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37438 Commits

Author SHA1 Message Date
Marius Bakke 52b24ba495
gnu: mariadb: Update to 10.1.37 [security fixes]. 
This release fixes CVE-2018-3282, CVE-2018-3174, CVE-2018-3143, CVE-2018-3156,
and CVE-2018-3251.  See
<https://mariadb.com/kb/en/library/mariadb-10137-release-notes/> for details.

* gnu/packages/databases.scm (mariadb): Update to 10.1.37.
 2018-11-24 02:03:12 +01:00
Marius Bakke 4d8f4a3f00
Merge branch 'master' into core-updates 2018-11-24 01:58:18 +01:00
Marius Bakke dc4851093c
gnu: libraw: Update to 0.19.1. 
* gnu/packages/photo.scm (libraw): Update to 0.19.1.
 2018-11-24 01:50:43 +01:00
Marius Bakke 43bcf392a7
gnu: libtorrent-rasterbar: Update to 1.1.11. 
* gnu/packages/bittorrent.scm (libtorrent-rasterbar): Update to 1.1.11.
 2018-11-24 01:50:43 +01:00
Nam Nguyen c2be790fb1
gnu: Add deluge. 
* gnu/packages/bittorrent.scm (deluge): New variable.

Co-authored-by: Mike Rosset <mike.rosset@gmail.com>
Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-24 01:50:43 +01:00
Nam Nguyen 39da44c2c0
gnu: libtorrent-rasterbar: Compile Python bindings in C++11 mode. 
* gnu/packages/bittorrent.scm (libtorrent-rasterbar)[arguments]: Add phase to
  substitute setup.py.

Co-authored-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-24 01:50:43 +01:00
Nam Nguyen 8afe166dd7
gnu: Add python-service-identity. 
* gnu/packages/python-crypto.scm (python-service-identity,
  python2-service-identity): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-24 01:50:42 +01:00
Nicolas Goaziou f12f70b1f2
gnu: Add emacs-matrix-client. 
* gnu/packages/emacs.scm (emacs-matrix-client): New variable.
 2018-11-23 21:43:15 +01:00
Nicolas Goaziou d4f7b7e127
gnu: Add emacs-a. 
* gnu/packages/emacs.scm (emacs-a): New variable.
 2018-11-23 21:43:15 +01:00
Nicolas Goaziou 8fc78612b5
gnu: Add emacs-tracking. 
* gnu/packages/emacs.scm (emacs-tracking): New variable.
 2018-11-23 21:43:14 +01:00
Nicolas Goaziou 87470116e6
gnu: Add emacs-ov. 
* gnu/packages/emacs.scm (emacs-ov): New variable.
 2018-11-23 21:43:14 +01:00
Paul Garlick 57d30004e5
gnu: python-slepc4py: Update to 3.10.0. 
* gnu/packages/maths.scm (python-slepc4py): Update to 3.10.0.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-23 20:27:15 +01:00
Paul Garlick cd3681a237
gnu: python-petsc4py: Update to 3.10.0. 
* gnu/packages/maths.scm (python-petsc4py): Update to 3.10.0.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-23 20:27:15 +01:00
Paul Garlick e93da160ca
gnu: slepc: Update to 3.10.1. 
* gnu/packages/maths.scm (slepc): Update to 3.10.1.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-23 20:27:15 +01:00
Paul Garlick e6951e4ee0
gnu: petsc: Update to 3.10.2 
* gnu/packages/maths.scm (petsc): Update to 3.10.2.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-23 20:27:15 +01:00
Luther Thompson dc240b6aa5
gnu: python-ilinkedlist: Update to 0.4.0. 
* gnu/packages/python.scm (python-ilinkedlist): Update to 0.4.0.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-11-23 20:17:23 +01:00
Ludovic Courtès c491f7f8de
gnu: pt-scotch, pt-scotch32: Add Open MPI setup phase. 
* gnu/packages/maths.scm (pt-scotch)[arguments]: Use 'invoke' instead of
'system*'.  Add 'mpi-setup' phase.
(pt-scotch32)[arguments]: Likewise.
 2018-11-23 18:44:47 +01:00
Ricardo Wurmus d57ec906ba
gnu: pigx-scrnaseq: Use latest snakemake. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4
with snakemake.
 2018-11-23 16:30:48 +01:00
Ricardo Wurmus 92d9a1e2c6
gnu: pigx-bsseq: Use latest snakemake. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4
with snakemake.
 2018-11-23 16:30:16 +01:00
Ricardo Wurmus c068d00746
gnu: pigx-chipseq: Use latest snakemake. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4
with snakemake.
 2018-11-23 16:29:35 +01:00
Ricardo Wurmus 936ea3d664
gnu: python-gevent: Update to 1.3.7. 
* gnu/packages/python.scm (python-gevent): Update to 1.3.7.
[arguments]: Find headers for greenlet in phase "do-not-use-bundled-sources".
[propagated-inputs]: Add python-objgraph.
 2018-11-23 16:01:21 +01:00
Ricardo Wurmus 72ffb51231
gnu: Add python-objgraph. 
* gnu/packages/python.scm (python-objgraph): New variable.
 2018-11-23 16:01:07 +01:00
Ricardo Wurmus 93d229cb86
gnu: python-loompy: Remove python-typing. 
* gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove
python-typing.
 2018-11-23 15:59:44 +01:00
Ludovic Courtès e9926f80c6
build: Binary tarball now populates the "current-guix" profile. 
* Makefile.am (guix-binary.%.tar.xz): Pass
'--profile-name=current-guix'.  Remove glibc and glibc-utf8-locales.
* doc/guix.texi (Binary Installation): Update accordingly.
* etc/guix-install.sh
* etc/guix-install.sh (sys_create_store, sys_enable_guix_daemon)
(sys_authorize_build_farms): Likewise.
* etc/guix-publish.conf.in, etc/guix-publish.service.in,
etc/guix-daemon.conf.in, etc/guix-daemon.service.in: Update file names
accordingly.
 2018-11-23 15:42:01 +01:00
Ludovic Courtès 08f410834b
pack: Add '--profile-name'. 
* guix/scripts/pack.scm (self-contained-tarball): Add #:profile-name and
honor it.
(squashfs-image, docker-image): Add #:profile-name.
(%default-options): Add 'profile-name'.
(%options, show-help): Add "--profile-name".
(guix-pack): Honor it.
* tests/guix-pack-localstatedir.sh: New file.
* Makefile.am (SH_TESTS): Add it.
* doc/guix.texi (Invoking guix pack): Document "--profile-name".
 2018-11-23 15:42:01 +01:00
Ludovic Courtès 4bd5b9707e
Update NEWS. 2018-11-23 15:42:01 +01:00
Ludovic Courtès 694e638e78
status: Display 'build-remote' events. 
* guix/status.scm (print-build-event): Add clause for 'build-remote'.
 2018-11-23 15:42:00 +01:00
Ludovic Courtès 60e1c1099f
Update Guile-SQLite3 URL everywhere. 
* README: Update Guile-SQLite3 URL.
* doc/guix.texi (Requirements): Likewise.
* guix/store/database.scm (sqlite-exec): Likewise.
* m4/guix.m4 (GUIX_CHECK_GUILE_SQLITE3): Likewise.
 2018-11-23 15:42:00 +01:00
Alex Vong 332443d429
gnu: emacs-picpocket: Update to 40. 
Fix version string as well:
<https://lists.gnu.org/archive/html/guix-devel/2018-11/msg00286.html>.

