[med-svn] [Git][med-team/bioperl-run][master] 4 commits: Revert "skip_tests_for_ncbi-blast+.patch: remove."
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Dec 1 09:58:41 GMT 2024
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 <emollier at debian.org> 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 <tille at debian.org>
+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 <ucko at debian.org>
+Reviewed-By: Étienne Mollier <emollier at debian.org>
+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
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