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Author SHA1 Message Date
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
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
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
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
Vasile Dumitrascu d232e02ecf
gnu: Add duperemove. 
* gnu/packages/disk.scm (duperemove): New variable.

Co-authored-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-03-29 15:17:35 +02:00
Ludovic Courtès 9c3f2c2e83
gnu: Add python-debug. 
Suggested by Pjotr Prins <pjotr.public12@thebird.nl>.

* gnu/packages/python.scm (python-debug): New variable.
 2018-03-29 15:17:35 +02:00
Efraim Flashner 594e5d7368
gnu: nano: Update to 2.9.5. 
* gnu/packages/nano.scm (nano): Update to 2.9.5.
 2018-03-29 16:08:06 +03:00
Roel Janssen c974008d91
gnu: Add r-idr. 
* gnu/packages/cran.scm (r-idr): New variable.
 2018-03-29 14:26:44 +02:00
Roel Janssen 996bed0608
gnu: Add r-amap. 
* gnu/packages/cran.scm (r-amap): New variable.
 2018-03-29 14:11:21 +02:00
Roel Janssen 6174db2b2c
gnu: Add r-venndiagram. 
* gnu/packages/cran.scm (r-venndiagram): New variable.
 2018-03-29 14:08:36 +02:00
Roel Janssen ddbf2a98ba
gnu: Add r-pastecs. 
* gnu/packages/cran.scm (r-pastecs): New variable.
 2018-03-29 13:54:30 +02:00
Ricardo Wurmus 017bffc1a3
gnu: libusb4java: Adjust for building with libusb 1.0.22. 
* gnu/packages/libusb.scm (libusb4java)[arguments]: Add phase to remove
"-Werror" flag.
 2018-03-29 12:26:38 +02:00
Ricardo Wurmus b0a4b6d957
gnu: libusb-for-axoloti: Update patch. 
* gnu/packages/patches/libusb-for-axoloti.patch: Update context for libusb
1.0.22.
 2018-03-29 12:26:38 +02:00
Chris Marusich 7874e9e047
gnu: Refactor boot-service-type and activation-service-type. 
* gnu/services.scm (boot-service-type) <compose>: Use the "identity"
  procedure instead of the "append" procedure because it more accurately
  reflects the intent, which is to simply return the single list of
  extensions to which fold-services applies the "compose" procedure.
  (activation-service-type) <compose>: Likewise.
 2018-03-29 08:38:49 +02:00
Chris Marusich 881c61d062
doc: Improve <service-type> documentation. 
* doc/guix.texi (Service Reference): Correct and clarify some statements
  regarding the "compose" and "extend" procedures of <service-type>.
 2018-03-29 07:29:49 +02:00
Chris Marusich 3cd4447f56
guix-install.sh: Explicitly set root's home directory. 
* etc/guix-install.sh (ROOT_HOME): New variable.
  (sys_create_store, sys_enable_guix_daemon, sys_authorize_build_farms):
  Use ROOT_HOME instead of ~root or the HOME environment variable.
* doc/guix.texi (Binary Installation): Instead of assuming that ~ and
  $HOME refer to root's directory simply because commands are being run
  as root, explicilty refer to it via ~root.

Fixes: <https://bugs.gnu.org/30728>
 2018-03-29 07:03:37 +02:00
Jelle Licht ce353a548f
gnu: node: Update to 9.10.0. 
* gnu/packages/node.scm (node): Update to 9.10.0.
 2018-03-28 23:33:53 +02:00
Jelle Licht b63af9b7c7
gnu: http-parser: Update to 2.8.0. 
* gnu/packages/web.scm (http-parser): Update to 2.8.0.
 2018-03-28 23:33:43 +02:00
Marius Bakke 0a8985f395
gnu: xf86-video-ati: Update to 18.0.1. 
* gnu/packages/xorg.scm (xf86-video-ati): Update to 18.0.1.
 2018-03-28 21:23:21 +02:00
Marius Bakke 4d967992d8
gnu: xf86-input-libinput: Update to 0.27.0. 
* gnu/packages/xorg.scm (xf86-input-libinput): Update to 0.27.0.
 2018-03-28 21:23:21 +02:00
Leo Famulari 935806b822
gnu: ntp: Update to 4.2.8p11 [security-fixes]. 
Fixes CVE-2016-1549 and CVE-2018-{7170,7182,7183,7184,7185}.

* gnu/packages/ntp.scm (ntp): Update to 4.2.8p11.
 2018-03-28 14:59:47 -04:00
Leo Famulari 590bdc149b
gnu: openssl: Replace with OpenSSL 1.0.2o [fixes CVE-2018-0739]. 
* gnu/packages/tls.scm (openssl)[replacement]: New field.
(openssl-1.0.2o): New variable.
 2018-03-28 14:07:45 -04:00
Konrad Hinsen 1cde746700
gnu: Add r-parsedate. 
* gnu/packages/cran.scm (r-parsedate): New variable.

Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-03-28 17:18:20 +02:00
Maxim Cournoyer 3481c714c6
gnu: mu: Fix tests failures triggered by DST. 
* gnu/packages/mail.scm (mu)[phases]: Add 'fix-date-tests.

Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-03-28 17:14:40 +02:00
Nadya Voronova 910deec66c
gnu: Add tcalc. 
* gnu/packages/maths.scm (tcalc): New variables.

Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-03-28 17:13:00 +02:00
Ludovic Courtès c5e7bca248
build: Build (guix ci) and (guix scripts weather) when HAVE_GUILE_JSON. 
* Makefile.am (MODULES): Move guix/ci.scm and guix/scripts/weather.scm
to the HAVE_GUILE_JSON-guarded block.
 2018-03-28 17:06:33 +02:00