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2023-11-30Merge pull request #186462 from apraga/bio-bigfile-1.07Doron Behar3-0/+118
bio-bigfile: init 1.07
2023-11-21perlPackages.BioBigFile: Addressing reviewer changeAlexis Praga2-7/+32
2023-11-21perlPackages.BioBigfile: init at 1.07Alexis Praga2-0/+93
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 - e027a5d8368a053e231 : packaging kent header - 2b2c6f4c287c6107acb : enabling patches in kent
2023-11-21perlPackages.Hailo: fix testsStig Palmquist1-0/+28
Add patch to tests that fixes compat with Getopt-Long-Description 0.106
2023-11-18perl538Packages.CSSDOM: fix testtu-maurice1-0/+1412
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.
2023-11-03perlPackages.Gtk2: fix build with clang 16Randy Eckenrode1-0/+86
Fix pointer casts to 32-bit integers.
2023-11-03Merge pull request #265043 from stigtsp/perl/mousex-getopts-fix-gldStig1-0/+143
[staging-next] perlPackages.MouseXGetopt: add patch
2023-11-02perlPackages.MouseXGetopt: add patchStig Palmquist1-0/+143
Adds patch to test suite to make it compatible with Getopt-Long-Descriptive >= 0.106
2023-11-02perlPackages.XMLLibXML: fix darwin buildStig Palmquist1-0/+47
2023-10-28perlPackages.IOTty: Fix build on DarwinTae Selene Sandoval Murgan1-0/+13
Co-authored-by: Stig <git@stig.io>
2023-10-26Merge branch 'staging-next' into perl-updatesStig Palmquist3-1/+55
2023-10-26Merge branch 'staging' into staging-nextVladimír Čunát1-1/+1
2023-10-23perlPackages.ArchiveLibarchive: init at 0.08TomaSajt1-0/+25
2023-10-23perlPackages.AlienFFI: init at 0.27TomaSajt1-0/+29
2023-10-23perlPackages.Paranoid: fix patchStig Palmquist1-17/+16
2023-10-23perlPackages.MHonArc: remove merged patchStig Palmquist1-26/+0
2023-10-23perlPackages.LWPProtocolHttps: update patch for NIX_SSL_CERT_FILEStig Palmquist1-26/+9
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.
2023-10-04treewide: refactor `.attrs.sh` detectionMaximilian Bosch1-1/+1
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`.
2023-09-21Merge pull request #256402 from puckipedia/fix-frozen-bubbleStig1-0/+64
perlPackages.SDL: fix on perl >= 5.38.0
2023-09-21perlPackages.SDL: import patchPuck Meerburg1-0/+64
2023-09-06perlPackages.Tk: fix build with clang 16Randy Eckenrode1-0/+11
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.
2023-08-02Merge #246585: Fix perlPackages breakageVladimír Čunát3-0/+77
...into staging-next
2023-08-01perlPackages.ExtUtilsConstant: add patch for failing testStig Palmquist1-0/+31
2023-08-01perlPackages.ExceptionBase: add patch for perl 5.38.0Stig Palmquist1-0/+20
2023-08-01perlPackages.DataClone: add patch for perl 5.38.0Stig Palmquist1-0/+26
2023-07-24perlPackages.DataUUID: Add patch for CVE-2013-4184Stig Palmquist1-0/+214
2023-06-22perlPackages.Po4a: disable tests on darwinTheodore Ni1-1/+3
2023-06-03strip-nondeterminism: fix zip handlerArtturin1-2/+1
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
2023-06-01perlPackages.TextBibTeX: always install libbtparse.so to /lib instead of /lib64Nick Cao1-1/+1
2023-04-19Merge pull request #224107 from Artturin/perl-use-mkscopewithsplicingArtturi1-3/+3
2023-04-11perlPackages: use makeScopeWithSplicingArtturin1-3/+3
2023-03-26Merge staging-next into staginggithub-actions[bot]1-0/+12
2023-03-26Merge staging-next into staginggithub-actions[bot]1-0/+12
2023-03-26perl536Packages.Po4a: remove texlive dependencyapfelkuchen061-3/+11
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.
2023-03-26perlPackages.CatalystAuthenticationStoreHtpasswd: add patch to avoid DES ↵Stig Palmquist1-0/+12
encrypted passwords in tests
2023-03-25perlPackages.Plack: add patch to avoid DES encrypted passwords in testsStig Palmquist1-0/+12
2023-03-02Merge pull request #218503 from Artturin/strictdeps4Artturi1-3/+5
2023-02-25perlPackages.Po4a: enable strictDepsArtturin1-3/+5
2023-02-14strip-nondeterminism: fix binary functioning on darwinArtturin1-3/+11
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
2023-02-09Merge pull request #215488 from alyssais/strip-nondeterminism-1.13.1Artturi1-2/+2
strip-nondeterminism: fix build
2023-02-09strip-nondeterminism: 1.13.0 -> 1.13.1Alyssa Ross1-2/+2
Fixes build.
2023-02-06ham: 2020-09-09 -> 2022-10-26Andreas Wiese1-8/+16
2023-01-21treewide: switch to nativeCheckInputsGuillaume Girol1-1/+1
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.
2023-01-09Merge master into staging-nextgithub-actions[bot]1-14/+35
2023-01-09strip-nondeterminism: 1.0.0 -> 1.13.0Artturin1-14/+35
https://salsa.debian.org/reproducible-builds/strip-nondeterminism/-/tags/1.13.0 move shortenPerlShebang to postBuild to fix tests
2022-12-08treewide: source .attrs in buildersArtturin1-3/+1
if theres a source $stdenv then this is needed for structuredAttrs
2022-12-08treewide: fix some core package structuredAttrsArtturin2-3/+9
2022-10-22Merge pull request #186464 from apraga/bioextalign-1.5.1Sandro2-0/+49
2022-10-20bioextalign: init at 1.5.1Alexis Praga2-0/+49
Part of BioPerl Extensions (BioPerl-Ext) distribution, a collection of Bioperl C-compiled extensions. These are no longer maintained but needed for Ensembl-VEP (annotation for genomics). Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
2022-10-02Merge master into staging-nextgithub-actions[bot]1-13/+0
generated by cgit-pink 1.4.1 (git 2.36.1) at 2024-08-19 21:51:20 +0000