* gnu/packages/emacs.scm (emacs-picpocket): Update to 40.
 2018-11-23 22:37:12 +08:00
Rutger Helling a605e3c68c
gnu: xpra: Update to 2.4.2. 
* gnu/packages/xorg.scm (xpra): Update to 2.4.2.
 2018-11-23 13:59:36 +01:00
Vagrant Cascadian 74e35e8c94
gnu: Add u-boot-pinebook. 
* gnu/packages/patches/u-boot-pinebook-a64-update-dts.patch: New file.
* gnu/packages/patches/u-boot-pinebook-syscon-node.patch: New file.
* gnu/packages/patches/u-boot-pinebook-mmc-calibration.patch: New file.
* gnu/packages/patches/u-boot-pinebook-video-bridge.patch: New file.
* gnu/packages/patches/u-boot-pinebook-r_i2c-controller.patch: New file.
* gnu/packages/patches/u-boot-pinebook-dts.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/bootloaders.scm (u-boot-pinebook): New exported variable.
* gnu/bootloader/u-boot.scm (u-boot-pinebook-bootloader): New exported
variable.
* gnu/system/install.scm (pinebook-installation-os): New exported variable.
 2018-11-22 21:59:05 +01:00
Ricardo Wurmus 37751b480f
gnu: podofo: Add patch to fix build. 
* gnu/packages/patches/podofo-cmake-3.12.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/pdf.scm (podofo)[source]: Add patch.
 2018-11-22 21:56:41 +01:00
Efraim Flashner 691d39a267
gnu: jalv: Build with python-2. 
* gnu/packages/audio.scm (jalv)[arguments]: Build with python-2.
 2018-11-22 22:06:29 +02:00
Pierre Neidhardt eff8e0b4d9
gnu: ccl: Fix missing command line argument support in wrapper. 
* gnu/packages/lisp.scm (ccl): Fix missing command line argument support in wrapper.
 2018-11-22 19:40:03 +01:00
Oleg Pykhalov 85e9c4b919
describe: Add recutils format. 
* guix/scripts/describe.scm (channel->recutils): New procedure.
(display-checkout-info, display-profile-info): Use this.
(%options): Add 'recutils' option.
* doc/guix.texi (Invoking guix describe): Document this.
 2018-11-22 21:17:55 +03:00
Oleg Pykhalov 81a40ee0cb
describe: Add json format. 
* guix/scripts/describe.scm (channel->json): New procedure.
(display-checkout-info, display-profile-info): Use this.
(%options): Add 'json' option.
* doc/guix.texi (Invoking guix describe): Document this.
 2018-11-22 21:17:54 +03:00
Oleg Pykhalov 8548f99549
describe: Use a procedure to format output. 
* guix/scripts/describe.scm (channel->sexp): New procedure.
(display-checkout-info, display-profile-info): Use this.
 2018-11-22 21:17:38 +03:00
Arun Isaac e3a2dd5559
gnu: gajim: Rename wrap-program phases. 
* gnu/packages/messaging.scm (gajim)[arguments]: Rename wrap-program phases to
wrap-gi-typelib-path and wrap-gsettings-schema-dir.
 2018-11-22 22:49:56 +05:30
Marius Bakke 7ff3f3d22c
gnu: python-scikit-learn: Update to 0.20.1. 
* gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch:
Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.20.1.
[source](patches): Remove.
[arguments]: Skip network tests with pytest instead of deleting files.  Make
sure $HOME is writable.
(python2-scikit-learn): Rewrite in terms of PACKAGE-WITH-PYTHON2.
 2018-11-22 17:02:47 +01:00
Nicolas Goaziou 561e3c1d0d
gnu: supercollider: Update to 3.9.3. 
* gnu/packages/audio.scm (supercollider): Update to 3.9.3.
 2018-11-22 13:00:15 +01:00
Nicolas Goaziou af90cc45ae
gnu: giac-xcas: Add a "doc" output 
* gnu/packages/algebra.scm (giac-xcas): Add "doc" output.
[arguments]: Add phase to install documentation in the appropriate directory.
 2018-11-22 12:18:52 +01:00
Nicolas Goaziou 90d5ec55ae
gnu: giac-xcas: Update to 1.5.0-19. 
* gnu/packages/algebra.scm (giac-xcas): Update to 1.5.0-19.
 2018-11-22 12:18:43 +01:00
Pierre Neidhardt 910ac0effe
gnu: ccl: Properly include x86-headers and remove missing "contrib" folder. 
* gnu/packages/lisp.scm (ccl): Include x86-headers and remove missing "contrib" folder.
[home-page]: Use HTTPS.
 2018-11-22 11:43:17 +01:00
Marius Bakke ec8130eb23
Merge branch 'master' into core-updates 2018-11-22 00:10:44 +01:00
Marius Bakke 437c78bcfb
gnu: python-tblib: Fix test failure with Python 3.7. 
* gnu/packages/python.scm (python-tblib)[arguments]: Add 'adjust-tests' phase.
 2018-11-22 00:00:44 +01:00
Ludovic Courtès d422cbb3d6
linux-initrd: 'expression->initrd' returns the complete file name. 
Previously 'expression->initrd' would return the directory that contains
the 'initrd' file; now it returns the complete file name for that file.

