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31210 Commits

Author SHA1 Message Date
Mark H Weaver 619d7bffa0
gnu: linux-libre@4.1: Update to 4.1.51. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.51.
 2018-03-30 17:31:15 -04:00
Julien Lepiller a7baa201cb
gnu: Update php to 7.2.4. 
* gnu/packages/php.scm (php): Update to 7.2.4.
 2018-03-30 23:22:18 +02:00
Ricardo Wurmus 4bd8a9d8e2
gnu: Define ao. 
This is a follow-up to commit 28f4d56dd3.

* gnu/packages/engineering.scm (ao): Restore variable definition.
 2018-03-30 22:54:51 +02:00
Ricardo Wurmus 28f4d56dd3
gnu: ao: Update to 0-2.9d857d1. 
* gnu/packages/engineering.scm (ao): Rename...
(libfive): ...to this new variable; update to 0-2.9d857d1.
[inputs]: Remove glfw, libepoxy, glm, guile-2.0; add qtbase, guile-2.2.
[home-page]: Use new libfive home page.
[description]: Adjust.
(ao): Redefine using 'deprecated-package'.
 2018-03-30 22:23:43 +02:00
Arun Isaac 6009cdb4e3
gnu: python-pycairo: Update to 1.16.3. 
* gnu/packages/gtk.scm (python-pycairo): Update to 1.16.3.
[source]: Remove patch.
[build-system]: Switch to python-build-system.
[native-inputs]: Remove python-waf.
[home-page]: Use HTTPS URI.
* gnu/packages/patches/pycairo-wscript.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Unregister it.
 2018-03-31 00:29:35 +05:30
Arun Isaac 7ad5c6dd78
gnu: python-pytest: Update to 3.5.0. 
* gnu/packages/python.scm (python-six): Replace system* with invoke.
(python-six-bootstrap, python2-six-bootstrap, python2-funcsigs-bootstrap): New
variables.
(python-more-itertools)[propagated-inputs]: Replace python-six with
python-six-bootstrap.
* gnu/packages/check.scm (python-pytest): Update to 3.5.0.
[propagated-inputs]: Add python-attrs-bootstrap,
python-more-itertools-bootstrap, python-pluggy and python-six-bootstrap.
[properties]: Add python2-variant.
(python2-pytest)[propagated-inputs]: Add python2-funcsigs.
(python-pytest-bootstrap)[properties]: Add python2-variant.
(python2-pytest-bootstrap)[propagated-inputs]: Add python2-funcsigs-bootstrap.
 2018-03-31 00:29:35 +05:30
Arun Isaac 32b92480b3
gnu: python-py: Update to 1.5.3. 
* gnu/packages/python.scm (python-py): Update to 1.5.3.
[home-page]: Update URI.
 2018-03-31 00:29:35 +05:30
Arun Isaac b19a960f5f
gnu: python-hypothesis: Update to 3.52.0. 
* gnu/packages/check.scm (python-hypothesis): Update to 3.52.0.
[propagated-inputs]: Add python-attrs and python-coverage.
[home-page]: Update URI.
* gnu/packages/python.scm (python-attrs-bootstrap, python2-attrs-bootstrap):
New variables.
 2018-03-31 00:29:35 +05:30
Arun Isaac 180b6f3baa
gnu: Add python-more-itertools. 
* gnu/packages/python.scm (python-more-itertools, python2-more-itertools): New
variables.
 2018-03-31 00:29:35 +05:30
Arun Isaac 21f76d40cc
gnu: python-pluggy: Update to 0.6.0. 
* gnu/packages/python.scm (python-pluggy): Update to 0.6.0.
 2018-03-31 00:29:35 +05:30
Arun Isaac 769f56d735
gnu: python-pyasn1: Update to 0.4.2. 
* gnu/packages/python.scm (python-pyasn1): Update to 0.4.2.
 2018-03-31 00:29:34 +05:30
Arun Isaac fbec83b81a
gnu: python-attrs: Update to 17.4.0. 
* gnu/packages/python.scm (python-attrs): Update to 17.4.0.
 2018-03-31 00:29:34 +05:30
Nicolas Goaziou 2d19a7e4f4
gnu: emacs-org: Change source and naming scheme. 
* gnu/packages/emacs.scm (emacs-org): Switch back to ELPA.  Adopt its naming
  scheme.
 2018-03-30 20:03:36 +02:00
Nicolas Goaziou 5ecd2d28d0
gnu: emacs-org-contrib: Fix build. 
* gnu/packages/emacs.scm (emacs-org-contrib): Update SHA256.
[version]: Add keyword.
[arguments]: Use new keyword.
 2018-03-30 20:03:31 +02:00
Roel Janssen fdc306879b
gnu: Add delly. 
* gnu/packages/bioinformatics.scm (delly): New variable.
* gnu/packages/patches/delly-use-system-libraries.patch: New file.
* gnu/local.mk: Include delly-use-system-libraries.patch.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-03-30 10:48:01 -04:00
Roel Janssen 183ce98849
gnu: Add r-regioner. 
* gnu/packages/bioconductor.scm (r-regioner): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-03-30 10:47:57 -04:00
