Étienne Mollier pushed to branch master at Debian Med / bioperl-run
Commits: 54adca05 by Étienne Mollier at 2024-12-01T10:28:42+01:00 Revert "skip_tests_for_ncbi-blast+.patch: remove." This reverts commit 226548d4f611390f9e6996b23f043605d1a552cd. - - - - - 72055700 by Étienne Mollier at 2024-12-01T10:31:52+01:00 Revert "d/control: remove build dependency on ncbi-blast+-legacy." This reverts commit 7047f684b6c17c01808b5eef076cb744a02fc8c9. - - - - - 8ed96aea by Étienne Mollier at 2024-12-01T10:55:20+01:00 update-blastdbcmd-error-output.patch: fix test regression. This patch updates the expected blastdbcmd error output parsed by the StandAloneBlastPlus.pm runner, fixing the corresponding test item in the maneuver. Thanks: Aaron M. Ucko Closes: #1077454 - - - - - 7a192d25 by Étienne Mollier at 2024-12-01T10:58:16+01:00 d/changelog: ready for upload to unstable. - - - - - 5 changed files: - debian/changelog - debian/control - debian/patches/series - + debian/patches/skip_tests_for_ncbi-blast+.patch - + debian/patches/update-blastdbcmd-error-output.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,15 @@ +bioperl-run (1.7.3-13) unstable; urgency=medium + + * Revert "skip_tests_for_ncbi-blast+.patch: remove." + * Revert "d/control: remove build dependency on ncbi-blast+-legacy." + * update-blastdbcmd-error-output.patch: fix test regression. + This patch updates the expected blastdbcmd error output parsed by the + StandAloneBlastPlus.pm runner, fixing the corresponding test item in + the maneuver. + Thanks to Aaron M. Ucko (Closes: #1077454) + + -- Étienne Mollier <[email protected]> Sun, 01 Dec 2024 10:57:53 +0100 + bioperl-run (1.7.3-12) unstable; urgency=medium * d/control: remove build dependency on ncbi-blast+-legacy. ===================================== debian/control ===================================== @@ -32,16 +32,7 @@ Build-Depends-Indep: perl, # failures in bioperl-run, so the package is excluded on !amd64 for now. bedtools [any-amd64], bedtools-test, -# FIXME: functionalities related to ncbi-blast+ are affected by Debian -# bug #1077454 starting with ncbi-blast+ 2.16.0. Issue open upstream[1] -# remains unanswered, so removing the build dependency skips the test -# and hides the problem under the carpet. This is not ideal and it has -# been considered to remove the package from the archive instead, but -# the package libbio-perl-run-perl still has high popcon reverse -# dependencies like psortb or the libbio-tools-*-perl packages. -# -# [1]: https://github.com/bioperl/bioperl-run/issues/62 -# ncbi-blast+-legacy, + ncbi-blast+-legacy, libbio-perl-perl, clustalw [any-amd64], emboss [any-amd64 arm64 mips64el ppc64el riscv64], ===================================== debian/patches/series ===================================== @@ -7,6 +7,7 @@ skip_tests_for_wise.patch skip_tests_for_phylip.patch skip_tests_for_phyml.patch skip_tests_for_infernal.patch +skip_tests_for_ncbi-blast+.patch hyphy.patch remove_tests_for_ensembl.patch skip_tests_for_soap.patch @@ -17,3 +18,4 @@ fix-whatis-entries.patch unscramble-erpin.patch fix-pod-conversion.patch adjust-muscle-test.patch +update-blastdbcmd-error-output.patch ===================================== debian/patches/skip_tests_for_ncbi-blast+.patch ===================================== @@ -0,0 +1,26 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Fri, 16 Dec 2016 09:17:37 +0100 +Description: Somehow tests are excluded automatically - adjust expected number of tests + +--- a/t/SABlastPlus.t ++++ b/t/SABlastPlus.t +@@ -8,7 +8,7 @@ use lib '../lib'; + our $home; + BEGIN { + use Bio::Root::Test; +- test_begin(-tests => 73, ++ test_begin(-tests => 71, + -requires_module => "IPC::Run"); + use_ok( 'Bio::Tools::Run::StandAloneBlastPlus' ); + use_ok( 'Bio::Tools::Run::WrapperBase' ); +@@ -43,8 +43,8 @@ SKIP : { + -create => 1 + ); + +- like($fac->program_version, qr/2\.\d+\.\d+/, 'program version'); +- like($fac->package_version, qr/2\.\d+\.\d+/, 'package version'); ++ # like($fac->program_version, qr/2\.\d+\.\d+/, 'program version'); ++ # like($fac->package_version, qr/2\.\d+\.\d+/, 'package version'); + + ok $fac->make_db, "named db made"; + ok $fac->check_db, "check_db"; ===================================== debian/patches/update-blastdbcmd-error-output.patch ===================================== @@ -0,0 +1,21 @@ +Description: update blastdbcmd error output. + AFAICT, the relevant change is in blastdbcmd error output and the + following patch suffices (perhaps with a line break thrown in): +Author: Aaron M. Ucko <[email protected]> +Reviewed-By: Étienne Mollier <[email protected]> +Bug: https://github.com/bioperl/bioperl-run/issues/62 +Bug-Debian: https://bugs.debian.org/1077454 +Last-Update: 2024-12-01 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- bioperl-run.orig/lib/Bio/Tools/Run/StandAloneBlastPlus.pm ++++ bioperl-run/lib/Bio/Tools/Run/StandAloneBlastPlus.pm +@@ -1106,7 +1106,7 @@ + $self->factory->no_throw_on_crash(1); + $self->factory->_run(); + $self->factory->no_throw_on_crash(0); +- return 0 if ($self->factory->stderr =~ /No alias or index file found/); ++ return 0 if ($self->factory->stderr =~ /No alias or index file found|Database memory map file error/); + return 1; + } + return; View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/60f0c2f7f2eac5438f879d4c6d13dc111400848d...7a192d251c38e1fceea12f95e38a51e60ee68e71 -- View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/60f0c2f7f2eac5438f879d4c6d13dc111400848d...7a192d251c38e1fceea12f95e38a51e60ee68e71 You're receiving this email because of your account on salsa.debian.org.
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