialogs when there is no choice. 
Previously, for a machine that only has wired networking, and only one
such network, we'd have to go through two selection boxes.  Now we just
skip both.

* gnu/installer/newt/ethernet.scm (run-ethernet-page): When
'ethernet-services' returns one element, return it directly without
opening a listbox selection.
* gnu/installer/newt/network.scm (run-technology-page): Likewise.
 2019-05-06 23:21:33 +02:00
Ludovic Courtès d1e5f758e1
installer: Shrink simple listboxes to their minimum height. 
* gnu/installer/newt/partition.scm (run-partioning-page): Pass
 #:listbox-height.
(run-scheme-page): Likewise.
(run-device-page): Likewise.
* gnu/installer/newt/network.scm (run-technology-page): Likewise.
* gnu/installer/newt/ethernet.scm (run-ethernet-page): Likewise.
 2019-05-06 23:21:33 +02:00
Ludovic Courtès 7ae9979cff
installer: Actually translate step descriptions. 
Until now, step descriptions in the menu that shows up when hitting
"Exit" would not be translated.  That's because the 'G_' procedure was
called once and for all when the installer was started.

* gnu/installer/steps.scm (<installer-step>)[description]: Add the
'thunked' attribute.
 2019-05-06 23:21:33 +02:00
Ludovic Courtès 1d8da896be
installer: Do not sort methods on the partitioning page. 
* gnu/installer/newt/partition.scm (run-partioning-page): Pass
 #:sort-listbox-items? #f so that methods always appear in the same
 order.
 2019-05-06 23:21:33 +02:00
Ludovic Courtès 04f4bdcd70
installer: Widen user dialog. 
* gnu/installer/newt/user.scm (run-user-add-page)[pad-label]: Increase
2nd argument to 25.
[entry-width]: Increase to 35.
 2019-05-06 23:21:32 +02:00
Ludovic Courtès 3bb293b6f3
gnu: mate-power-manager: License is GPLv2+. 
Reported by Guy fleury <hoonandon@gmail.com>.

* gnu/packages/mate.scm (mate-power-manager): Change to GPL2+.
 2019-05-06 23:21:32 +02:00
Brian Leung d6a68e9048
gnu: emacs-evil-nerd-commenter: Update to 3.3.7. 
* gnu/packages/emacs-xyz.scm (emacs-evil-nerd-commenter): Update to 3.3.7.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-05-06 16:56:39 +02:00
Brian Leung 869eb264ac
gnu: emacs-elfeed: Update to 3.1.0. 
* gnu/packages/emacs-xyz.scm (emacs-elfeed): Update to 3.1.0.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-05-06 16:56:13 +02:00
Brian Leung e77787ca91
gnu: emacs-hl-todo: Update to 3.0.0. 
* gnu/packages/emacs-xyz.scm (emacs-hl-todo): Update to 3.0.0.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-05-06 16:55:32 +02:00
Mark H Weaver 46ce12d0a3
gnu: icecat: Move the snippet and patches out of the 'source'. 
This commit changes the 'source' field of the 'icecat' package to
simply be 'icecat-source', which aims to be suitable for use on any
system that IceCat supports.

* gnu/packages/gnuzilla.scm (icecat)[source]: Change to simply
be 'icecat-source'.
[native-inputs]: Add 'patch', along with the Guix-specific patches
that were previously applied within 'source'.
[arguments]: Remove the 'ensure-no-mtimes-pre-1980' phase.
Add 'apply-guix-specific-patches' and 'remove-bundled-libraries'
phases.  Touch 'configure' in the bootstrap phase.  Return #t from
the 'augment-CPLUS_INCLUDE_PATH' phase.  Reindent.
 2019-05-06 10:33:20 -04:00
Mark H Weaver 3e605b6998
gnu: icecat-source: Make sure 'makeicecat' is the right version. 
* gnu/packages/gnuzilla.scm (icecat-source): Check to make sure the
value of FFMAJOR in the 'makeicecat' script matches the major version
of IceCat being generated.