Nikolai Merinov f342bb58fe
gnu: rust: Update rust to 1.24.1. 
* gnu/packages/rust.scm (rust-bootstrap): Freeze bootstrap version to 1.22.1.
Reorganize bootstrap binaries to match new "rust" package structure with two
ouputs "out" with Rust compiler and "cargo" with Cargo package manager.
Replace all "system*" by "invoke".
(rust-1.23): Rename "rustc" to "rust".  Update sha256 for tarball.  Add cargo
related dependencies.  Install "cargo" as separate "rust" output.  Remove
substitutes for parts that were fixed in "rustc" source code.  Install
documentation to separate "doc" output.  Update configuration according to
changes in "rustc" source code.  Replace all "system*" by "invoke".
(rust): Create package for 1.24.1 rust release based on rust-1.23 release.
* guix/build-system/cargo.scm (default-rust): Replace "default-cargo" and
"default-rustc" functions with "default-rust" function.
(cargo-build-system): Take only one package as "rust" source.  Use "rustc" of
default output of "rust" package, use "cargo" as "cargo" output of "rust"
package.
 2018-03-30 15:46:53 +02:00
Ben Woodcroft 8456a4c5cb
gnu: ruby-2.2: Update to 2.2.10. 
* gnu/packages/ruby.scm (ruby-2.2): Update to 2.2.10.
 2018-03-30 12:27:57 +10:00
Ben Woodcroft 049edeb24c
gnu: ruby-2.3: Update to 2.3.7. 
* gnu/packages/ruby.scm (ruby-2.3): Update to 2.3.7.
 2018-03-30 12:24:59 +10:00
Ben Woodcroft f38ac742e6
gnu: mash: Update to 2.0. 
* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
 2018-03-30 12:18:35 +10:00
Ben Woodcroft c7a8aa131d
gnu: mafft: Update to 7.394. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
 2018-03-30 12:18:35 +10:00
Ben Woodcroft 9a40b8d9b2
gnu: diamond: Update to 0.9.19. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
 2018-03-30 12:18:35 +10:00
Leo Famulari 9b018ada13
gnu: tzdata: Update to 2018d. 
* gnu/packages/base.scm (tzdata): Update to 2018d.
 2018-03-29 20:15:49 -04:00
Ricardo Wurmus 315ed91efb
gnu: pybitmessage: Update to 0.6.3.2 [security fixes]. 
* gnu/packages/messaging.scm (pybitmessage): Update to 0.6.3.2.
[source]: Fetch from git.
 2018-03-29 22:43:37 +02:00
Ricardo Wurmus 80808d678a
gnu: hydrogen: Update to 1.0.0-beta1. 
* gnu/packages/music.scm (hydrogen): Update to 1.0.0-beta1.
[source]: Fetch from git.
[arguments]: Add phase to fix installation directory for pixmaps.
[inputs]: Remove qt-4; add qtbase and qtxmlpatterns.
 2018-03-29 22:40:30 +02:00
Ricardo Wurmus 9f1ac4fa49
gnu: mod-host: Update to 0.10.6-3.1726ad06b. 
* gnu/packages/music.scm (mod-host): Update to 0.10.6-3.1726ad06b.
 2018-03-29 22:26:59 +02:00
Ricardo Wurmus 9602ac76b4
gnu: drumkv1: Update to 0.9.0. 
* gnu/packages/music.scm (drumkv1): Update to 0.9.0.
 2018-03-29 22:22:50 +02:00
Ricardo Wurmus 2a5d08daf4
gnu: samplv1: Update to 0.9.0. 
* gnu/packages/music.scm (samplv1): Update to 0.9.0.
 2018-03-29 22:22:50 +02:00
Ricardo Wurmus 4503b18701
gnu: padthv1: Update to 0.9.0. 
* gnu/packages/music.scm (padthv1): Update to 0.9.0.
 2018-03-29 22:22:50 +02:00
Ricardo Wurmus 7c60a23cb1
gnu: synthv1: Update to 0.9.0. 
* gnu/packages/music.scm (synthv1): Update to 0.9.0.
 2018-03-29 22:22:50 +02:00
Ricardo Wurmus 15c5541bc8
gnu: qtractor: Update to 0.9.0. 
* gnu/packages/music.scm (qtractor): Update to 0.9.0.
 2018-03-29 22:22:50 +02:00
Marius Bakke cee6d90f73
gnu: awesome: Remove obsolete snippet. 
* gnu/packages/wm.scm (awesome)[source](snippet): Remove.
 2018-03-29 21:30:15 +02:00
Marius Bakke 40fb6b84f9
gnu: xcb-util-xrm: Update to 1.3. 
* gnu/packages/xdisorg.scm (xcb-util-xrm): Update to 1.3.
 2018-03-29 21:30:15 +02:00
Marius Bakke d2fd5c6532
gnu: mbedtls-apache: Update to 2.7.2. 
* gnu/packages/tls.scm (mbedtls-apache): Update to 2.7.2.
[source](snippet): Remove.
 2018-03-29 21:30:15 +02:00
Leo Famulari b6beda1d6b
gnu: Add botan. 
* gnu/packages/crypto.scm (botan): New variable.
 2018-03-29 14:40:34 -04:00
Tonton d4e0ebd016
gnu: Add fpm2. 
* gnu/packages/password-utils.scm (fpm2): New variable.

