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Author SHA1 Message Date
Marius Bakke 8d653c08b7
gnu: LLVM, Clang, LLD: Update to 14.0.4. 
* gnu/packages/llvm.scm (%llvm-monorepo-hashes): Adjust for 14.0.4.
(%llvm-patches): Likewise.
(llvm-14, clang-14, lld-14): Update to 14.0.4.
* gnu/packages/patches/clang-14.0-libc-search-path.patch: Adjust for upstream
changes.
 2022-06-01 21:41:23 +02:00
Tobias Geerinckx-Rice 82b06436b4
daemon: Clarify ‘--check’ error when outputs are missing. 
Drop the confusing ‘invalid’ jargon and display a hint like we do
for ‘--fallback’.

* nix/libstore/build.cc (DerivationGoal::outputsSubstituted): Rewrite error message.
 2022-05-29 02:00:00 +02:00
Tobias Geerinckx-Rice a08c21f206
gnu: libmicrohttpd: Update to 0.9.75. 
* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.75.
 2022-05-29 02:00:13 +02:00
Tobias Geerinckx-Rice 9009189994
gnu: libmicrohttpd: Use G-expressions. 
* gnu/packages/gnunet.scm (libmicrohttpd)[arguments]:
Rewrite as G-expressions.
 2022-05-29 02:00:13 +02:00
Tobias Geerinckx-Rice 00411836d9
gnu: pgpdump: Update to 0.35. 
* gnu/packages/gnupg.scm (pgpdump): Update to 0.35.
 2022-05-29 02:00:13 +02:00
Tobias Geerinckx-Rice 45fdd1d5e5
gnu: ocrfeeder: Update to 0.8.5. 
* gnu/packages/gnome.scm (ocrfeeder): Update to 0.8.5.
[arguments]: Don't explicitly return #t from phases.
 2022-05-29 02:00:13 +02:00
Jonathan Brielmaier 16a0aea02d
gnu: icedove: Use updated clang and llvm. 
* gnu/packages/gnuzilla.scm (icedove)[native-inputs]: Replace `clang-11`
and `clang-11` with the default version, which is now 13.
 2022-06-01 15:12:39 +02:00
Jonathan Brielmaier a8228a6253
gnu: icedove: Update to 91.10.0 [fixes CVE-2022-1834]. 
* gnu/packages/gnuzilla.scm (icedove): Update to 91.10.0.
 2022-06-01 15:12:39 +02:00
Danial Behzadi 91861046f2
gnu: tractor: Update to 3.13. 
* gnu/packages/tor.scm (tractor): Update to 3.13.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2022-05-29 02:00:00 +02:00
Tobias Geerinckx-Rice f696bbb707
gnu: fortune-mod: Fix fortune directory. 
It now matches the one given in the fortune(6) man page.

* gnu/packages/games.scm (fortune-mode)[arguments]:
Install to /share rather than /local/share/games.
Shorten the 'fix-install-directory phase.
 2022-05-29 02:00:00 +02:00
Ricardo Wurmus b540e5e6bb
gnu: pigx-scrnaseq: Update to 1.1.9. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
 2022-06-01 12:57:22 +02:00
Ricardo Wurmus 93c97bfffb
gnu: pigx-bsseq: Update to 0.1.7. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.7.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove automake and autoconf.
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2022-06-01 12:41:59 +02:00
Ricardo Wurmus 6e54ce9ca9
gnu: pigx-chipseq: Update to 0.1.0. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.1.0.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2022-06-01 12:19:48 +02:00
Efraim Flashner 75af73e1b7
gnu: vim: Update to 8.2.5048. 
* gnu/packages/vim.scm (vim): Update to 8.2.5048.
[arguments]: Patch another instance of '/bin/sh'.
 2022-06-01 12:15:06 +03:00
Ricardo Wurmus cd95d7ddd1
gnu: pigx-rnaseq: Update to 0.1.0. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0.
[arguments]: Remove phase 'patch-knitr.
 2022-06-01 11:07:27 +02:00
Ricardo Wurmus 0aae2f7f01
gnu: pigx-rnaseq: Update to 0.0.21. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21.