 2019-05-06 10:33:18 -04:00
Mark H Weaver ebff346945
gnu: icecat: Update to 60.6.2-guix1. 
* gnu/packages/gnuzilla.scm (%icecat-version): Update to 60.6.2-guix1.
(icecat-source)[upstream-firefox-source]: Update hash.
 2019-05-06 10:33:12 -04:00
Ricardo Wurmus 1c404e6c1a
gnu: r-gridgraphics: Update to 0.4-0. 
* gnu/packages/cran.scm (r-gridgraphics): Update to 0.4-0.
 2019-05-06 16:11:45 +02:00
Ricardo Wurmus 639334a962
gnu: r-checkmate: Update to 1.9.3. 
* gnu/packages/statistics.scm (r-checkmate): Update to 1.9.3.
 2019-05-06 16:11:33 +02:00
Ricardo Wurmus 93f8a00964
gnu: r-rgadem: Update to 2.32.0. 
* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.32.0.
 2019-05-06 16:11:17 +02:00
Ricardo Wurmus 94249db825
gnu: python2-terminado: Add missing input. 
* gnu/packages/python-web.scm (python2-terminado)[propagated-inputs]: Add
python2-futures.
 2019-05-06 12:57:10 +02:00
Brian Leung fc7d632829
gnu: Add emacs-miniedit. 
* gnu/packages/emacs-xyz.scm (emacs-miniedit): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 11:17:23 +02:00
Brian Leung cc1d1fc8b7
gnu: Add emacs-sudo-edit. 
* gnu/packages/emacs-xyz.scm (emacs-sudo-edit): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 11:15:31 +02:00
Brian Leung d2ca86f308
gnu: Add emacs-docker-compose-mode. 
* gnu/packages/emacs-xyz.scm (emacs-docker-compose-mode): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 11:14:47 +02:00
Brian Leung a02198133a
gnu: Add emacs-elisp-demos. 
* gnu/packages/emacs-xyz.scm (emacs-elisp-demos): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 11:14:10 +02:00
Brian Leung 0209661ee6
gnu: Add emacs-flycheck-flow. 
* gnu/packages/emacs-xyz.scm (emacs-flycheck-flow): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 11:10:21 +02:00
Brian Leung df7d0dce4b
gnu: Add emacs-evil-textobj-syntax. 
* gnu/packages/emacs-xyz.scm (emacs-evil-textobj-syntax): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 11:09:10 +02:00
Brian Leung a08530df08
gnu: Add emacs-names. 
* gnu/packages/emacs-xyz.scm (emacs-names): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 11:08:34 +02:00
Ludovic Courtès 5e319c15c1
gnu: mate-power-manager: Placate 'guix lint'. 
Reported by guy fleury iteriteka <hoonandon@gmail.com>.

* gnu/packages/mate.scm (mate-power-manager)[source]: Use mirror:// URL.
[synopsis, description]: Adjust to placate 'guix lint'.
 2019-05-06 11:06:37 +02:00
Alex Griffin 623d4b4662
gnu: Add git-annex-remote-rclone. 
* gnu/packages/version-control.scm (git-annex-remote-rclone): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 10:43:45 +02:00
Brendan Tildesley 5d6bab9e00
gnu: quickswitch-i3: Fix license field to use license:wtfpl2. 
* gnu/packages/wm.scm (quickswitch-i3): Fix license field to use
  license:wtfpl2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 10:32:28 +02:00
Brendan Tildesley 6f38ef73a5
gnu: tmux-themepack: Fix license field to refer to license:wtfpl2. 
* gnu/packages/tmux.scm (tmux-themepack): Fix license field to refer to
  license:wtfpl2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 10:32:28 +02:00
Brendan Tildesley 41ee377305
gnu: Use license: prefix in tmux.scm. 
* gnu/packages/tmux.scm Use license: prefix in tmux.scm.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 10:32:28 +02:00
Brendan Tildesley 492e3a7a76
gnu: python-pyyaml: Fix license field to refer to license:wtfpl2. 
