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
a1dcaacb7b
gnu: Add brial.
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* gnu/packages/sagemath.scm (brial): New variable.
2019-06-19 23:57:49 +02:00
37edfb0f1c
gnu: Add m4ri.
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* gnu/packages/algebra.scm (m4ri): New variable.
2019-06-19 23:45:29 +02:00
3f9a027ce2
gnu: Add crispy-doom.
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* gnu/packages/games.scm (crispy-doom): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-06-19 22:56:28 +02:00
8785a71faf
gnu: emacs-unpackaged-el: Add patch for missing require statement.
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* 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
a7a3182761
gnu: Add numix-theme.
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* gnu/packages/gnome.scm (numix-theme): New variable
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-06-19 22:56:27 +02:00
aad086d871
grafts: Avoid 'query-valid-derivers' RPC.
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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
2ef22a9f37
derivations: Add 'derivation-input-derivation'.
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* guix/derivations.scm (derivation-input-derivation): New procedure.
(derivation-prerequisites): Use it.
2019-06-19 22:56:27 +02:00
74247b80e5
gnu: Add python-pandocfilters.
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* gnu/packages/textutils.scm (python-pandocfilters): New variable.
2019-06-19 22:01:53 +02:00
0c842e3a59
gnu: Add ratpoints.
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* 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
7c5f623192
gnu: Add gf2x.
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* gnu/packages/algebra.scm (gf2x): New variable.
2019-06-19 18:56:55 +02:00
01822e3ebf
gnu: Add zn_poly.
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* gnu/packages/sagemath.scm (zn_poly): New variable.
2019-06-19 18:56:55 +02:00
3923e9d942
gnu: Add pynac.
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* gnu/packages/sagemath.scm (pynac): New variable.
2019-06-19 18:56:55 +02:00
538230c933
gnu: python-gmpy2: Update to 2.1.0b1.
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The gmpy2 package has become a standard package in sage-8.7, and the latest
stable release is too old.
* gnu/packages/sagemath.scm (python-gmpy2): Update to 2.1.0b1.
2019-06-19 18:56:55 +02:00
f58b10cb30
gnu: balsa: Update to 2.5.7.
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* gnu/packages/mail.scm (balsa): Update to 2.5.7.
[inputs]: Build with gtksourceview@3.
2019-06-19 17:58:48 +02:00
c8a67f13c9
gnu: nano: Update to 4.3.
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* gnu/packages/nano.scm (nano): Update to 4.3.
2019-06-19 17:50:44 +02:00
76472ed959
gnu: notmuch: Update to 0.29.1.
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* gnu/packages/mail.scm (notmuch): Update to 0.29.1.
2019-06-19 17:50:44 +02:00
903bc2672d
gnu: mpd: Update to 0.21.10.
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* gnu/packages/mpd.scm (mpd): Update to 0.21.10.
2019-06-19 17:50:44 +02:00
2dcde3c733
gnu: perl-xml-sax: Update to 1.02.
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* gnu/packages/xml.scm (perl-xml-sax): Update to 1.02.
2019-06-19 17:50:43 +02:00
1f6dd7e9c2
gnu: shadow: Update home page.
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* gnu/packages/admin.scm (shadow)[home-page]: Update to new project home.
2019-06-19 17:50:43 +02:00
bb3dc8025a
gnu: shadow: Update to 4.7.
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* gnu/packages/admin.scm (shadow): Update to 4.7.
2019-06-19 17:50:43 +02:00
a6dc3cc197
gnu: ansible: Update to 2.8.1.
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* gnu/packages/admin.scm (ansible): Update to 2.8.1.
2019-06-19 17:50:43 +02:00
Marius Bakke