Commit Graph

344 Commits

Author SHA1 Message Date
Peder Bergebakken Sundt
261314120c
Merge pull request #265750 from herrwiese/for-master/ham-20231006
ham: unstable-2022-10-26 -> unstable-2023-10-06
2024-01-19 17:02:59 +01:00
Doron Behar
df20638983
Merge pull request #186462 from apraga/bio-bigfile-1.07
bio-bigfile: init 1.07
2023-11-30 13:39:01 +00:00
Alexis Praga
75fc8ae0f4 perlPackages.BioBigFile: Addressing reviewer change 2023-11-21 23:16:39 +01:00
Alexis Praga
cc4bd30387 perlPackages.BioBigfile: init at 1.07
Perl interface to manipulate BigWig and BigBeg files (for genomics)
This will be used to package VEP : uttps://www.ensembl.org/info/docs/tools/vep/script/vep_download.html

For that, only kent version 335 works at the moment.
For this commit, 2 commits for kent are needed
- e027a5d836 : packaging kent header
- 2b2c6f4c28 : enabling patches in kent
2023-11-21 23:16:12 +01:00
Stig Palmquist
78cbf53e82
perlPackages.Hailo: fix tests
Add patch to tests that fixes compat with Getopt-Long-Description 0.106
2023-11-21 13:34:04 +01:00
tu-maurice
462ae9fadc perl538Packages.CSSDOM: fix test
t/css-dom.t was deactivated because it failed due to deprecated syntax. This
commit uses an upstream patch to fix the syntax and activate the test again.
2023-11-18 23:08:46 +01:00
Andreas Wiese
28cfd573de ham: unstable-2022-10-26 -> unstable-2023-10-06 2023-11-06 00:18:59 +01:00
Randy Eckenrode
1a2c0b89c6
perlPackages.Gtk2: fix build with clang 16
Fix pointer casts to 32-bit integers.
2023-11-03 13:45:18 -04:00
Stig
0dca32340c
Merge pull request #265043 from stigtsp/perl/mousex-getopts-fix-gld
[staging-next] perlPackages.MouseXGetopt: add patch
2023-11-03 17:57:02 +01:00
Stig Palmquist
79309b35b6
perlPackages.MouseXGetopt: add patch
Adds patch to test suite to make it compatible with
Getopt-Long-Descriptive >= 0.106
2023-11-02 16:32:39 +01:00
Stig Palmquist
aa6ed10765
perlPackages.XMLLibXML: fix darwin build 2023-11-02 13:21:50 +01:00
Tae Selene Sandoval Murgan
daba2eb22d perlPackages.IOTty: Fix build on Darwin
Co-authored-by: Stig <git@stig.io>
2023-10-28 20:56:30 +02:00
Stig Palmquist
f99ac6d6f7 Merge branch 'staging-next' into perl-updates 2023-10-26 14:09:03 +02:00
Vladimír Čunát
d811555465
Merge branch 'staging' into staging-next 2023-10-26 10:36:50 +02:00
TomaSajt
d12237ef2f
perlPackages.ArchiveLibarchive: init at 0.08 2023-10-23 14:04:17 +02:00
TomaSajt
9a4eb3234a
perlPackages.AlienFFI: init at 0.27 2023-10-23 14:04:14 +02:00
Stig Palmquist
a03242816f perlPackages.Paranoid: fix patch 2023-10-23 05:15:21 +02:00
Stig Palmquist
123c9259db perlPackages.MHonArc: remove merged patch 2023-10-23 05:15:20 +02:00
Stig Palmquist
ae4c0e392d perlPackages.LWPProtocolHttps: update patch for NIX_SSL_CERT_FILE
Update patch that supports NIX_SSL_CERT_FILE env variable so it's
compatible with LWP::Protocol::https 6.11

The new patch does not handle SSL_CERT_FILE or default cert store paths
as this is managed by IO::Socket::SSL.
2023-10-23 05:15:09 +02:00
Maximilian Bosch
8bc5104a6e
treewide: refactor .attrs.sh detection
When specifying the `builder` attribute in `stdenv.mkDerivation`, this
will be effectively transformed into

    builtins.derivation {
      builder = stdenv.shell;
      args = [ "-e" builder ];
    }

This also means that `default-builder.sh` is never sourced and as a
result it's not guaranteed that `$NIX_ATTRS_SH_FILE` is set to a correct
location[1].

Also, we need to source `.attrs.sh` to source `$stdenv`. So, the
following is done now:

* If `$NIX_ATTRS_SH_FILE` points to a correct location, then use it.
  Directly using `.attrs.sh` is problematic for `nix-shell(1)` usage
  (see previous commit for more context), so prefer the environment
  variable if possible.

* Otherwise, if `.attrs.sh` exists, then use it. See [1] for when this
  can happen.

* If neither applies, it can be assumed that `__structuredAttrs` is
  turned off and thus nothing needs to be done.