* gnu/packages/python-xyz.scm (python-pyyaml): Fix license field to refer to
  license:wtfpl2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 10:32:27 +02:00
Brendan Tildesley ac44b39a19
gnu: envstore: Fix license field to refer to license:wtfpl2. 
* gnu/packages/shellutils.scm (envstore): Fix license field to refer to
  license:wtfpl2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 10:32:27 +02:00
Brendan Tildesley e3e8924d23
gnu: Use license: prefix in shellutils.scm. 
* gnu/packages/shellutils.scm Use license: prefix in all packages.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 10:32:27 +02:00
Brendan Tildesley f62e7ce442
gnu: zimg: Fix license field to refer to license:wtfpl2. 
* gnu/packages/image.scm (zimg): Fix license field to refer to license:wtfpl2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 10:32:21 +02:00
Carl Dong 0e293f75f1
gnu: gcc@9: Fix limits.h include for cross builds. 
This allows us to supply gcc-9 as an optional argument to cross-gcc,
successfully constructing gcc-9-based cross-compilers.

* gnu/packages/gcc.scm (gcc-9)[source](patches): Add
  "gcc-9-asan-fix-limits-include.patch".
* gnu/packages/patches/gcc-9-asan-fix-limits-include.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add the patch.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 10:22:00 +02:00
Carl Dong 83b0a7f41b
gnu: cross-base: Apply gcc 8 patch to gcc >= 8. 
* gnu/packages/cross-base.scm (cross-gcc): Apply gcc 8 patch to gcc >= 8.
* gnu/packages/patches/gcc-8-cross-environment-variables.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add the patch.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 10:21:38 +02:00
Carl Dong bdfc327639
gnu: gcc: Add 9.1.0. 
* gnu/packages/gcc.scm (gcc-9): New variable.
* gnu/packages/commencement.scm (gcc-toolchain-9): New variable.
* gnu/packages/patches/gcc-9-strmov-store-file-names.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add the patch.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-05-06 10:18:15 +02:00
Mark H Weaver 654332f00f
gnu: linux-libre: Update to 5.0.13. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 5.0.13.
(%linux-libre-hash): Update hash.
 2019-05-06 02:13:19 -04:00
Mark H Weaver 90f4cc4bc7
gnu: linux-libre@4.19: Update to 4.19.40. 
* gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.40.
(%linux-libre-4.19-hash): Update hash.
 2019-05-06 02:12:31 -04:00
Mark H Weaver d40684e827
gnu: linux-libre@4.14: Update to 4.14.116. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.116.
(%linux-libre-4.14-hash): Update hash.
 2019-05-06 02:11:37 -04:00
Mark H Weaver 60065f5bd3
gnu: linux-libre@4.9: Update to 4.9.173. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.173.
 2019-05-06 02:10:51 -04:00
Maxim Cournoyer 59781b32d8
gnu: docker: Refer to xz by its absolute path. 
* gnu/packages/docker.scm (docker)[inputs]: Add xz.
[phases]{patch-paths}: Patch the reference to xz.
 2019-05-05 21:21:02 -04:00
Maxim Cournoyer 80fec17f39
gnu: docker: Patch the reference to the docker proxy. 
* gnu/packages/docker.scm (docker)[inputs]: Add docker-libnetwork-cmd-proxy.
* gnu/packages/docker.scm (docker)[phases]{patch-paths}: Patch proxy.go to
refer to the docker-proxy binary by its absolute path.
 2019-05-05 21:21:02 -04:00
Maxim Cournoyer a01d54f3bd
gnu: docker: Optimize substitution macros. 
This change halves the time needed to patch the paths.

* gnu/packages/docker.scm (docker)[phases]{patch-paths}: Allow passing
multiple SOURCE-TEXT, PACKAGE and RELATIVE-PATH tuples so that the rewrite
rules can be generated and processed by a single use of the SUBSTITUTE*
macro.  Rename SUBSTITUTE-LOOKPATH to SUBSTITUTE-LOOKPATH* and
substitute-Command to SUBSTITUTE-COMMAND* to denote the change.  Adapt the
uses of SUBSTITUTE-LOOKPATH* and SUBSTITUTE-COMMAND*.
