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Author SHA1 Message Date
Roel Janssen
48efbde7a9
gnu: virtuoso-ose: Update to 7.2.7. 
* gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.7; Run autogen
  after applying the patch below.
* gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch:
  New file.
 2022-05-30 09:03:02 +02:00
Mark H Weaver
7f63a6aefc
gnu: icecat: Update to 91.9.1-guix0-preview1 [security fixes]. 
Includes fixes for CVE-2022-1529 and CVE-2022-1802.

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
 2022-05-29 23:21:41 -04:00
Wiktor Zelazny
acb08304c8
gnu: Add python-gpy. 
* gnu/packages/python-science.scm (python-gpy): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-29 23:56:06 +02:00
Wiktor Zelazny
6400f08d07
gnu: Add python-paramz. 
* gnu/packages/python-science.scm (python-paramz): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-29 23:56:05 +02:00
Wiktor Zelazny
6dacd15381
gnu: Add python-climin. 
* gnu/packages/python-science.scm (python-climin): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-29 23:56:05 +02:00
Felix Gruber
3d1b2bc740
gnu: wla-dx: Update to 10.1. 
* gnu/packages/assembly.scm (wla-dx): Update to 10.1.
[native-inputs]: Use new style.
[arguments]: Add custom 'check phase to run run_tests.sh.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-29 23:56:05 +02:00
Ludovic Courtès
40530ffd15
store: Record cache lookups in 'references/cached'. 
* guix/store.scm (references/cached): Add call to
'record-cache-lookup!'.
 2022-05-29 23:56:01 +02:00
Danny Milosavljevic
98e2f4fbeb
gnu: openjdk: Update to 17.0.3. 
* gnu/packages/java.scm (openjdk17): Update to 17.0.3.
 2022-05-29 22:57:19 +02:00
Julien Lepiller
d1f4b6dc83
gnu: python-translate-toolkit: Update to 3.6.2. 
* gnu/packages/python-xyz.scm (python-translate-toolkit): Update to
  3.6.2.
 2022-05-29 22:20:15 +02:00
Julien Lepiller
31a9d8677c
gnu: python-user-agents: Update to 2.2.0. 
* gnu/packages/python-xyz.scm (python-user-agents): Update to 2.2.0.
 2022-05-29 21:30:45 +02:00
Julien Lepiller
92a83f38b5
gnu: python-ua-parser: Update to 0.10.0. 
* gnu/packages/python-xyz.scm (python-ua-parser): Update to 0.10.0.
 2022-05-29 21:30:16 +02:00
Efraim Flashner
e8b2219152
gnu: lagrange: Update to 1.13.6. 
* gnu/packages/web-browsers.scm (lagrange): Update to 1.13.6.
[source]: Adjust snippet to remove another bundled library.
 2022-05-29 19:26:47 +03:00
Efraim Flashner
9cd22702b8
gnu: wget: Update to 1.21.3. 
* gnu/packages/wget.scm (wget): Update to 1.21.3.
 2022-05-29 16:31:59 +03:00
Efraim Flashner
1ed40eee39
gnu: mutt: Update to 2.2.5. 
* gnu/packages/mail.scm (mutt): Update to 2.2.5.
 2022-05-29 16:31:59 +03:00
Efraim Flashner
46ed423e28
gnu: git-annex: Update to 10.20220525. 
* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20220525.
 2022-05-29 16:31:59 +03:00
Efraim Flashner
e4fe344a5c
gnu: nmap: Honor tests? flag. 
* gnu/packages/admin.scm (nmap)[arguments]: In custom 'check phase honor
the #:tests? flag.
 2022-05-29 16:31:09 +03:00
Efraim Flashner
50970a28b7
gnu: wgetpaste: Remove trailing #t from phases. 
* gnu/packages/wget.scm (wgetpaste)[arguments]: Remove trailing #t from
phases.
 2022-05-29 16:31:09 +03:00
Efraim Flashner
c62be7d530
gnu: wgetpaste: Add missing input. 
* gnu/packages/wget.scm (wgetpaste)[inputs]: Add bash-minimal.
 2022-05-29 16:23:48 +03:00
cage
69af8a6837
gnu: telescope: Update to 0.8.1. 
* gnu/packages/web-browsers.scm (telescope): Update to 0.8.1.
[home-page]: Update to new upstream home-page.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-05-29 16:10:34 +03:00
Efraim Flashner
d540e686ef
gnu: Add pbuilder. 
* gnu/packages/debian.scm (pbuilder): New variable.
 2022-05-29 16:01:02 +03:00
Rene Saavedra
b456086c65
gnu: apostrophe: Build with correct webkitgtk. 
* gnu/packages/gnome.scm (apostrophe)[inputs]: Replace webkitgtk with
webkitgtk-with-libsoup2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2022-05-29 15:53:48 +03:00
Ricardo Wurmus
e640da33f3
Merge branch 'wip-r' 2022-05-29 11:49:03 +02:00
Ricardo Wurmus
89e9262012
gnu: r-bsgenome-hsapiens-ucsc-hg19-masked: Update to 1.3.993. 
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): Update to 1.3.993.
 2022-05-29 11:44:09 +02:00
Efraim Flashner
926fcb488b
gnu: clang-from-llvm: Fix building on riscv64-linux. 
* gnu/packages/llvm.scm (clang-from-llvm)[arguments]: When building for
riscv64-linux add configure-flags and make-flags to ensure linking with
'-latomic'.
 2022-05-29 08:46:17 +03:00
Mădălin Ionel Patrașcu
a5f4c03df1
gnu: Add r-scmap. 
* gnu/packages/bioconductor.scm (r-scmap): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-05-29 00:43:05 +02:00
Ricardo Wurmus
cb115ba722
gnu: pigx-sars-cov-2: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add
'autoreconf phase to patch build system.
 2022-05-29 00:39:19 +02:00
Ricardo Wurmus
df3e5cfa05
gnu: pigx-bsseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system
in 'autoreconf phase.
 2022-05-29 00:34:29 +02:00
Ricardo Wurmus
b64f4a1245
gnu: pigx-scrnaseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Add autoreconf
step to work around m4 macro bug and missing VERSION file.
[native-inputs]: Add autoconf and automake.
 2022-05-29 00:29:19 +02:00
Ricardo Wurmus
add551f651
gnu: pigx-chipseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build
system.
 2022-05-29 00:18:48 +02:00
Mădălin Ionel Patrașcu
a4b90009c7
gnu: Add r-googlevis. 
* gnu/packages/cran.scm (r-googlevis): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-05-29 00:01:47 +02:00
Ricardo Wurmus
371a83b764
scripts/import: Use pretty printer from (guix scripts style). 
* guix/scripts/import.scm (guix-import): Use pretty-print-with-comments.
(newline-rewriting-port): Remove procedure.
 2022-05-29 00:01:46 +02:00
Ludovic Courtès
f383838a09
services: elogind: When started by dbus-daemon, wait for the Shepherd service. 
Fixes <https://issues.guix.gnu.org/55444>.

