b556abe416
gnu: khmer: Update to 3.0.0a3.
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* 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].
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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.
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* 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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/algebra.scm (symmetrica): Add -fPIC compiler flag.
2019-06-21 09:49:57 +02:00
c68ec87ca7
gnu: iml: Enable shared library.
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* gnu/packages/algebra.scm (iml): Add configure flag --enable-shared.
2019-06-21 09:33:30 +02:00
fedb9571eb
gnu: Add lcalc.
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* 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.
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* 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.
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* 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
010689e706
gnu: python-sphinx: Update to 2.1.2.
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* gnu/packages/sphinx.scm (python-sphinx): Update to 2.1.2.
2019-06-20 23:19:09 +02:00
651478aa18
Merge branch 'master' into staging
2019-06-20 23:08:16 +02:00
9a2e5fe5fd
gnu: ungoogled-chromium: Disable parallel build.
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* 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].
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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
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* gnu/licenses.scm (hpnd): New variable.
2019-06-20 18:24:49 +02:00
eacf29835d
gnu: Add iml.
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* gnu/packages/algebra.scm (iml): New variable.
2019-06-20 17:36:39 +02:00
264334716f
gnu: Add ppl.
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* 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.
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* 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.
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* 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.
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* 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.
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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.
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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.
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* gnu/packages/algebra.scm (lrcalc): New variable.
2019-06-20 12:21:11 +02:00
66c67e7ba1
gnu: Add eclib.
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* gnu/packages/algebra.scm (eclib): New variable.
2019-06-20 12:21:04 +02:00
6cbedbd2f2
gnu: Add m4rie.
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* 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.
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* 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
c5c51bda0b
gnu: bind: Update to 9.14.3 [fixes CVE-2019-6471].
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* gnu/packages/dns.scm (isc-bind): Update to 9.14.3.
2019-06-20 00:28:14 +02:00
80ee7c4a48
gnu: zn_poly: Rename to zn-poly, according to our naming conventions.
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Reported by Nicolas Goaziou <mail@nicolasgoaziou.fr>.
This is a follow-up to commit 01822e3ebf
2019-06-20 00:03:46 +02:00
Ricardo Wurmus