 2019-05-05 21:21:02 -04:00
Maxim Cournoyer 079f0eb3d2
gnu: docker: Make macros use a relative path as argument. 
* gnu/packages/docker.scm (docker)[phases]: Move implementation detail inside
the SUBSTITUTE-LOOKPATH and SUBSTITUTE-COMMAND macros definition, so that the
relative path argument can be given as a relative path.
 2019-05-05 21:21:01 -04:00
Maxim Cournoyer 3f280d3950
gnu: docker: Harmonize LookPath regexes. 
* gnu/packages/docker.scm (docker)[phases]: In the patch-paths phase, update
the regexes used by SUBSTITUTE-LOOKPATH and SUBSTITUTE-COMMAND to match at the
start of the word, like it's done later.
 2019-05-05 21:21:01 -04:00
Maxim Cournoyer 1b14e1bccd
gnu: docker: Cleanup extraneous comments. 
* gnu/packages/docker.scm (docker): Remove "parenthesis-balancing" comments.
 2019-05-05 21:21:01 -04:00
Maxim Cournoyer c627932639
gnu: docker: Fix indentation. 
* gnu/packages/docker.scm (docker): Fix indentation using Emacs.
 2019-05-05 21:20:58 -04:00
Maxim Cournoyer 7a31d93a61
services: docker: Add new fields to support proxy. 
The Docker proxy enables inter-container and outside-to-container loopback,
and is required by the Docker registry server.

* gnu/services/docker.scm (docker-configuration)[proxy,
enable-proxy?]: Add fields.
(docker-shepherd-service): Use them.
(serialize-boolean): New function.
 2019-05-05 20:14:15 -04:00
Maxim Cournoyer 0b94911add
gnu: Add docker-libnetwork-cmd-proxy. 
* gnu/packages/docker.scm (docker-libnetwork-cmd-proxy): New variable.
 2019-05-05 20:14:15 -04:00
Maxim Cournoyer 9c0244abbd
gnu: Add docker-libnetwork. 
* gnu/packages/docker.scm (docker-libnetwork): New private variable.
 2019-05-05 20:14:15 -04:00
Maxim Cournoyer 626de0d13a
gnu: Add go-netlink. 
* gnu/packages/linux.scm (go-netlink): New variable.
 2019-05-05 20:14:15 -04:00
Maxim Cournoyer 03981f9064
gnu: Add go-netns. 
* gnu/packages/networking.scm (go-netns): New variable.
 2019-05-05 20:14:14 -04:00
Maxim Cournoyer 523533ed09
gnu: Add go-sctp. 
* gnu/packages/networking.scm (go-sctp): New variable.
 2019-05-05 20:14:14 -04:00
Ricardo Wurmus 85c1d20fa6
gnu: r-chippeakanno: Update to 3.18.0. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.18.0.
[propagated-inputs]: Add r-rtracklayer.
 2019-05-06 00:14:59 +02:00
Ricardo Wurmus c24adbbf07
gnu: r-arrmnormalization: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.24.0.
 2019-05-06 00:14:59 +02:00
Ricardo Wurmus c2bfb978bf
gnu: r-progeny: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-progeny): Update to 1.6.0.
 2019-05-06 00:14:59 +02:00
Ricardo Wurmus 7d33d36c52
gnu: r-rbowtie2: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-rbowtie2): Update to 1.6.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus 02530c2821
gnu: r-zfpkm: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.6.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus 67bc9255d5
gnu: r-webbioc: Update to 1.56.0. 
* gnu/packages/bioconductor.scm (r-webbioc): Update to 1.56.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus c881b9ef3a
gnu: r-widgettools: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-widgettools): Update to 1.62.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus a6edf33533
gnu: r-wiggleplotr: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.8.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus 07597c85d8
gnu: r-wrench: Update to 1.2.0. 
