a65f1e8eab
gnu: Move ratpoints into "sagemath.scm"
...
* gnu/packages/algebra.scm (ratpoints): Move package from here...
* gnu/packages/sagemath.scm (ratpoints): ... to here.
2019-06-21 22:57:19 +02:00
64dc8e9e59
gnu: Add openjdk12.
...
* gnu/packages/java.scm(openjdk12): New variable.
2019-06-21 22:50:25 +02:00
38d4c21502
gnu: emacs-fish-completion: Update to 1.1.
...
* gnu/packages/emacs-xyz.scm (emacs-fish-completion): Update to 1.1.
2019-06-21 19:52:54 +02:00
e6049c84da
gnu: zn-poly: Install all libraries.
...
* gnu/packages/sagemath.scm (zn-poly): Install the static and the dynamic
library with its symlinks, and end a phase with #t.
2019-06-21 16:35:27 +02:00
b556abe416
gnu: khmer: Update to 3.0.0a3.
...
* gnu/packages/bioinformatics.scm (khmer): Update to 3.0.0a3.
[source]: Remove patch; remove seqan in snippet.
[inputs]: Add seqan-1.
* gnu/packages/patches/khmer-use-libraries.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2019-06-21 11:41:54 +02:00
c2c4ac0f69
gnu: icecat: Update to 60.7.2-guix1 [security fixes].
...
Includes fixes for CVE-2019-11707 and CVE-2019-11708.
* gnu/packages/gnuzilla.scm (%icecat-version): Update to 60.7.2-guix1.
(icecat-source)[upstream-firefox-source]: Update hash.
2019-06-21 05:20:36 -04:00
c94cc6de39
gnu: ungoogled-chromium: Increase build timeout.
...
* gnu/packages/chromium.scm (ungoogled-chromium)[properties]: New field.
2019-06-21 11:05:05 +02:00
6dc29ab4e2
gnu: linux-libre: Update to 5.1.12.
...
* gnu/packages/linux.scm (%linux-libre-version): Update to 5.1.12.
(%linux-libre-hash): Update hash.
2019-06-21 04:35:26 -04:00
5e9452a41d
gnu: linux-libre@4.19: Update to 4.19.53.
...
* gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.53.
(%linux-libre-4.19-hash): Update hash.
2019-06-21 04:34:41 -04:00
16854b97ee
gnu: linux-libre@4.14: Update to 4.14.128.
...
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.128.
(%linux-libre-4.14-hash): Update hash.
2019-06-21 04:33:39 -04:00
468bfd13a0
gnu: ratpoints: Generate position-independent code.
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* gnu/packages/algebra.scm (ratpoints): Add "CCFLAGS=-fPIC" to make flags.
2019-06-21 09:55:13 +02:00
e6eafd4277
gnu: symmetrica: Generate position-independent code.
...
* gnu/packages/algebra.scm (symmetrica): Add -fPIC compiler flag.
2019-06-21 09:49:57 +02:00
c68ec87ca7
gnu: iml: Enable shared library.
...
* gnu/packages/algebra.scm (iml): Add configure flag --enable-shared.
2019-06-21 09:33:30 +02:00
fedb9571eb
gnu: Add lcalc.
...
* gnu/packages/sagemath.scm (lcalc): New variable.
* gnu/packages/patches/lcalc-default-parameters-1.patch,
gnu/packages/patches/lcalc-default-parameters-2.patch,
gnu/packages/patches/lcalc-lcommon-h.patch,
gnu/packages/patches/lcalc-using-namespace-std.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register patches.
2019-06-21 09:28:07 +02:00
88f913e8ad
gnu: lrcalc: Add a patch for identifying include files.
...
* gnu/packages/patches/lrcalc-includes.patch: New file.
* gnu/packages/algebra.scm (lrcalc): Use patch.
* gnu/local.mk (dist_patch_DATA): Register patch.
2019-06-21 09:28:07 +02:00
2c12be76cd
gnu: python-mpi4py: Update to 3.0.2.