 2022-06-01 10:46:00 +02:00
Ricardo Wurmus 0c26c8da9d
gnu: pigx-rnaseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.
 2022-06-01 10:46:00 +02:00
Tobias Geerinckx-Rice 1600d5cd3a
gnu: gnome-commander: Update to 1.14.2. 
* gnu/packages/gnome.scm (gnome-commander): Update to 1.14.2.
 2022-05-29 02:00:27 +02:00
Tobias Geerinckx-Rice 6c345a2465
gnu: angband: Update to 4.2.4. 
* gnu/packages/games.scm (angband): Update to 4.2.4.
[arguments]: Don't explicitly return #t from phases.
 2022-05-29 02:00:26 +02:00
Tobias Geerinckx-Rice a01cc9f97f
gnu: freeipmi: Update to 1.6.9. 
* gnu/packages/freeipmi.scm (freeipmi): Update to 1.6.9.
 2022-05-29 02:00:26 +02:00
Tobias Geerinckx-Rice 22f56dda8e
import: minetest: Fix typo. 
* guix/import/minetest.scm (important-dependencies): Fix ‘choosen’ typo.
 2022-05-29 02:00:07 +02:00
Tobias Geerinckx-Rice a3ea97976b
gnu: corefreq: Update to 1.90.1. 
* gnu/packages/linux.scm (corefreq): Update to 1.90.1.
 2022-05-29 02:00:06 +02:00
Tobias Geerinckx-Rice dc6d92ac93
bash completion: Fix & unify option parsing. 
We now correctly recognise ‘guix -Abcdef’ as equivalent to ‘guix -f’.

* etc/completion/bash/guix (_guix_is_short_option, guix_is_long_option):
New functions.
(_guix_is_dash_f, _guix_is_dash_l, _guix_is_dash_L, _guix_is_dash_m)
(_guix_is_dash_C, _guix_is_dash_p): Use them.
 2022-05-29 02:00:20 +02:00
Tobias Geerinckx-Rice 4cb6994790
gnu: services: Update setuid service description. 
* gnu/services.scm (setuid-program-service-type)[description]:
Remove ‘root’, add ‘setgid’.
 2022-05-29 02:00:19 +02:00
Tobias Geerinckx-Rice 4ac15e44e5
gnu: libfprint: Update to 1.94.4. 
* gnu/packages/freedesktop.scm (libfprint): Update to 1.94.4.
 2022-05-29 02:00:19 +02:00
Tobias Geerinckx-Rice 72b2412add
gnu: fprintd: Update to 1.94.2. 
* gnu/packages/freedesktop.scm (fprintd): Update to 1.94.2.
 2022-05-29 02:00:01 +02:00
Tobias Geerinckx-Rice 78879b10c2
gnu: fprintd: Remove input labels. 
* gnu/packages/freedesktop.scm (fprintd)[native-inputs]:
Remove input labels.
 2022-05-29 02:00:01 +02:00
Tobias Geerinckx-Rice eded213cbc
gnu: fprintd: Fix build. 
* gnu/packages/freedesktop.scm (fprintd)[native-inputs]: Add python.
 2022-05-29 02:00:01 +02:00
Tobias Geerinckx-Rice 5610778266
gnu: beancount: Update to 2.3.5. 
* gnu/packages/finance.scm (beancount): Update to 2.3.5.
 2022-05-29 02:00:01 +02:00
Tobias Geerinckx-Rice c6c32ab966
gnu: caf: Update to 0.18.6. 
* gnu/packages/cpp.scm (caf): Update to 0.18.6.
 2022-05-29 02:00:00 +02:00
Tobias Geerinckx-Rice 3f4850f0ae
gnu: quazip: Update to 1.3. 
* gnu/packages/compression.scm (quazip): Update to 1.3.
 2022-05-29 02:00:00 +02:00
Tobias Geerinckx-Rice bc95e0c8d6
gnu: foomatic-filters: Use project home page. 
* gnu/packages/cups.scm (foomatic-filters)[home-page]: Point upstream.
 2022-05-29 02:00:00 +02:00
Ricardo Wurmus b279e778ab
gnu: Add sylamer. 
* gnu/packages/bioinformatics.scm (sylamer): New variable.
