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Author SHA1 Message Date
Tobias Geerinckx-Rice
7d0370ede4
gnu: r-learnr: Update to 0.9.2.1. 
* gnu/packages/cran.scm (r-learnr): Update to 0.9.2.1.
 2018-07-04 02:45:38 +02:00
Ricardo Wurmus
fab43c6b84
gnu: Add r-loomr. 
* gnu/packages/bioinformatics.scm (r-loomr): New variable.
 2018-07-03 17:58:55 +02:00
Ricardo Wurmus
3568b8234a
gnu: Add r-itertools. 
* gnu/packages/cran.scm (r-itertools): New variable.
 2018-07-03 17:58:55 +02:00
Björn Höfling
a51cf16031
gnu: Update stellarium to 0.18.0. 
[[PGP Signed Part:Good signature from BF286CB6593E5FFD Björn Höfling <bjoern.hoefling@bjoernhoefling.de> (trust undefined) created at 2018-06-29T20:39:51+0200 using DSA]]

* gnu/packages/astronomy.scm (stellarium): Update to 0.18.0.
[home-page]: Update URL.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-07-03 17:50:05 +02:00
Pierre Neidhardt
c1220498b0
gnu: emacs-helm-system-packages: Update to 1.10.0. 
* gnu/packages/emacs.scm (emacs-helm-system-packages): Update to 1.10.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-07-03 17:50:04 +02:00
Fis Trivial
53fc7a09f6
gnu: Add pocl. 
* gnu/packages/opencl.scm (pocl): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-07-03 17:50:04 +02:00
Ludovic Courtès
3c78f5b5c3
tests: basic: Wait for /var/run/shepherd/socket to be ready. 
* gnu/tests/base.scm (run-basic-test)["shepherd socket ready"]: New test.
 2018-07-03 17:50:04 +02:00
Ludovic Courtès
86eee976f5
Revert "packages: Optimize 'package-transitive-supported-systems'." 
This reverts commit 24420f5ffa.

This broke 'package-transitive-supported-systems', which would return
the union of supported systems instead of the intersection.
 2018-07-03 17:50:04 +02:00
Ludovic Courtès
f3f1d0a557
guix system: Make 'init' idempotent again. 
This fixes a regression introduced in
df2f6400b1: since the new
'register-path' (actually 'reset-timestamps') would make files
read-only, 'delete-file-recursively' would fail to delete them.  Thus,
re-running 'guix system init' on an already-populated store would fail
with a 'delete-file' EPERM.

* guix/scripts/system.scm (copy-item): Use 'lstat' instead of
'file-exists?'.  Call 'make-file-writable' on each directory below
DEST.
 2018-07-03 17:50:04 +02:00
Ludovic Courtès
90b144d22d
ui: Report file names in 'system-error' exceptions from 'delete-file'. 
* guix/ui.scm (delete-file): New error-reporting wrapper.
 2018-07-03 17:50:04 +02:00
Ludovic Courtès
e5e5119855
database: 'reset-timestamps' now correctly handles symlinks. 
* guix/store/database.scm (reset-timestamps): Use 'utime' with
AT_SYMLINK_NOFOLLOW for symlinks.
 2018-07-03 17:50:04 +02:00
Ludovic Courtès
25c7ff6a3e
syscalls: Define AT_SYMLINK_NOFOLLOW et al. 
* guix/build/syscalls.scm (AT_FDCWD, AT_SYMLINK_NOFOLLOW, AT_REMOVEDIR)
(AT_SYMLINK_FOLLOW, AT_NO_AUTOMOUNT, AT_EMPTY_PATH): New variables.
* tests/syscalls.scm ("utime with AT_SYMLINK_NOFOLLOW"): New test.
 2018-07-03 17:50:04 +02:00
Ludovic Courtès
a5b34d9d24
deduplication: Remove 'false-if-system-error', now unused. 
* guix/store/deduplication.scm (false-if-system-error): Remove.
 2018-07-03 17:50:04 +02:00
Ricardo Wurmus
13f5eb3494
gnu: pigx-bsseq: Update to 0.0.10. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.10.
[arguments]: Remove "wrap-executable" phase.
 2018-07-03 17:33:51 +02:00
Ricardo Wurmus
c7d5cd6ca5
gnu: pigx-rnaseq: Update to 0.0.4. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.4.
[arguments]: Remove "wrap-executable" phase.
 2018-07-03 16:20:28 +02:00
Ricardo Wurmus
29cbf8178f
gnu: pigx-chipseq: Update to 0.0.20. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.20.
 2018-07-03 16:20:28 +02:00
Paul Garlick
631bc3a666
gnu: ikiwiki: Include auto setup files in output. 
* gnu/packages/web.scm(ikiwiki)[arguments]: Add patch-Makefile phase.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-07-03 15:45:41 +02:00
Peter Mikkelsen
abf3a33178
gnu: emacs-use-package: Update to commit da8c9e2. 
This update is needed because the release tarball from github does not
contain all the files needed for us to build the package.

