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Author SHA1 Message Date
Ricardo Wurmus
6c32e9b4dc
gnu: bedtools: Update to 2.29.2. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.29.2.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Change to Expat.
 2020-02-27 17:38:17 +01:00
Ricardo Wurmus
d24b3b0213
gnu: rseqc: Update to 3.0.1. 
* gnu/packages/bioinformatics.scm (rseqc): Update to 3.0.1.
[source]: Remove snippet.
[arguments]: Remove to build with Python 3.
[inputs]: Replace python2-cython, python2-pysam, and python2-numpy with
python-cython, python-pysam, and python-numpy, respectively; add
python-bx-python and python-pybigwig.
[native-inputs]: Replace python2-nose with python-nose.
 2020-02-27 17:38:17 +01:00
Maxim Cournoyer
faa0fa3978
gnu: earlyoom: Update to latest commit to resolve a test failure. 
* gnu/packages/linux.scm (earlyoom): Update to commit
7bd4b2c9a285d2b9a4ef6e7a080e83ab95fcdeea.
 2020-02-27 09:34:46 -05:00
Maxim Cournoyer
e64c5a8fe4
gnu: git-repo: Really disable self update. 
* gnu/packages/android.scm (git-repo)[phases]{do-not-self-update}: Rename
phase from 'do-not-clone-this-source.  Rework the patching done to prevent
repo from self updating.
{set-executable-paths}: Do not patch the reference to GnuPG, as it is only
necessary for the self update mechanism, which is disabled.
[inputs]: Remove gnupg.
 2020-02-27 09:34:46 -05:00
Maxim Cournoyer
0c0156089c
gnu: git-repo: Update to 2.4.1. 
* gnu/packages/android.scm (git-repo): Update to 2.4.1.
 2020-02-27 09:34:46 -05:00
Brice Waegeneire
e7075353e0
gnu: kicad: Add translations and search paths. 
* gnu/packages/engineering.scm (kicad)[arguments]<#:phases>[install-translations]: New phase.
[native-search-paths]: Add specification for KICAD_TEMPLATE_DIR,
KICAD_SYMBOL_DIR, KISYSMOD and KISYS3DMOD.
[native-inputs]: Add desktop-file-utils and kicad-i18l.
[inputs]: Remove desktop-file-utils.  Replace python by
python-wrapper.
(kicad-i18l): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2020-02-27 14:31:26 +01:00
Brice Waegeneire
badc3c6783
gnu: kicad-symbols: Update synopsis and description. 
* gnu/packages/engineering.scm (kicad-symbols)[synopsis]: Update.
[description]: Update.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2020-02-27 14:31:26 +01:00
Brice Waegeneire
0528474223
gnu: Remove kicad-library. 
* gnu/packages/engineering.scm (kicad-library): Remove variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2020-02-27 14:31:26 +01:00
Brice Waegeneire
ca839f3c18
gnu: Add kicad-templates. 
* gnu/packages/engineering.scm (kicad-templates): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2020-02-27 14:31:26 +01:00
Brice Waegeneire
c595150709
gnu: Add kicad-packages3d. 
* gnu/packages/engineering.scm (kicad-packages3d): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2020-02-27 14:31:26 +01:00
Brice Waegeneire
259e65aac1
gnu: Add kicad-footprints. 
* gnu/packages/engineering.scm (kicad-footprints): New variable.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2020-02-27 14:31:23 +01:00
Pierre Neidhardt
a69bc7386f
gnu: Add lttng-ust. 
* gnu/packages/linux.scm (lttng-ust): New variable.
 2020-02-27 14:06:57 +01:00
Pierre Neidhardt
e10587c5a5
gnu: gnome-shell-extension-noannoyance: Fix synopsis and description. 
* gnu/packages/gnome-xyz.scm (gnome-shell-extension-noannoyance)[synopsis]:
  Use imperative form.
  [description]: Remove spurious comma.
 2020-02-27 11:33:49 +01:00
Leo Prikler
c456d18b50
gnu: gnome-shell-extension-noannoyance: Use the copy-build-system. 
* gnu/packages/gnome-xyz.scm (gnome-shell-extension-noannoyance):
Use the copy-build-system.
 2020-02-27 11:31:19 +01:00
Leo Prikler
f6a151cdc6
gnu: gnome-shell-extension-appindicator: Use the copy-build-system. 
* gnu/packages/gnome-xyz.scm (gnome-shell-extension-appindicator):
Use the copy-build-system.
 2020-02-27 11:29:03 +01:00
Alex Griffin
fdd4813547
gnu: Add gnome-shell-extension-gsconnect. 
* gnu/packages/gnome-xyz.scm (gnome-shell-extension-gsconnect): New variable.
 2020-02-27 10:58:46 +01:00
Pierre Neidhardt
b7d0590bb2
gnu: emacs-evil-collection: Update to 20200219. 
* gnu/packages/emacs-xyz.scm (emacs-evil-collection): Update to 20200219.
 2020-02-27 10:57:57 +01:00
Arun Isaac
83ee1e91b0
gnu: Add emacs-password-generator. 
* gnu/packages/emacs-xyz.scm (emacs-password-generator): New variable.
 2020-02-27 10:45:47 +01:00
Arun Isaac
b4e0f0dc37
gnu: Add emacs-exiftool. 
* gnu/packages/emacs-xyz.scm (emacs-exiftool): New variable.
 2020-02-27 10:42:14 +01:00
Vagrant Cascadian
2d9b05817d
gnu: opensbi-qemu-sifive-u: Mark as deprecated. 
* gnu/packages/firmware (opensbi-qemu-sifive-u): Deprecated by
  opensbi-sifive-fu540.
 2020-02-26 23:48:06 -08:00
Vagrant Cascadian
5eeb70a709
gnu: opensbi: Update to 0.6. 
* gnu/packages/firmware (make-opensbi-package): Update to 0.6.
 2020-02-26 23:47:49 -08:00
Vagrant Cascadian
d854ab1595
gnu: python-construct: Update to 2.10.56. 
* gnu/packages/python-xyz (python-construct): Update to 2.10.56.
 2020-02-26 22:24:31 -08:00
Vagrant Cascadian
760dfc67cd
gnu: u-boot-pinebook: Fix LCD video output. 
* gnu/packages/bootloaders (u-boot-pinebook): Add phase applying patch
  submitted upstream.
 2020-02-26 22:23:17 -08:00
Nicolas Goaziou
c3435e2e60
gnu: Add emacs-org-superstar. 
* gnu/packages/emacs-xyz.scm (emacs-org-superstar): New variable.
 2020-02-26 22:31:46 +01:00
Jakub Kądziołka
37db2370db
gnu: icecat: Remove about:buildconfig store references. 
* gnu/packages/gnuzilla.scm (icecat)[arguments]:
  New ‘neutralise-store-references’ phase.