* gnu/packages/bioconductor.scm (r-wrench): Update to 1.2.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus 298f7f112f
gnu: r-xcms: Update to 3.6.0. 
* gnu/packages/bioconductor.scm (r-xcms): Update to 3.6.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus 7c888138ef
gnu: r-massspecwavelet: Update to 1.50.0. 
* gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.50.0.
 2019-05-06 00:14:58 +02:00
Ricardo Wurmus 88469def75
gnu: r-xbseq: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-xbseq): Update to 1.16.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus 0334b203d7
gnu: r-roar: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-roar): Update to 1.20.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus 7f4957b24e
gnu: r-yarn: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-yarn): Update to 1.10.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus 2feea2d22a
gnu: r-quantro: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-quantro): Update to 1.18.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus f48e29daa3
gnu: r-yaqcaffy: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-yaqcaffy): Update to 1.44.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus 38c5d13a73
gnu: r-simpleaffy: Update to 2.60.0. 
* gnu/packages/bioconductor.scm (r-simpleaffy): Update to 2.60.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus 56576bea97
gnu: r-gcrma: Update to 2.56.0. 
* gnu/packages/bioconductor.scm (r-gcrma): Update to 2.56.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus edba69b2ff
gnu: r-yapsa: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.10.0.
 2019-05-06 00:14:57 +02:00
Ricardo Wurmus 3cdc5d1a7b
gnu: r-somaticsignatures: Update to 2.20.0. 
* gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.20.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus 128c6d59f0
gnu: r-gtrellis: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.16.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus 1269a926c0
gnu: r-yamss: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-yamss): Update to 1.10.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus 2a6d838337
gnu: r-ebimage: Update to 4.26.0. 
* gnu/packages/bioconductor.scm (r-ebimage): Update to 4.26.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus b68a9e80f4
gnu: r-aucell: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-aucell): Update to 1.6.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus 9da2021f49
gnu: r-allelicimbalance: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.22.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus ee1a45d719
gnu: r-annotationtools: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.58.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus 69a2ec5447
gnu: r-annotationfuncs: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-annotationfuncs): Update to 1.34.0.
 2019-05-06 00:14:56 +02:00
Ricardo Wurmus e2e1dea2bb
gnu: r-abaenrichment: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-abaenrichment): Update to 1.14.0.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus bab06a6ff3
gnu: r-gofuncr: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.4.0.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus bcc233c1a6
gnu: r-atacseqqc: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.8.0.
[propagated-inputs]: Add r-edger.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus 19ee76379c
gnu: r-genomicscores: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 1.8.0.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus aa0ebfd2eb
gnu: r-motifstack: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-motifstack): Update to 1.28.0.
[propagated-inputs]: Replace r-grimport with r-grimport2.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus f7a495b159
gnu: r-motiv: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-motiv): Update to 1.40.0.
 2019-05-06 00:14:55 +02:00
Ricardo Wurmus a5860ebe87
gnu: r-rgadem: Update to 2.31.0. 
* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.31.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus e33c25ff2c
gnu: r-bacon: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-bacon): Update to 1.12.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus b7ddf0f048
gnu: r-abseqr: Update to 1.2.0. 
* gnu/packages/bioconductor.scm (r-abseqr): Update to 1.2.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus 1aadddeaa9
gnu: r-a4: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4): Update to 1.32.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus ae1730ae1a
gnu: r-a4base: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4base): Update to 1.32.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus e5a36543ac
gnu: r-a4reporting: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.32.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus 0b6091621f
gnu: r-a4preproc: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.32.0.
 2019-05-06 00:14:54 +02:00
Ricardo Wurmus 82de77da5a
gnu: r-a4classif: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4classif): Update to 1.32.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus b077e3db2a
gnu: r-a4core: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-a4core): Update to 1.32.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus 8bef9df4d4
gnu: r-annaffy: Update to 1.56.0. 
* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.56.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus 8265a1115e
gnu: r-mlinterfaces: Update to 1.64.0. 
* gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.64.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus 1a3e33be23
gnu: r-clusterprofiler: Update to 3.12.0. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.12.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus 77d28d665c
gnu: r-enrichplot: Update to 1.4.0. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.4.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus 1990ff9d10
gnu: r-dose: Update to 3.10.0. 
* gnu/packages/bioconductor.scm (r-dose): Update to 3.10.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus ebffd24c10
gnu: r-fgsea: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-fgsea): Update to 1.10.0.
[propagated-inputs]: Add r-bh.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus 3e5ee6f69f
gnu: r-sigpathway: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.52.0.
 2019-05-06 00:14:53 +02:00
Ricardo Wurmus 0a41b5db95
gnu: r-anota: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-anota): Update to 1.32.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus 24cf7bad99
gnu: r-gosemsim: Update to 2.10.0. 
* gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.10.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus 376d1fe759
gnu: r-heatplus: Update to 2.30.0. 
* gnu/packages/bioconductor.scm (r-heatplus): Update to 2.30.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus c2effdedc0
gnu: r-varianttools: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-varianttools): Update to 1.26.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus bc083ecab8
gnu: r-triform: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-triform): Update to 1.26.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus 2ee91179d1
gnu: r-ioniser: Update to 2.8.0. 
* gnu/packages/bioconductor.scm (r-ioniser): Update to 2.8.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus 48c2a7eb39
gnu: r-linnorm: Update to 2.8.0. 
* gnu/packages/bioconductor.scm (r-linnorm): Update to 2.8.0.
 2019-05-06 00:14:52 +02:00
Ricardo Wurmus 5551b07cde
gnu: r-lumi: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-lumi): Update to 2.36.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus 2986b51ffe
gnu: r-methylumi: Update to 2.30.0. 
* gnu/packages/bioconductor.scm (r-methylumi): Update to 2.30.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus 8c0fae3cd4
gnu: r-minfi: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-minfi): Update to 1.30.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus 693a98056c
gnu: r-bumphunter: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.26.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus 409f4dd652
gnu: r-siggenes: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-siggenes): Update to 1.58.0.
[propagated-inputs]: Add r-scrime.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus fadc6db82d
gnu: r-illuminaio: Update to 0.26.0. 
* gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.26.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus 2d4430877a
gnu: r-geoquery: Update to 2.52.0. 
* gnu/packages/bioconductor.scm (r-geoquery): Update to 2.52.0.
 2019-05-06 00:14:51 +02:00
Ricardo Wurmus 26c72fffc1
gnu: r-scone: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-scone): Update to 1.8.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus 7baa59ed4d
gnu: r-scdd: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-scdd): Update to 1.8.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus 6a2c58b7e0
gnu: r-noiseq: Update to 2.28.0. 
* gnu/packages/bioconductor.scm (r-noiseq): Update to 2.28.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus 78b6326785
gnu: r-monocle: Update to 2.12.0. 
* gnu/packages/bioconductor.scm (r-monocle): Update to 2.12.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus a0ff725d6a
gnu: r-mast: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-mast): Update to 1.10.0.
[propagated-inputs]: Add r-blme.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus 3fd2ea8883
gnu: r-icobra: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-icobra): Update to 1.12.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus bcd8b7a9bd
gnu: r-ihw: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-ihw): Update to 1.12.0.
 2019-05-06 00:14:50 +02:00
Ricardo Wurmus 61c79d55e3
gnu: r-lpsymphony: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.12.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus 4a3c47e940
gnu: r-ebseq: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-ebseq): Update to 1.24.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus 301c4ff12a
gnu: r-deds: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-deds): Update to 1.58.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus d5f3c0d09e
gnu: r-dnacopy: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.58.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus d941918599
gnu: r-copynumber: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-copynumber): Update to 1.24.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus 58a43fc28e
gnu: r-chipexoqual: Update to 1.8.0. 
* gnu/packages/bioconductor.scm (r-chipexoqual): Update to 1.8.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus 8d3d0c3abe
gnu: r-savr: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-savr): Update to 1.22.0.
 2019-05-06 00:14:49 +02:00
Ricardo Wurmus 0aa72f2d1e
gnu: r-destiny: Update to 2.14.0. 
