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42411 Commits

Author SHA1 Message Date
Ricardo Wurmus 83546785b2
gnu: r-rcas: Add upstream name. 
* gnu/packages/bioinformatics.scm (r-rcas)[properties]: Add upstream name.
 2019-04-03 17:42:18 +02:00
Ricardo Wurmus 9800d859a7
gnu: Add r-zfpkm. 
* gnu/packages/bioconductor.scm (r-zfpkm): New variable.
 2019-04-03 17:42:18 +02:00
Ricardo Wurmus 6b12f21363
gnu: Add r-webbioc. 
* gnu/packages/bioconductor.scm (r-webbioc): New variable.
 2019-04-03 17:42:18 +02:00
Ricardo Wurmus 7b5101c5bf
gnu: Add r-widgettools. 
* gnu/packages/bioconductor.scm (r-widgettools): New variable.
 2019-04-03 17:42:17 +02:00
Ricardo Wurmus b9b8b447ec
gnu: Add r-wiggleplotr. 
* gnu/packages/bioconductor.scm (r-wiggleplotr): New variable.
 2019-04-03 17:42:17 +02:00
Ricardo Wurmus 8830664d61
gnu: Add r-wrench. 
* gnu/packages/bioconductor.scm (r-wrench): New variable.
 2019-04-03 17:42:17 +02:00
guy fleury iteriteka 807900804d
gnu: gnu-mate-icon-theme-faenza: Update to 1.20.0. 
* gnu/packages/mate.scm (gnu-mate-icon-theme-faenza): Update to 1.20.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:10 +02:00
guy fleury iteriteka 1e4999de71
gnu: mate-polkit: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-polkit): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:10 +02:00
guy fleury iteriteka 4e5b1221e7
gnu: mate-system-monitor: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-system-monitor): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:08 +02:00
guy fleury iteriteka b3dcbc0408
gnu: pluma: Update to 1.22.0. 
* gnu/packages/mate.scm (pluma): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:08 +02:00
guy fleury iteriteka 56689aa5fb
gnu: engrampa: Update to 1.22.0. 
* gnu/packages/mate.scm (engrampa): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:08 +02:00
guy fleury iteriteka b85d568203
gnu: eom: Update to 1.22.0. 
* gnu/packages/mate.scm (eom): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:08 +02:00
Guy fleury 24eee2c025
gnu: mate-utils: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-utils): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:08 +02:00
guy fleury iteriteka d3440c5313
gnu: mate-screensaver: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-screensaver): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:07 +02:00
guy fleury iteriteka 5150ba6f17
gnu: mate-netbook: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-netbook): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:07 +02:00
guy fleury iteriteka 9c688deccc
gnu: backgrounds: Update to 1.22.0. 
* gnu/packages/mate.scm (backgrounds): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:07 +02:00
guy fleury iteriteka d96a83b883
gnu: mate-calc: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-calc): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:07 +02:00
guy fleury iteriteka 59c410dd3e
gnu: mate-user-guide: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-user-guide): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:07 +02:00
guy fleury iteriteka 0e4c492d4d
gnu: mate-control-center: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-control-center): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:05 +02:00
guy fleury iteriteka 4373626b5a
gnu: caja-extensions: Update to 1.22.0. 
* gnu/packages/mate.scm (caja-extensions): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:05 +02:00
guy fleury iteriteka 98b81c2e9e
gnu: atril: Update to 1.22.0. 
* gnu/packages/mate.scm (atril): Update to 1.22.0.
[arguments]<#:configure-flags>: Remove pre-GTK3 option.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:04 +02:00
guy fleury iteriteka cca6216bfc
gnu: marco: Update to 1.22.0. 
* gnu/packages/mate.scm (marco): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:04 +02:00
guy fleury iteriteka 296c42b9e8
gnu: caja: Update to 1.22.0. 
* gnu/packages/mate.scm (caja): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:04 +02:00
guy fleury iteriteka da5ef2a085
gnu: mate-media: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-media): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:04 +02:00
guy fleury iteriteka 75a9f76066
gnu: mate-applets: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-applets): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:04 +02:00
guy fleury iteriteka e568d8339b
gnu: mate-panel: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-panel): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:04 +02:00
guy fleury iteriteka 45bafe5501
gnu: mate-menus: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-menus): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:03 +02:00
guy fleury iteriteka a628389fa9
gnu: libmatekbd: Update to 1.22.0. 
* gnu/packages/mate.scm (libmatekbd): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:03 +02:00
guy fleury iteriteka 660aa5d9f8
gnu: libmatemixer: Update to 1.22.0. 
* gnu/packages/mate.scm (libmatemixer): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:00 +02:00
guy fleury iteriteka 541dfa45da
gnu: mate-settings-daemon: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-settings-daemon): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:00 +02:00
guy fleury iteriteka bc96f8c4a7
gnu: mate-session-manager: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-session-manager): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:26:00 +02:00
guy fleury iteriteka 27d4e820d1
gnu: mate-terminal: Update to 1.22.0 
* gnu/packages/mate.scm (mate-terminal): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:25:59 +02:00
guy fleury iteriteka 595abe8688
gnu: libmatewether: Update to 1.22.0. 
* gnu/packages/mate.scm (libmatewether): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:25:59 +02:00
guy fleury iteriteka 2dc975d7c0
gnu: mate-desktop: Update to 1.22.2. 
* gnu/packages/mate.scm (mate-desktop): Update to 1.22.0.
[inputs]: Add iso-codes.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:25:59 +02:00
guy fleury iteriteka b465500686
gnu: mate-themes: Update to 3.22.19. 
* gnu/packages/mate.scm (mate-themes): Update to 3.22.19.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:25:59 +02:00
guy fleury iteriteka 80e8305146
gnu: mate-icon-theme: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-icon-theme): Update to 1.20.3.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:25:59 +02:00
guy fleury iteriteka 8b493c7cf0
gnu: mate-common: Update to 1.22.0. 
* gnu/packages/mate.scm (mate-common): Update to 1.22.0.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2019-04-03 15:25:57 +02:00
Ricardo Wurmus 44e06f9cf3
gnu: Add brlaser. 
* gnu/packages/printers.scm (brlaser): New variable.
 2019-04-02 22:04:08 +02:00
Kei Kebreau 932d6e276b
gnu: wxmaxima: Update to 19.03.1. 
* gnu/packages/maths.scm (wxmaxima): Update to 19.03.1.
 2019-04-02 14:45:22 -04:00
Leo Famulari a6f9f18c7e
gnu: livemedia-utils: Update to 2019.03.06. 
* gnu/packages/video.scm (livemedia-utils): Update to 2019-03-06.
[source]: Remove snippet.
 2019-04-02 14:44:14 -04:00
Leo Famulari 295197500f
gnu: Syncthing: Update to 1.1.1. 
* gnu/packages/syncthing.scm (syncthing): Update to 1.1.1.
 2019-04-02 13:07:03 -04:00
Leo Famulari 9c1b4316dc
gnu: Go standard crypto library: Update to 0.0.0-3.b7391e9 [security fixes]. 
Fixes a vulnerability in 'golang.org/x/crypto/salsa20' where, if more than 256
GiB of keystream is generated, or if the counter otherwise grows greater than 32
bits, the amd64 implementation will first generate incorrect output, and then
cycle back to previously generated keystream.