 2022-06-01 00:17:05 +02:00
Leo Famulari 95792a26c3
gnu: linux-libre 5.10: Update to 5.10.119. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.119.
(linux-libre-5.10-pristine-source): Update hash.
 2022-05-31 18:04:02 -04:00
Leo Famulari da30df085e
gnu: linux-libre 5.15: Update to 5.15.44. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.44.
(linux-libre-5.15-pristine-source): Update hash.
 2022-05-31 18:04:02 -04:00
Leo Famulari cae7ed2aed
gnu: linux-libre: Update to 5.17.12. 
* gnu/packages/linux.scm (linux-libre-5.17-version): Update to 5.17.12.
(linux-libre-5.17-pristine-source): Update hash.
 2022-05-31 18:03:58 -04:00
Ricardo Wurmus c4e03f8204
gnu: Add r-gsalib. 
* gnu/packages/cran.scm (r-gsalib): New variable.
 2022-05-31 23:43:37 +02:00
Ricardo Wurmus 6d8a3aa9c9
gnu: Add glibc-locales-2.32. 
* gnu/packages/base.scm (glibc-locales-2.32): New variable.
 2022-05-31 22:32:17 +02:00
Ricardo Wurmus 16ff4bc024
gnu: Add glibc-locales-2.31. 
* gnu/packages/base.scm (glibc-locales-2.31): New variable.
 2022-05-31 22:32:17 +02:00
Ricardo Wurmus 70f88d53b6
gnu: Add glibc-locales-2.30. 
* gnu/packages/base.scm (glibc-locales-2.30): New variable.
 2022-05-31 22:32:17 +02:00
Ricardo Wurmus a484e019d3
gnu: Add glibc-2.32. 
* gnu/packages/base.scm (glibc-2.32): New variable.
 2022-05-31 22:32:14 +02:00
Maxim Cournoyer c35e508b4a
gnu: Remove python2-biopython. 
* gnu/packages/bioinformatics.scm (python2-biopython): Delete variable.
 2022-05-31 14:54:17 -04:00
Maxim Cournoyer ad030a0b7d
gnu: Remove pplacer-scripts. 
* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable.
 2022-05-31 14:54:17 -04:00
Maxim Cournoyer d397cb6207
gnu: Remove pplacer. 
* gnu/packages/bioinformatics.scm (pplacer): Delete variable.
 2022-05-31 14:54:16 -04:00
Maxim Cournoyer 962d02904f
gnu: Remove python2-pytest-cov. 
* gnu/packages/check.scm (python2-pytest-cov): Delete variable.
 2022-05-31 14:54:16 -04:00
Maxim Cournoyer f7cfb57bb5
gnu: Remove python2-called-python. 
* gnu/packages/python.scm (python2-called-python): Delete variable.
 2022-05-31 14:54:16 -04:00
Maxim Cournoyer 96c0c18c3e
gnu: Remove python-prompt-toolkit-2. 
* gnu/packages/python-xyz.scm (python-prompt-toolkit-2): Delete variable.
(python-prompt-toolkit)[properties]: Delete field.
(python-jupyter-console): Replace python-prompt-toolkit-2 with
python-prompt-toolkit.
 2022-05-31 14:54:16 -04:00
Maxim Cournoyer 5d8fb87127
gnu: Remove python2-setuptools. 
* gnu/packages/python-xyz.scm (python2-setuptools): Delete variable.
(python-setuptools)[properties]: Delete field.
* gnu/packages/syncthing.scm (syncthing-gtk): Delete commented native input.
* guix/lint.scm (check-inputs-should-not-be-an-input-at-all): Remove obsolete entries.
 2022-05-31 14:54:16 -04:00
Maxim Cournoyer 026fca8b5b
gnu: Remove python2-checkm-genome. 
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Delete variable.
 2022-05-31 14:54:15 -04:00
Maxim Cournoyer 12a16c3166
gnu: qtwebengine: Re-style inputs. 
* gnu/packages/qt.scm (qtwebengine)[phases]: Delete trailing #t.
{substitute-source}: Use search-input-file.
[inputs, native-inputs]: Use new style.
 2022-05-31 14:54:15 -04:00