Co-authored-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2020-02-26 22:29:22 +01:00
Ludovic Courtès
2e4011465b
git-authenticate: Remove duplicate entry. 
* build-aux/git-authenticate.scm (%committers): Remove duplicate of snape.
 2020-02-26 22:11:19 +01:00
Ludovic Courtès
a73a530df2
git-authenticate: Add sub-key for thomasd. 
This is a followup to commit 7dc0f1d5a8,
signed with sub-key "3D2C DA58 819C 08C2 A649  D43D 5C3B 064C 724A 5726".

* build-aux/git-authenticate.scm (%committers): Provide fingerprint of
subkey for thomasd.
 2020-02-26 22:09:44 +01:00
Pierre Neidhardt
fb7eec3a84
scripts: Emit GC hint if free space is lower than absolute and relative threshold. 
* guix/scripts.scm (%disk-space-warning-absolute): New variable.
(warn-about-disk-space): Test against %disk-space-warning-absolute.
Fix error in display-hint due to extraneous 'profile' argument.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-02-26 22:05:56 +01:00
Ludovic Courtès
513c0a0f46
daemon: Drop 'AT_STATX_DONT_SYNC' flag upon EINVAL. 
Fixes <https://bugs.gnu.org/39727>.
Reported by Paul Garlick <pgarlick@tourbillion-technology.com>.

* nix/libstore/gc.cc (LocalStore::removeUnusedLinks) [HAVE_STATX]: Add
'statx_flags' static variables.  Clear 'AT_STATX_DONT_SYNC' flag from
'statx_flags' when 'statx' returns EINVAL.
 2020-02-26 22:05:56 +01:00
Evan Straw
e524b57740
gnu: awscli: Update to 1.18.6. 
* gnu/packages/python-web.scm (awscli): Update to 1.18.6.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2020-02-26 21:52:48 +01:00
Jack Hill
cae3b3774e
gnu: vim-full: Describe differences from vim. 
* gnu/packages/vim.scm (vim-full)[description]: New field. Explain what
  vim-full provides over vim.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2020-02-26 21:52:48 +01:00
Vincent Legoll
233332c2e9
gnu: musl: Update to 1.2.0. 
* gnu/packages/musl (musl): Update to 1.2.0.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2020-02-26 21:52:48 +01:00
Vincent Legoll
176dd26b38
gnu: benchmark: Add bonnie++. 
* gnu/packages/benchmark.scm (bonnie++): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2020-02-26 21:52:48 +01:00
Kyle Meyer
b18d3c5268
gnu: emacs-eacl: Fix typo in description. 
* gnu/packages/emacs-xyz.scm (emacs-eacl)[description]: Correct misspelling of
"commands".