* gnu/packages/emacs.scm (emacs-use-package): Update to commit da8c9e2.
[source]: change to git.
[arguments]: Enable tests.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-07-03 15:45:41 +02:00
Peter Mikkelsen
b5f746d2da
gnu: Add emacs-atom-one-dark-theme. 
* gnu/packages/emacs.scm (emacs-atom-one-dark-theme): New variable

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2018-07-03 15:45:41 +02:00
Marius Bakke
27b73b4999
gnu: libuninameslist: Update to 20180701. 
* gnu/packages/fontutils.scm (libuninameslist): Update to 20180701.
[source]: Change URI to use release tarball.  Remove FILE-NAME.
[native-inputs]: Remove.
 2018-07-03 15:45:40 +02:00
Marius Bakke
b19c92ef7e
gnu: libuninameslist: Correct license. 
* gnu/packages/fontutils.scm (libuninameslist)[license]: Remove GPL2.  Add
BSD-3 and X11-STYLE.
 2018-07-03 15:45:40 +02:00
Danny Milosavljevic
74ba3a6830
gnu: Add vsftpd. 
* gnu/packages/ftp.scm (vsftpd): New variable.
 2018-07-03 15:32:51 +02:00
Rutger Helling
4786f51576
gnu: vkd3d: Add vulkan-headers. 
* gnu/packages/vulkan.scm (vkd3d)[inputs]: Add vulkan-headers.
 2018-07-03 11:23:47 +02:00
Rutger Helling
4108886b09
gnu: vkquake: Add vulkan-headers. 
* gnu/packages/games.scm (vkquake)[inputs]: Add vulkan-headers.
 2018-07-03 11:23:47 +02:00
Rutger Helling
08899ee91b
gnu: mpv: Add vulkan-headers. 
* gnu/packages/video.scm (mpv)[inputs]: Add vulkan-headers.
 2018-07-03 11:23:47 +02:00
Rutger Helling
b1eb1ba99c
gnu: vulkan-loader: Update to 1.1.77.0. 
* gnu/packages/vulkan.scm (vulkan-loader): Update to 1.1.77.0.
[inputs]: Add 'vulkan-headers.
[home-page]: Correct URL.
 2018-07-03 11:23:47 +02:00
Rutger Helling
cf09bed4f5
gnu: Add vulkan-headers. 
* gnu/packages/vulkan.scm (vulkan-headers): New variable.
 2018-07-03 11:23:47 +02:00
Rutger Helling
940c2c5c14
gnu: openrct2: Update to 0.2.0. 
* gnu/packages/games.scm (openrct2): Update to 0.2.0.
[configure-flags]: Add -DDOWNLOAD_OBJECTS=OFF configure flag.
[arguments]: Add 'fixgcc7, 'get-rid-of-errors phases.
[native-inputs]: Add gcc@7.
 2018-07-03 11:01:21 +02:00
Rutger Helling
fab8d41c64
gnu: dolphin-emu: Update to commit 806c1ee. 
* gnu/packages/emulators.scm (dolphin-emu): Update to commit 806c1ee.
[source]: Don't delete removed externals.
[arguments]: Remove unused variables.
[inputs]: Add 'pugixml. Remove 'wxwidgets-gtk2-3.1.
 2018-07-03 09:13:55 +02:00
Oleg Pykhalov
a6a2ef27a3
gnu: Add keynav. 
* gnu/packages/xorg.scm (keynav): New variable.
 2018-07-03 07:29:30 +03:00
Oleg Pykhalov
ae6fa00af0
import: elpa: Check if 'fetch-elpa-package' rest argument is null. 
* guix/import/elpa.scm (fetch-elpa-package): Check if 'rest' is null.
 2018-07-03 07:19:13 +03:00
Oleg Pykhalov
3a15d0aa9c
bash completion: Complete files names after 'guix weather -m'. 
* etc/completion/bash/guix (_guix_complete): Complete files names after 'guix
weather -m'.
 2018-07-03 06:58:51 +03:00
Oleg Pykhalov
9b0a755f64
bash completion: Complete files names after 'guix build -L'. 
* etc/completion/bash/guix (_guix_complete): Complete files names after 'guix
build -L'.
 2018-07-03 06:58:51 +03:00
Kei Kebreau
6104f922ee
gnu: units: Update to 2.17. 
* gnu/packages/maths.scm (units): Update to 2.17.
 2018-07-02 21:12:55 -04:00
Gábor Boskovits
673135df30
gnu: icedtea Work around gcc segfault. 
* gnu/packages/java.scm (icedtea-8)[native-inputs]: Add icedtea-7
patch to hotspot.
 2018-07-03 02:07:14 +02:00
Leo Famulari
86163a017b
gnu: libgit2: Update to 0.26.4 [fixes CVE-2018-11235]. 
* gnu/packages/version-control.scm (libgit2): Update to 0.26.4.
(source): Adjust patch name.
* gnu/packages/patches/libgit2-0.25.1-mtime-0.patch: Rename to ...
* gnu/packages/patches/libgit2-mtime-0.patch: ... this.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
 2018-07-02 19:47:46 -04:00
Gábor Boskovits
db024183c9
gnu: icedtea: Work around gcc segfault. 
* gnu/packages/java.scm (icedtea-7)[native-inputs]: Add patch to hotspot.
* gnu/packages/patches/icedtea-7-hotspot-gcc-segfault-workaround.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2018-07-03 00:53:56 +02:00
Ludovic Courtès
3dbf331942
deduplication: Place link files under /gnu/store/.links. 
Previously they'd always be placed next to TO-REPLACE, which would lead
to EPERM in some cases.