...
* gnu/packages/mpi.scm (python-mpi4py): Update to 3.0.2.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-06-21 09:04:37 +02:00
9a2e5fe5fd
gnu: ungoogled-chromium: Disable parallel build.
...
* gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Set
#:parallel-build? #f. Adjust 'build' phase to account for it.
2019-06-20 22:49:32 +02:00
0605d939a9
gnu: samba: Update to 4.10.5 [fixes CVE-2019-12435, CVE-2019-12436].
...
* gnu/packages/samba.scm (samba): Update to 4.10.5.
2019-06-20 22:49:32 +02:00
cee835897b
gnu: ungoogled-chromium: Update to 75.0.3770.100-0.5d8abc3.
...
* gnu/packages/chromium.scm (%chromium-version): Set to 75.0.3770.100.
(%chromium-origin): Update hash.
2019-06-20 22:49:32 +02:00
e4386b334a
gnu: openh264: Update to 2.0.0.
...
* gnu/packages/video.scm (openh264): Update to 2.0.0.
[source](uri): Adjust file name.
2019-06-20 22:49:32 +02:00
3df7b15e6c
gnu: ungoogled-chromium: Install icons.
...
* gnu/packages/chromium.scm (ungoogled-chromium)[arguments]: Install icons.
Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2019-06-20 22:49:32 +02:00
b549a05353
gnu: Use HTTPS for sphinx-doc.org.
...
* gnu/packages/sphinx.scm (python-sphinx,
python-sphinxcontrib-websupport)[home-page]: Use HTTPS.
2019-06-20 22:49:31 +02:00
bd9d72067e
gnu: python-unidecode: Update to 1.1.0.
...
* gnu/packages/python-xyz.scm (python-unidecode): Update to 1.1.0.
2019-06-20 22:49:31 +02:00
377bd155ea
gnu: dbus: Fix CVE-2019-12749.
...
* gnu/packages/patches/dbus-CVE-2019-12749.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/glib.scm (dbus)[replacement]: New field.
(dbus/fixed): New variable.
2019-06-20 22:49:31 +02:00
28618b05f0
gnu: pigx-rnaseq: Update to 0.0.7.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7.
[inputs]: Add coreutils and sed.
2019-06-20 22:29:43 +02:00
78407a27cf
licenses: Add Historical Permission Notice and Disclaimer license
...
* gnu/licenses.scm (hpnd): New variable.
2019-06-20 18:24:49 +02:00
eacf29835d
gnu: Add iml.
...
* gnu/packages/algebra.scm (iml): New variable.
2019-06-20 17:36:39 +02:00
264334716f
gnu: Add ppl.
...
* gnu/packages/maths.scm (ppl): New variable.
2019-06-20 16:46:37 +02:00
ace8e269a4
services: opensmtpd: Extend the PAM service.
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* gnu/services/mail.scm (%opensmtpd-pam-services): New variable.
(opensmtpd-service-type)[extensions]: Add it, extending
PAM-ROOT-SERVICE-TYPE.
Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2019-06-20 15:54:51 +02:00
30adfd3600
gnu: ngs-sdk: Update to 2.9.6.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6.
2019-06-20 14:33:57 +02:00
20874b7044
gnu: sra-tools: Update to 2.9.6.
...
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6.
2019-06-20 14:33:57 +02:00
7cb44fb571
gnu: ncbi-vdb: Update to 2.9.6.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.6.
[arguments]: Pass HAVE_HDF5 make flag; add build phase "patch-krypto-flags".
2019-06-20 14:33:57 +02:00
b46a9b9a5e
import: hackage: Add two expected failing test cases.
...
This adds failing test cases for two hackage import bugs:
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=25138
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=35743
* tests/hackage.scm: Make comment style consistent. Add two
cabal parsing tests, marked as expected failures.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-06-20 14:07:01 +02:00
3149c00264
utils: canonical-newline-port: Fix handling of carriage return at buffer end.
...