Signed-off-by: Tonton <tonton@riseup.net>
Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-03-29 18:43:09 +02:00
Tonton af1e3dfe27
gnu: Add screen-message. 
* gnu/packages/xdisorg.scm (screen-message): New variable.

Signed-off-by: Tonton <tonton@riseup.net>
Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-03-29 18:35:46 +02:00
Ludovic Courtès d0a2db47fb
ld-wrapper: Allow linking with non-store libraries by default. 
This was suggested on several occasions, notably
<https://bugs.gnu.org/24544>.

* gnu/packages/ld-wrapper.in (%allow-impurities?): Default to #t and
parse the value of 'GUIX_LD_WRAPPER_ALLOW_IMPURITIES'.
* guix/build/gnu-build-system.scm (set-paths): Set
'GUIX_LD_WRAPPER_ALLOW_IMPURITIES'.
 2018-03-29 17:58:16 +02:00
Ludovic Courtès 1a5e07c3b5
ld-wrapper: Don't talk about "impure library". 
* gnu/packages/ld-wrapper.in (rpath-arguments): Clarify message instead
of saying "impure library".
 2018-03-29 17:58:16 +02:00
Ludovic Courtès 6764538327
ld-wrapper: Make sure debugging output goes through. 
* gnu/packages/ld-wrapper.in (ld-wrapper): Add call to 'force-output'.
 2018-03-29 17:58:16 +02:00
Ludovic Courtès c90fd42020
gremlin: Fix typo in export list. 
* guix/build/gremlin.scm: Really export 'elf-dynamic-info-soname'.
 2018-03-29 17:58:15 +02:00
Ludovic Courtès 5294836d6a
gnu: libarchive: Add '-L' flags in 'libarchive.pc'. 
* gnu/packages/backup.scm (libarchive)[arguments]: Add
'add--L-in-libarchive-pc' phase.
 2018-03-29 17:58:15 +02:00
Tobias Geerinckx-Rice 95fb6b0413
gnu: r-lme4: Update to 1.1-16. 
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-16.
 2018-03-29 17:45:45 +02:00
Tobias Geerinckx-Rice dc8450c178
gnu: r-curl: Update to 3.2. 
* gnu/packages/web.scm (r-curl): Update to 3.2.
 2018-03-29 17:36:57 +02:00
Tobias Geerinckx-Rice f36685b058
gnu: bspwm: Update to 0.9.4. 
* gnu/packages/wm.scm (bspwm): Update to 0.9.4.
 2018-03-29 17:36:50 +02:00
Tobias Geerinckx-Rice 4bb5bdd963
gnu: rss-bridge: Update to 2018-03-11. 
* gnu/packages/web.scm (rss-bridge): Update to 2018-03-11.
 2018-03-29 17:36:39 +02:00
Marius Bakke 5576cfabf3
Merge branch 'master' into core-updates 2018-03-29 17:34:41 +02:00
Marius Bakke 12cb6c31df
gnu: cmake: Update to 3.11.0. 
* gnu/packages/cmake.scm (cmake): Update to 3.11.0.
[arguments]: Enable fixed test.  Adjust file substitutions.  Run tests and
"./configure" in parallel.
(cmake-3.11): Remove variable.
* gnu/packages/storage.scm (ceph)[arguments]: Remove #:cmake.
 2018-03-29 16:54:52 +02:00
Roel Janssen e086d2f68b
gnu: r-mutationalpatterns: Update to 1.4.3. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3;
  [propagated-inputs]: Remove r-gridextra.
 2018-03-29 15:50:44 +02:00
Roel Janssen 53e42694e5
gnu: kaiju: Update to 1.6.2. 
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2;
  [inputs]: Add zlib.
 2018-03-29 15:40:52 +02:00