[1] It's possible that it doesn't exist at all - in case of Nix 2.3 or
    it can point to a wrong location on older Nix versions with a bug in
    `__structuredAttrs`.
2023-10-04 18:36:57 +02:00
Stig
c9a667043f
Merge pull request #256402 from puckipedia/fix-frozen-bubble
perlPackages.SDL: fix on perl >= 5.38.0
2023-09-21 13:58:37 +02:00
Puck Meerburg
5742d5a8fd perlPackages.SDL: import patch 2023-09-21 09:14:44 +00:00
Randy Eckenrode
42f749145d
perlPackages.Tk: fix build with clang 16
The jpeg `configure` script fails to detect clang as a functioning C
compiler because it uses a test with a `main` that returns an implicit
`int`, which results in an error with clang 16.
2023-09-06 18:30:41 -04:00
Vladimír Čunát
c58c344fca
Merge #246585: Fix perlPackages breakage
...into staging-next
2023-08-02 10:09:38 +02:00
Stig Palmquist
42dde6e410
perlPackages.ExtUtilsConstant: add patch for failing test 2023-08-01 17:01:54 +02:00
Stig Palmquist
5a9c09f2f7
perlPackages.ExceptionBase: add patch for perl 5.38.0 2023-08-01 17:01:54 +02:00
Stig Palmquist
5be1087e8f
perlPackages.DataClone: add patch for perl 5.38.0 2023-08-01 17:01:47 +02:00
Stig Palmquist
a287870f99
perlPackages.DataUUID: Add patch for CVE-2013-4184 2023-07-24 17:11:59 +02:00
Theodore Ni
867f6fc82d
perlPackages.Po4a: disable tests on darwin 2023-06-22 13:07:51 -07:00
Artturin
449a46278e strip-nondeterminism: fix zip handler
https://salsa.debian.org/reproducible-builds/strip-nondeterminism/-/blob/master/lib/File/StripNondeterminism/handlers/zip.pm#L29

it was working on linux because the tests are run on linux
2023-06-03 23:43:41 +03:00
Nick Cao
d9bf21544e
perlPackages.TextBibTeX: always install libbtparse.so to /lib instead of /lib64 2023-06-01 16:32:17 +08:00
Artturi
e0ac8942bd
Merge pull request #224107 from Artturin/perl-use-mkscopewithsplicing 2023-04-19 01:53:05 +03:00
Artturin
af0fc32127 perlPackages: use makeScopeWithSplicing 2023-04-11 18:49:10 +03:00
github-actions[bot]
97b2abc678
Merge staging-next into staging 2023-03-26 12:02:02 +00:00
github-actions[bot]
72fc224baa
Merge staging-next into staging 2023-03-26 06:01:39 +00:00
apfelkuchen06
8e40747e62 perl536Packages.Po4a: remove texlive dependency
The motivation behind this is wanting to reduce the reverse closure size of
texlive.

When internationalizing tex files, Po4a attempts to follow included files. In
order to find the correct files, po4a uses texlive's file-finding utility
kpsewhich. This commit replaces texlive with a tiny shell script, which is
precisely good enough to run the tests.

This does not change the resulting package in any way, it only affects how the
test is run.
2023-03-26 01:11:05 -04:00
Stig Palmquist
33b7b0bf88
perlPackages.CatalystAuthenticationStoreHtpasswd: add patch to avoid DES encrypted passwords in tests 2023-03-26 04:14:40 +02:00
Stig Palmquist
301d70dae8
perlPackages.Plack: add patch to avoid DES encrypted passwords in tests 2023-03-25 23:20:55 +01:00
Artturi
44fd51cd47
Merge pull request #218503 from Artturin/strictdeps4 2023-03-02 18:45:34 +02:00
Artturin
07064726bf perlPackages.Po4a: enable strictDeps 2023-02-25 21:47:55 +02:00
Artturin
d707691b35 strip-nondeterminism: fix binary functioning on darwin
result/bin/strip-nondeterminism: bad interpreter: /nix/store/mym5b5zbzgny17ixqr8kgwmndc3k4y2r-perl-5.36.0/bin/perl -I/nix/store/mym5b5zbzgny17ixqr8kgwmndc3k4y2r-perl-5.36.0/lib: exec format error
2023-02-14 05:47:43 +02:00
Artturi
56c4f27b18
Merge pull request #215488 from alyssais/strip-nondeterminism-1.13.1
strip-nondeterminism: fix build
2023-02-09 17:21:53 +02:00
Alyssa Ross
92e6b205ed
strip-nondeterminism: 1.13.0 -> 1.13.1
Fixes build.
2023-02-09 10:35:27 +00:00
Andreas Wiese
fd3dc83046 ham: 2020-09-09 -> 2022-10-26 2023-02-06 16:18:49 +01:00
Guillaume Girol
33afbf39f6 treewide: switch to nativeCheckInputs
checkInputs used to be added to nativeBuildInputs. Now we have
nativeCheckInputs to do that instead. Doing this treewide change allows
to keep hashes identical to before the introduction of
nativeCheckInputs.
2023-01-21 12:00:00 +00:00
github-actions[bot]
33aa224777
Merge master into staging-next 2023-01-09 18:01:24 +00:00
Artturin
d5febb8d7a strip-nondeterminism: 1.0.0 -> 1.13.0
https://salsa.debian.org/reproducible-builds/strip-nondeterminism/-/tags/1.13.0

move shortenPerlShebang to postBuild to fix tests
2023-01-09 18:33:56 +02:00
Artturin
c01f509e44 treewide: source .attrs in builders
if theres a source $stdenv then this is needed

for structuredAttrs
2022-12-08 21:09:02 +02:00
Artturin
adc8900df1 treewide: fix some core package structuredAttrs 2022-12-08 21:05:28 +02:00
Sandro
05c703fde0
Merge pull request #186464 from apraga/bioextalign-1.5.1 2022-10-22 00:34:42 +02:00