Prior to this change the added test fails for me locally at byte
1024. It might depend on some default buffer sizes.
Fixes <https://bugs.gnu.org/35863 >.
* tests/utils.scm ("canonical-newline-port-1024"): Add test.
* guix/utils.scm (canonical-newline-port): Correct comments on CR/LF.
Remove CR even when they're at the end of the buffer.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-06-20 14:07:01 +02:00
c050f18700
gnu: guile: Add 2.2.5.
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* gnu/packages/guile.scm (guile-2.2.5): New variable.
2019-06-20 14:07:01 +02:00
becb9cbfe1
gnu: python-jupyter-console: Update to 6.0.0.
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* gnu/packages/python-xyz.scm (python-jupyter-console): Update to 6.0.0.
[arguments]: Enable tests.
[propagated-inputs]: Replace python-prompt-toolkit-1 with
python-prompt-toolkit.
2019-06-20 13:14:16 +02:00
8e590c8153
gnu: python2-jupyter-console: Split from python-jupyter-console.
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* gnu/packages/python-xyz.scm (python2-jupyter-console): Implement without
package-with-python2.
2019-06-20 13:14:16 +02:00
e2ab228b46
Revert "gnu: Add libgd."
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This reverts commit 059e4c9a15
2019-06-20 12:39:21 +02:00
197ebc36be
gnu: Add lrcalc.
...
* gnu/packages/algebra.scm (lrcalc): New variable.
2019-06-20 12:21:11 +02:00
66c67e7ba1
gnu: Add eclib.
...
* gnu/packages/algebra.scm (eclib): New variable.
2019-06-20 12:21:04 +02:00
6cbedbd2f2
gnu: Add m4rie.
...
* gnu/packages/algebra.scm (m4rie): New variable.
2019-06-20 12:20:11 +02:00
9553a41dbe
gnu: weechat: update to 2.5
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* gnu/packages/irc.scm (weechat): update to 2.5
Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
2019-06-20 11:55:09 +02:00
25cbaa9e70
gnu: Add python-fpylll.
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* gnu/packages/algebra.scm (python-fpylll): New variable.
2019-06-20 11:07:12 +02:00
1de48e8f8a
gnu: fplll: Update to 5.2.1.
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* gnu/packages/algebra.scm (fplll): Update to 5.2.1.
[source]: Use Github tagged release: the original tarball no longer exists.
[native-inputs]: Add Autoconf and al.
[homepage]: Update it, the previous one no longer exists.
[description]: Expound description.
2019-06-20 11:03:37 +02:00
f7dbf186b4
services: Fix typo in (gnu services mail) exports.
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* gnu/services/mail.scm (define-module):
Re-spell ‘%default-imap4d-config-file’.
2019-06-20 10:43:25 +02:00
75a73bb024
gnu: Add symmetrica.
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* gnu/packages/algebra.scm (symmetrica): New variable.
* gnu/packages/patches/symmetrica-bruch.patch:
* gnu/packages/patches/symmetrica-int32.patch:
* gnu/packages/patches/symmetrica-return_values.patch:
* gnu/packages/patches/symmetrica-sort_sum_rename.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add patches.
2019-06-20 10:19:12 +02:00
a42cb6f1f1
gnu: zathura: Install icons.
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* gnu/packages/pdf.scm (zathura)[native-inputs]: Add librsvg to build and
install the application icons.
Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
2019-06-20 10:10:31 +02:00
059e4c9a15
gnu: Add libgd.
...
* gnu/packages/image.scm (libgd): New variable.
2019-06-20 10:09:17 +02:00
ab398380eb
gnu: Move ratpoints into a different module.
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* gnu/packages/maths.scm (ratpoints): Move...
* gnu/packages/algebra.scm: ...here.
2019-06-20 09:20:29 +02:00
5543d3bb09
gnu: spdlog: Clarify license.
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* gnu/packages/logging.scm (spdlog): Clarify license of the bundled fmt
library.
Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
2019-06-20 05:38:58 +02:00
Nicolas Goaziou