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Author SHA1 Message Date
Thiago Jung Bauermann 1e1de83719
gnu: public-inbox: Update to 1.8.0. 
Some fixes are needed in both the testsuite and the package itself before
tests can pass so disable them for now.

Also, the lei command needs curl to work, so add it to the PATH in
‘wrap-program’.

* gnu/packages/mail.scm (public-inbox)[version]: Change to 1.8.0.
[source]: Update hash.
[arguments]<#:tests?>: Set to #f.
[arguments]<#:phases>{wrap-programs}: Add curl to PATH.
[inputs]: Add curl and perl-socket-msghdr.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-06-01 23:28:14 +02:00
Thiago Jung Bauermann 8ba33143ac
gnu: Add perl-socket-msghdr 
* gnu/packages/perl.scm (perl-socket-msghdr): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-06-01 22:44:12 +02:00
Thiago Jung Bauermann c017acec34
gnu: public-inbox: Some packaging fixes 
The file ‘script/public-inbox-compact’ doesn't call ‘xapian-compact’ directly
anymore, so the substitution in the ‘qualify-paths’ phase doesn't do anything.

Now there's a reference to ‘xapian-compact’ in ‘lib/PublicInbox/Xapcmd.pm’,
so substitute the path there.

And move xapian from native-inputs to inputs and use its input path in the
substitution, since ‘xapian-compact’ is called during normal execution of
public-inbox.

Also add ‘bash-minimal’ to the package's inputs, since it uses ‘wrap-program’.

Finally, take the opportunity to change build phases to not return #t
unconditionally, since that isn't necessary anymore.

* gnu/packages/mail.scm (public-inbox)[arguments]<#:phases>: Don't return #t
from each phase.
{qualify-paths}: Substitute ‘xapian-compact’ path in the correct file.  Use
‘search-input-file’ rather than ‘which’ to find it.
[native-inputs]: Move ‘xapian’ from here ...
[inputs]: ... to here. Add ‘bash-minimal’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-06-01 22:44:09 +02:00
Fredrik Salomonsson 47792b9b56
gnu: Add emacs-bfuture. 
* gnu/packages/emacs-xyz.scm (emacs-bfuture): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-06-01 22:43:52 +02:00
Ludovic Courtès 2acc83daa5
shell: '--export-manifest -D x -D y' generates a valid manifest. 
* guix/scripts/shell.scm (manifest->code*): Add missing 'list' in
generated 'concatenate-manifests' call.
* tests/guix-shell-export-manifest.sh: Add test.
 2022-06-01 22:22:19 +02:00
Efraim Flashner 572bc6d7bd
gnu: Remove unreferenced patch. 
This is a follow-up to a08c21f206.

* gnu/packages/patches/libmicrohttpd-0.9.73-test-ssl3.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2022-06-01 22:55:27 +03:00
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