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45697 Commits

Author SHA1 Message Date
Andreas Enge c68ec87ca7
gnu: iml: Enable shared library. 
* gnu/packages/algebra.scm (iml): Add configure flag --enable-shared.
 2019-06-21 09:33:30 +02:00
Andreas Enge 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
Andreas Enge 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
Paul Garlick 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke 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
Alex Griffin 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
Marius Bakke 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
Marius Bakke 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
Marius Bakke 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
Ricardo Wurmus 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
Giovanni Biscuolo 78407a27cf
licenses: Add Historical Permission Notice and Disclaimer license 
* gnu/licenses.scm (hpnd): New variable.
 2019-06-20 18:24:49 +02:00
Andreas Enge eacf29835d
gnu: Add iml. 
* gnu/packages/algebra.scm (iml): New variable.
 2019-06-20 17:36:39 +02:00
Andreas Enge 264334716f
gnu: Add ppl. 
* gnu/packages/maths.scm (ppl): New variable.
 2019-06-20 16:46:37 +02:00
Kristofer Buffington ace8e269a4
services: opensmtpd: Extend the PAM service. 
* 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Robert Vollmert 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
Robert Vollmert 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
Ludovic Courtès c050f18700
gnu: guile: Add 2.2.5. 
* gnu/packages/guile.scm (guile-2.2.5): New variable.
 2019-06-20 14:07:01 +02:00
Ricardo Wurmus becb9cbfe1
gnu: python-jupyter-console: Update to 6.0.0. 
* 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
Ricardo Wurmus 8e590c8153
gnu: python2-jupyter-console: Split from python-jupyter-console. 
* gnu/packages/python-xyz.scm (python2-jupyter-console): Implement without
package-with-python2.
 2019-06-20 13:14:16 +02:00
Nicolas Goaziou e2ab228b46
Revert "gnu: Add libgd." 
This reverts commit 059e4c9a15.
 2019-06-20 12:39:21 +02:00
Andreas Enge 197ebc36be
gnu: Add lrcalc. 
* gnu/packages/algebra.scm (lrcalc): New variable.
 2019-06-20 12:21:11 +02:00
Andreas Enge 66c67e7ba1
gnu: Add eclib. 
* gnu/packages/algebra.scm (eclib): New variable.
 2019-06-20 12:21:04 +02:00
Andreas Enge 6cbedbd2f2
gnu: Add m4rie. 
* gnu/packages/algebra.scm (m4rie): New variable.
 2019-06-20 12:20:11 +02:00
Josh Holland 9553a41dbe
gnu: weechat: update to 2.5 
* 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
Nicolas Goaziou 25cbaa9e70
gnu: Add python-fpylll. 
* gnu/packages/algebra.scm (python-fpylll): New variable.
 2019-06-20 11:07:12 +02:00
Nicolas Goaziou 1de48e8f8a
gnu: fplll: Update to 5.2.1. 
* 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
Tobias Geerinckx-Rice f7dbf186b4
services: Fix typo in (gnu services mail) exports. 
* gnu/services/mail.scm (define-module):
Re-spell ‘%default-imap4d-config-file’.
 2019-06-20 10:43:25 +02:00
Nicolas Goaziou 75a73bb024
gnu: Add symmetrica. 
* 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
Alex Griffin a42cb6f1f1
gnu: zathura: Install icons. 
* 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
Nicolas Goaziou 059e4c9a15
gnu: Add libgd. 
* gnu/packages/image.scm (libgd): New variable.
 2019-06-20 10:09:17 +02:00
Nicolas Goaziou ab398380eb
gnu: Move ratpoints into a different module. 
* gnu/packages/maths.scm (ratpoints): Move...
* gnu/packages/algebra.scm: ...here.
 2019-06-20 09:20:29 +02:00
Meiyo Peng 5543d3bb09
gnu: spdlog: Clarify license. 
* 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
Tobias Geerinckx-Rice c5c51bda0b
gnu: bind: Update to 9.14.3 [fixes CVE-2019-6471]. 
* gnu/packages/dns.scm (isc-bind): Update to 9.14.3.
 2019-06-20 00:28:14 +02:00
Andreas Enge 80ee7c4a48
gnu: zn_poly: Rename to zn-poly, according to our naming conventions. 
Reported by Nicolas Goaziou <mail@nicolasgoaziou.fr>.

This is a follow-up to commit 01822e3ebf.
* gnu/packages/sagemath.scm (zn_poly): Rename to...
* gnu/packages/sagemath.scm (zn-poly): ...this.
 2019-06-20 00:03:46 +02:00
Andreas Enge a1dcaacb7b
gnu: Add brial. 
* gnu/packages/sagemath.scm (brial): New variable.
 2019-06-19 23:57:49 +02:00
Andreas Enge 37edfb0f1c
gnu: Add m4ri. 
* gnu/packages/algebra.scm (m4ri): New variable.
 2019-06-19 23:45:29 +02:00
Dan Frumin 3f9a027ce2
gnu: Add crispy-doom. 
* gnu/packages/games.scm (crispy-doom): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-06-19 22:56:28 +02:00
Brian Leung 8785a71faf
gnu: emacs-unpackaged-el: Add patch for missing require statement. 
* gnu/packages/emacs-xyz.scm (emacs-unpackaged-el)[source]: Add patch.
* gnu/packages/patches/emacs-unpackaged-req.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-06-19 22:56:27 +02:00
Giacomo Leidi a7a3182761
gnu: Add numix-theme. 
* gnu/packages/gnome.scm (numix-theme): New variable

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-06-19 22:56:27 +02:00
Ludovic Courtès aad086d871
grafts: Avoid 'query-valid-derivers' RPC. 
Previously we'd make 502 'query-valid-derivers' RPCs for
"guix build vim -d", and after this patch, we don't do any.

Furthermore, the previous strategy was "stateful" in the sense that
'item->deriver' could return a derivation that is not the one that was
actually computed by this process, but an "equivalent" one (due to
fixed-output derivations); which one is chosen would depend on the state
of the store.

This in turn means that we'd have to call 'read-derivation-from-file' to
actually read .drv files (as opposed to getting them from
%DERIVATION-CACHE).  This is costly and doesn't work with
GUIX_DAEMON_SOCKET=ssh://….

* guix/grafts.scm (item->deriver): Remove.
(reference-origin): New procedure.
(cumulative-grafts): Use it instead of 'item->deriver'.
 2019-06-19 22:56:27 +02:00
Ludovic Courtès 2ef22a9f37
derivations: Add 'derivation-input-derivation'. 
* guix/derivations.scm (derivation-input-derivation): New procedure.
(derivation-prerequisites): Use it.
 2019-06-19 22:56:27 +02:00
Nicolas Goaziou 74247b80e5
gnu: Add python-pandocfilters. 
* gnu/packages/textutils.scm (python-pandocfilters): New variable.
 2019-06-19 22:01:53 +02:00
Nicolas Goaziou 0c842e3a59
gnu: Add ratpoints. 
* gnu/packages/maths.scm (ratpoints): New variable.
* gnu/packages/patches/ratpoints-sturm_and_rp_private.patch: New file.
* gnu/local.mk (dist_patch_DATA): Reference patch.
 2019-06-19 21:43:12 +02:00
Andreas Enge 7c5f623192
gnu: Add gf2x. 
* gnu/packages/algebra.scm (gf2x): New variable.
 2019-06-19 18:56:55 +02:00