* gnu/packages/bioconductor.scm (r-destiny): Update to 2.14.0.
[propagated-inputs]: Remove r-fnn and r-hmisc; add r-ggplot2.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus 6fc161fc3e
gnu: r-biocneighbors: Update to 1.2.0. 
* gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.2.0.
[propagated-inputs]: Add r-biocgenerics and r-rcpphnsw.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus d8771f5fd6
gnu: r-ruvseq: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.18.0.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus 774e499cec
gnu: r-dnabarcodes: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.14.0.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus 3649d046a6
gnu: r-inspect: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-inspect): Update to 1.14.0.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus 5dce71535f
gnu: r-plgem: Update to 1.56.0. 
* gnu/packages/bioconductor.scm (r-plgem): Update to 1.56.0.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus 5bf7eb49f6
gnu: r-rots: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-rots): Update to 1.12.0.
 2019-05-06 00:14:48 +02:00
Ricardo Wurmus 07252952b7
gnu: r-glimma: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-glimma): Update to 1.12.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus 40f0ee43a0
gnu: r-goseq: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-goseq): Update to 1.36.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus 7a5d729af1
gnu: r-ctc: Update to 1.58.0. 
* gnu/packages/bioconductor.scm (r-ctc): Update to 1.58.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus 1236ce8e22
gnu: r-genomicinteractions: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.18.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus 176a264c7c
gnu: r-interactionset: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.12.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus eff6b2eb12
gnu: r-riboseqr: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.18.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus 7d5acf7a25
gnu: r-riboprofiling: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.14.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus 1ddd4af5a0
gnu: r-chipcomp: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.14.0.
 2019-05-06 00:14:47 +02:00
Ricardo Wurmus c38de81594
gnu: r-bayseq: Update to 2.18.0. 
* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.18.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus 4f4bed7de5
gnu: r-qdnaseq: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.20.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus 2317730994
gnu: r-cghcall: Update to 2.46.0. 
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.46.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus 8efb842f11
gnu: r-cghbase: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.44.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus bcb95b7aac
gnu: r-marray: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-marray): Update to 1.62.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus a61bcb28f7
gnu: r-graph: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-graph): Update to 1.62.0.
 2019-05-06 00:14:46 +02:00
Ricardo Wurmus 588b63c2af
gnu: r-multtest: Update to 2.40.0. 
* gnu/packages/bioconductor.scm (r-multtest): Update to 2.40.0.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus 0968a44874
gnu: r-ripseeker: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.24.0.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus 4c221b3bbf
gnu: r-diffbind: Update to 2.12.0. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.12.0.
[propagated-inputs]: Add r-rhtslib; remove r-zlibbioc.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus e02162f7ba
gnu: r-qvalue: Update to 2.16.0. 
* gnu/packages/bioconductor.scm (r-qvalue): Update to 2.16.0.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus 3e1bc88c1f
gnu: r-geneplotter: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.62.0.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus 4b53d55e98
gnu: r-regioner: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.16.0.
 2019-05-06 00:14:45 +02:00
Ricardo Wurmus 43a23a0733
gnu: r-hpar: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.26.0.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus 0c53332a27
gnu: r-annotate: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-annotate): Update to 1.62.0.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus 81a1c45df5
gnu: r-biocgenerics: Update to 0.30.0. 
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.30.0.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus 3addf736d5
gnu: r-systempiper: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.0.
[propagated-inputs]: Replace r-batchjobs with r-batchtools; add r-yaml.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus 9bcbca135b
gnu: r-rsamtools: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.0.
[propagated-inputs]: Add r-rhtslib.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus 82d9340b0c
gnu: r-impute: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.58.0.
[inputs]: Move gfortran from here...
[native-inputs]: ...to here.
 2019-05-06 00:14:44 +02:00
Ricardo Wurmus 2b4ac1d77e
gnu: r-rcas: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.0.
[propagated-inputs]: Add ghc-pandoc.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus 8322c860f9
gnu: r-methylkit: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.10.0.