* guix/store/deduplication.scm (replace-with-link): Add #:swap-directory
parameter and honor it.  Add call to 'make-file-writable'.  Catch
'system-error' around 'rename-file'.
(deduplicate): Pass #:swap-directory and remove uses of
'false-if-system-error'.
* tests/store-deduplication.scm ("deduplicate"): Add 'chmod' call.
 2018-07-03 00:39:11 +02:00
Ludovic Courtès
af2f8ae5f1
deduplication: Fix incorrect use of 'throw'. 
* guix/store/deduplication.scm (get-temp-link): In handler, fix call to
'throw'.
 2018-07-03 00:39:11 +02:00
Ludovic Courtès
71bf6cb700
guix system: init: Check the available space before copying. 
* guix/scripts/system.scm (copy-closure): Call 'query-path-info*' on
TO-COPY and REFS.  Compute the total size.  Call 'check-available-space'.
 2018-07-03 00:39:11 +02:00
Ludovic Courtès
8120b23e51
ui: Make 'check-available-space' public. 
* guix/ui.scm (check-available-space): Add optional 'directory'
parameter, defaulting to (%store-prefix).  Honor it.  Make public.
 2018-07-03 00:39:10 +02:00
Ludovic Courtès
0744a9f002
store: Add 'query-path-info*'. 
* guix/scripts/size.scm (query-path-info*): Move to...
* guix/store.scm (query-path-info*): ... here.
 2018-07-03 00:39:10 +02:00
Ludovic Courtès
24420f5ffa
packages: Optimize 'package-transitive-supported-systems'. 
This version is 13% faster than the one above when timing:

  (fold-packages (lambda (p x)
		   (package-transitive-supported-systems p))
		 '())

* guix/packages.scm (package-transitive-supported-systems): Make
'systems' a set instead of calling 'lset-intersection' repeatedly.
 2018-07-03 00:39:10 +02:00
Nicolas Goaziou
c729901583
gnu: python-duniterpy: Change module. 
* gnu/packages/python-crypto.scm (python-duniterpy): Move...
* gnu/packages/finance.scm: ... here.
 2018-07-02 23:27:07 +02:00
Nicolas Goaziou
929d4d2f4a
gnu: python-pylibscrypt: Improve speed. 
* gnu/packages/python-crypto.scm (python-pylibscrypt): Use "libscrypt"
  implementation instead of "openssl".

"hashlib.scrypt" requires Python 3.6+ and OpenSSL 1.1+.  Since Python is built
with OpenSSL 1.0, the library is unavailable. "pylibscrypt" defaults to a slow
pure Python implementation.  Instead, rely on the much faster "libscrypt".
 2018-07-02 23:12:40 +02:00
Nicolas Goaziou
84be0e9a74
gnu: Add libscrypt. 
* gnu/packages/crypto.scm (libscrypt): New variable.
 2018-07-02 23:12:14 +02:00
Kei Kebreau
2926e950ce
gnu: Add freedink-dfarc. 
* gnu/packages/games.scm (freedink-dfarc): New variable.
 2018-07-02 14:42:36 -04:00
Tobias Geerinckx-Rice
63e708f468
gnu: bambam: Don't use unstable tarball. 
* gnu/packages/games.scm (bambam)[source]: Use GIT-FETCH.
 2018-07-02 20:19:08 +02:00
Tobias Geerinckx-Rice
a62764bdbb
gnu: zstd: Update to 1.3.5. 
* gnu/packages/compression.scm (zstd): Update to 1.3.5.
[source]: Add two patches to make the test suite pass.
* gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch,
gnu/packages/patches/zstd-fix-stdin-list-test.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add both.
 2018-07-02 20:19:07 +02:00
Tobias Geerinckx-Rice
8ef7ecf469
gnu: acpica: Update to 20180629. 
* gnu/packages/admin.scm (acpica): Update to 20180629.
 2018-07-02 20:19:07 +02:00