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2020-02-26 21:52:47 +01:00
Kyle Meyer
66ed570a05
gnu: emacs-elixir-mode: Fix capitalization in description. 
* gnu/packages/emacs-xyz.scm (emacs-elixir-mode)[description]: Downcase
incorrectly capitalized word.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2020-02-26 21:52:47 +01:00
Marius Bakke
5041cc28cb
gnu: clang: Move version conditionals out of the builder. 
* gnu/packages/llvm.scm (clang-from-llvm)[arguments]: Rewrite phase
'set-glibc-file-names' to use VERSION>=? from (guix utils) and splice in the
relevant build code, instead of doing the comparison at build time.
 2020-02-26 21:52:47 +01:00
Marius Bakke
f5cc5de8b6
gnu: clang: Fix C++ search path handling on non-x86_64. 
* gnu/packages/llvm.scm (clang-from-llvm)[arguments]: Add phase
'add-missing-triplets'.
 2020-02-26 21:52:47 +01:00
Marius Bakke
5cfc6a88e9
gnu: node: Disable failing tests on armhf-linux. 
* gnu/packages/node.scm (node)[arguments]: When building on
armhf-linux, disable several zlib tests.
 2020-02-26 21:52:47 +01:00
Marius Bakke
458c3ff552
gnu: node: Update to 10.19.0. 
* gnu/packages/node.scm (node): Update to 10.19.0.
[inputs]: Remove LIBUV and NGHTTP2:LIB.  Add LIBUV/LATEST and
NGHTTP2-1.40:LIB.
 2020-02-26 21:52:47 +01:00
Marius Bakke
bbd804b29b
gnu: nghttp2: Add version 1.40.0. 
* gnu/packages/web.scm (nghttp2-1.40): New public variable.
 2020-02-26 21:52:46 +01:00
Marius Bakke
ae9cfc647d
gnu: LibUV: Add version 1.34.2. 
* gnu/packages/libevent.scm (libuv/latest): New public variable.
 2020-02-26 21:52:46 +01:00
Marius Bakke
6fda3a6cb4
gnu: pocl: Build with LLVM@9. 
* gnu/packages/opencl.scm (pocl)[inputs]: Change from LLVM-8 to LLVM.
 2020-02-26 21:52:46 +01:00
Evan Straw
b68f5a68f8
gnu: Add emacs-company-emoji. 
[[PGP Signed Part:No public key for F530C3B4A2A9F06D created at 2020-02-23T04:48:54+0100 using RSA]]
From 6c23c5966a3c7ed01c784874e410d5fe3009bfc5 Mon Sep 17 00:00:00 2001
From: Evan Straw <evan.straw99@gmail.com>
Date: Sat, 22 Feb 2020 19:47:19 -0800
Subject: [PATCH] gnu: Add emacs-company-emoji.

* gnu/packages/emacs-xyz.scm (emacs-company-emoji): New variable.
 2020-02-26 15:44:28 +01:00
Ricardo Wurmus
146430ea0e
gnu: proteinortho: Update to 6.0.14. 
* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.0.14.
[source]: Fetch from git; remove pre-built scripts.
[arguments]: Set make-flags; update wrap-programs phase to wrap all scripts.
[inputs]: Add guile-3.0, diamond, python-wrapper, lapack, and openblas; remove
python-2.
[native-inputs]: Add which.
[license]: Update to GPLv3+
 2020-02-26 14:07:32 +01:00
Ricardo Wurmus
9207575669
gnu: diamond: Update to 0.9.30. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
 2020-02-26 14:07:32 +01:00
Ricardo Wurmus
b38dd34f40
gnu: crossmap: Update to 0.3.8. 
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.3.8.
[arguments]: Remove to build with default Python.
[inputs]: Add python-pybigwig; replace python2-bx-python, python2-numpy, and
python2-pysam with their Python 3 variants.
[native-inputs]: Replace python2-cython and python2-nose with their Python 3
variants.
 2020-02-26 14:07:32 +01:00
Valentin Ignatev
a86fc40dc3
gnu: Add rust-libressl-pnacl-sys-2. 
* gnu/packages/crates-io.scm (rust-libressl-pnacl-sys-2): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2020-02-26 14:00:55 +02:00
Valentin Ignatev
754917c903
gnu: Add rust-pnacl-build-helper-1.4. 
* gnu/packages/crates-io.scm (rust-pnacl-build-helper-1.4):
New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2020-02-26 14:00:55 +02:00
Valentin Ignatev
b7c40a9713
gnu: Add rust-zip-0.5. 
* gnu/packages/crates-io.scm (rust-zip-0.5): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2020-02-26 14:00:55 +02:00
Valentin Ignatev
f4b8c27297
gnu: Add rust-bzip2-0.3. 
* gnu/packages/crates-io.scm (rust-bzip2-0.3): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2020-02-26 14:00:55 +02:00