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44172 Commits

Author SHA1 Message Date
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 a321312e3a
build: go-build-system: Follow-up to commit f42e4ebb56. 
This follows commit f42e4ebb56, which made it so that the unpack phase return
value could be left unspecified.

* guix/build/go-build-system.scm (unpack): Ensure that the value returned upon
a successful completion of the phase is #t.
 2019-05-05 23:01:03 -04:00
Maxim Cournoyer 2edec51c5e
build: go-build-system: Follow-up commit. 
There was an extraneous pair of parens in commit 7e84d3eef7.  Thanks for Mark
Weaver for reporting the issue.

* guix/build/go-build-system.scm (unpack): Remove the extraneous pair of
  parentheses surrounding the `display' function call.
 2019-05-05 22:41:11 -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
Maxim Cournoyer f42e4ebb56
build: go-build-system: Ensure uniform unpacking directory. 
Depending on whether the source is a directory or an archive, we strip the
source directory or preserve it, respectively.  This change makes it so that
whether the type of the source, it is unpacked at the expected location given
by the IMPORT-PATH of the Go build system.

* guix/build/go-build-system.scm: Add the (ice-9 ftw) module.
(unpack): Add inner procedure to maybe strip the top level directory of an
archive, document it and use it.
 2019-05-05 20:06:19 -04:00
Maxim Cournoyer 7e84d3eef7
build: go-build-system: Use WHEN for side-effect conditionals. 
* guix/build/go-build-system.scm (unpack): Replace single branch `if' by
`when'.
 2019-05-05 20:06:18 -04:00
Maxim Cournoyer b5f0528354
build: go-build-system: Re-ident. 
* guix/build/go-build-system.scm (unpack): Fix indentation.
 2019-05-05 20:06:18 -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