https://go.googlesource.com/crypto/+/b7391e95e576cacdcdd422573063bc057239113d

* gnu/packages/golang.scm (go-golang-org-x-crypto-bcrypt,
go-golang-org-x-crypto-blowfish, go-golang-org-x-crypto-pbkdf2,
go-golang-org-x-crypto-tea, go-golang-org-x-crypto-salsa20,
go-golang-org-x-crypto-cast5, go-golang-org-x-crypto-twofish,
go-golang-org-x-crypto-xtea, go-golang-org-x-crypto-ed25519,
go-golang-org-x-crypto-ripemd160, go-golang-org-x-crypto-blake2s,
go-golang-org-x-crypto-sha3, go-golang-org-x-crypto-ssh-terminal): Update to
0.0.0-3.b7391e9.
(go-golang-org-x-crypto-blake2s)[propagated-inputs]: Add
go-golang-org-x-sys-cpu.
(go-golang-org-x-crypto-blowfish, go-golang-org-x-crypto-pbkdf2,
go-golang-org-x-crypto-tea, go-golang-org-x-crypto-salsa20,
go-golang-org-x-crypto-cast5, go-golang-org-x-crypto-twofish,
go-golang-org-x-crypto-xtea, go-golang-org-x-crypto-ssh-terminal):
Inherit from go-golang-org-x-crypto-bcrypt.
 2019-04-02 13:07:03 -04:00
Leo Famulari 4a136536e8
gnu: Add go-golang-org-x-sys-cpu. 
* gnu/packages/golang.scm (go-golang-org-x-sys-cpu): New variable.
 2019-04-02 13:07:03 -04:00
Ludovic Courtès 1ccc0f807d
environment: '-C' creates namespaces where the user is not root. 
* guix/scripts/environment.scm (launch-environment/container): Add UID
and GID.  Use them in PASSWD and GROUPS.  Pass them as #:guest-uid and
 #:guest-gid to 'call-with-container'.
* tests/guix-environment-container.sh: Test the inner UID.
In '--user' test, replace hard-coded 0 with 1000.
* doc/guix.texi (Invoking guix environment): Adjust accordingly.
 2019-04-02 18:15:37 +02:00
Ludovic Courtès af76c020bf
linux-container: Make the guest UID and GID a parameter. 
* gnu/build/linux-container.scm (initialize-user-namespace): Add
 #:guest-uid and #:guest-gid parameters and honor them.
(run-container): Likewise.
(call-with-container): Likewise.
* tests/containers.scm ("call-with-container, user namespace, guest UID/GID"):
New test.
 2019-04-02 18:15:37 +02:00
Ludovic Courtès 36d69ac993
nls: Update 'de' translation of the manual. 2019-04-02 18:15:37 +02:00
Ricardo Wurmus cbe40b8b24
gnu: pigx-scrnaseq: Use older loompy. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
python-loompy with python-loompy-for-pigx-scrnaseq.
 2019-04-02 16:11:23 +02:00
Ricardo Wurmus dc112a0fe2
gnu: Add python-loompy-for-pigx-scrnaseq. 
* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): New variable.
 2019-04-02 16:11:12 +02:00
Ricardo Wurmus 82cc117450
gnu: pigx-chipseq: Update to 0.0.40. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.40.
 2019-04-02 15:53:23 +02:00
Ricardo Wurmus b4a33870f6
gnu: python-scanpy: Add python-louvain to inputs. 
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Sort
inputs and add python-louvain.
[arguments]: Do not delete test that depends on louvain.
 2019-04-02 15:11:45 +02:00