[propagated-inputs]: Add r-mgcv.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus b173dbe617
gnu: r-annotationhub: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.0.
[propagated-inputs]: Add r-biocfilecache, r-dplyr, and r-rappdirs.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus a8abc8dd3a
gnu: r-fastseg: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.30.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus e699e8e599
gnu: r-keggrest: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus c798455d87
gnu: r-gage: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.34.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus d4ef1d59cc
gnu: r-genomicfiles: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.20.0.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus 70a3e4499d
gnu: r-complexheatmap: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.0.0.
[propagated-inputs]: Add r-clue and r-png.
 2019-05-06 00:14:43 +02:00
Ricardo Wurmus e2cb23404c
gnu: r-dirichletmultinomial: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.26.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus 0af6efa3c5
gnu: r-ensembldb: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus 96f98c5b72
gnu: r-organismdbi: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.26.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus a98c3b4ae4
gnu: r-biovizbase: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.32.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus d38fbacad1
gnu: r-ggbio: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.32.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus 623be1a443
gnu: r-gqtlbase: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.16.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus ed7de45655
gnu: r-snpstats: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.34.0.
 2019-05-06 00:14:42 +02:00
Ricardo Wurmus 3c5f5b4154
gnu: r-erma: Update to 1.0.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.0.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus 89ba9a7226
gnu: r-ldblock: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus a349d57a46
gnu: r-gqtlstats: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.16.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus 105d9e2cb4
gnu: r-gviz: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus 1b454f9f69
gnu: r-gwascat: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.0.
[propagated-inputs]: Remove r-annotationhub, r-ggbio, r-ggplot2, r-gqtlstats,
r-graph, r-gviz, r-snpstats, r-summarizedexperiment, and r-variantannotation.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus 256609eb46
gnu: r-sushi: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.22.0.
 2019-05-06 00:14:41 +02:00
Ricardo Wurmus 7705165882
gnu: r-fithic: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.10.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus e998a26e1d
gnu: r-hitc: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.28.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus 65925573be
gnu: r-hdf5array: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus d5625b3a9e
gnu: r-rhdf5lib: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus 583b4fd6e3
gnu: r-beachmat: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.0.0.
[inputs]: Remove hdf5 and zlib.
[propagated-inputs]: Rmeove r-hdf5array, r-rcpp, r-rhdf5, and r-rhdf5lib.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus 029cefdd90
gnu: r-singlecellexperiment: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.6.0.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus 70d04dc183
gnu: r-scater: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.0.
[propagated-inputs]: Add r-biocneighbors and r-biocsingular; remove r-plyr,
r-reshape2, and r-rhdf5lib.
 2019-05-06 00:14:40 +02:00
Ricardo Wurmus 4540727a21
gnu: r-scran: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.12.0.
[propagated-inputs]: Add r-bh, r-biocsingular, and r-dqrng; remove r-rhdf5lib.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus f2a63d1588
gnu: r-delayedmatrixstats: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus fbf3494972
gnu: Add r-biocfilecache. 
* gnu/packages/bioconductor.scm (r-biocfilecache): New variable.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus fab5f7c8d9
gnu: r-interactivedisplaybase: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.22.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus 975b72fa10
gnu: r-edaseq: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.18.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus b765fc4a4c
gnu: r-deseq: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.36.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus 95f3a46630
gnu: r-aroma-light: Update to 3.14.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.14.0.
 2019-05-06 00:14:39 +02:00
Ricardo Wurmus dd03589939
gnu: r-msnid: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.0.
 2019-05-06 00:14:38 +02:00
Ricardo Wurmus b65c264907
gnu: r-msnbase: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.10.0.
 2019-05-06 00:14:38 +02:00
Ricardo Wurmus ee386fcb1a
gnu: r-pcamethods: Update to 1.76.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.76.0.
 2019-05-06 00:14:38 +02:00
Ricardo Wurmus f955afdabf
gnu: r-mzid: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.22.0.
 2019-05-06 00:14:38 +02:00