Previously shepherd and dbus-daemon would race to start elogind.  In
some cases (for instance if one logs in quickly enough on the tty),
dbus-daemon would "win" and start elogind before shepherd has had a
chance to do it.  Consequently, shepherd would fail to start elogind and
mark it as stopped and disabled, in turn preventing services that depend
on it such as 'xorg-server' from starting.

* gnu/services/desktop.scm (elogind-dbus-service): Rewrite to refer to a
wrapper that waits for the 'elogind' Shepherd service.
 2022-05-28 23:23:36 +02:00
Ludovic Courtès
b04ae71def
services: herd: Add 'wait-for-service'. 
* gnu/services/herd.scm (wait-for-service): New procedure.
 2022-05-28 23:23:36 +02:00
Ricardo Wurmus
66bfe55848
gnu: Add r-msdata. 
* gnu/packages/bioconductor.scm (r-msdata): New variable.
 2022-05-28 23:19:48 +02:00
Ricardo Wurmus
79158a5624
gnu: r-tcgabiolinksgui-data: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.16.0.
 2022-05-28 23:19:48 +02:00
Ricardo Wurmus
9d538de266
gnu: r-curatedtcgadata: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.18.0.
[native-inputs]: Add r-knitr.
 2022-05-28 23:19:47 +02:00
Ricardo Wurmus
1c4d0fc9a9
gnu: r-gagedata: Update to 2.34.0. 
* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.34.0.
 2022-05-28 23:19:47 +02:00
Ricardo Wurmus
c56b553e97
gnu: r-affydata: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-affydata): Update to 1.44.0.
 2022-05-28 23:19:47 +02:00
Ricardo Wurmus
e06ee7a745
gnu: r-all: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-all): Update to 1.38.0.
 2022-05-28 23:19:47 +02:00
Ricardo Wurmus
15e10974ef
gnu: r-hsmmsinglecell: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.16.0.
 2022-05-28 23:19:47 +02:00
Ricardo Wurmus
3ff4e48e85
gnu: r-pasilla: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-pasilla): Update to 1.24.0.
[propagated-inputs]: Remove r-biocstyle, r-knitr, and r-rmarkdown.
[native-inputs]: Add r-knitr.
 2022-05-28 23:19:47 +02:00
Ricardo Wurmus
4f2ac5f19f
gnu: r-genomationdata: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-genomationdata): Update to 1.28.0.
 2022-05-28 23:19:47 +02:00
Ricardo Wurmus
d24b0702b6
gnu: r-genelendatabase: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.32.0.
 2022-05-28 23:19:47 +02:00
Ricardo Wurmus
7a58c9af46
gnu: r-copyhelper: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.28.0.
 2022-05-28 23:19:47 +02:00
Ricardo Wurmus
e437cf10a4
gnu: r-chromstardata: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-chromstardata): Update to 1.22.0.
 2022-05-28 23:19:47 +02:00
Ricardo Wurmus
1413f9f214
gnu: r-celldex: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-celldex): Update to 1.6.0.
 2022-05-28 23:19:46 +02:00
Ricardo Wurmus
3ce819d563
gnu: r-biscuiteerdata: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.10.0.
 2022-05-28 23:19:46 +02:00
Ricardo Wurmus
ccb66a16a0
gnu: r-arrmdata: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.32.0.
 2022-05-28 23:19:46 +02:00
Ricardo Wurmus
9db43e4979
gnu: r-aneufinderdata: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-aneufinderdata): Update to 1.24.0.
 2022-05-28 23:19:46 +02:00
Ricardo Wurmus
c89eb68ede
gnu: r-adductdata: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-adductdata): Update to 1.12.0.
 2022-05-28 23:19:46 +02:00