* gnu/system/linux-initrd.scm (expression->initrd)[builder]: Change
output file name to "initrd.cpio.gz".  Tail-call 'file-append' to return
the complete file name.
* gnu/system.scm (operating-system-initrd-file): Remove 'file-append'
call.
* gnu/build/linux-initrd.scm (write-cpio-archive): Check whether OUTPUT
already has the ".gz" suffix; rename if before invoking GZIP if it does,
and otherwise after.
* gnu/system/vm.scm (expression->derivation-in-linux-vm)[builder]: Do
not append "/initrd" to #$initrd.
 2018-11-21 23:26:59 +01:00
Ludovic Courtès a29ce1f97d
guix system: Fix 'init' again. 
Fixes a regression introduced in
52ee4479ef, whereby 'install' would now be
passed a procedure instead of a lowerable object.

* guix/scripts/system.scm (perform-action): Pass BOOTLOADER-SCRIPT as
the #:bootloader-installer argument of 'install'.
 2018-11-21 23:26:58 +01:00
Marius Bakke 148caae049
gnu: python-numpy: Update to 1.15.4. 
* gnu/packages/python.scm (python-numpy): Update to 1.15.4.
 2018-11-21 23:15:21 +01:00
Marius Bakke d9f8e846b6
gnu: mbedtls-apache: Update to 2.14.0. 
* gnu/packages/tls.scm (mbedtls-apache): Update to 2.14.0.
 2018-11-21 23:06:08 +01:00
Marius Bakke b344a3a937
gnu: termite: Update to 14. 
* gnu/packages/terminals.scm (termite): Update to 14.
 2018-11-21 23:01:38 +01:00