Étienne Mollier pushed to branch master at Debian Med / bioperl-run
Commits: 7047f684 by Étienne Mollier at 2024-11-20T22:31:54+01:00 d/control: remove build dependency on ncbi-blast+-legacy. This skips the failing test reported in bug #1077454. - - - - - 226548d4 by Étienne Mollier at 2024-11-20T22:33:00+01:00 skip_tests_for_ncbi-blast+.patch: remove. The workaround in this patch gets to interfere with the test run once ncbi-blast+-legacy is not available anymore. - - - - - 402eb28a by Étienne Mollier at 2024-11-20T22:34:41+01:00 d/control: declare compliance to standards version 4.7.0. - - - - - 02288638 by Étienne Mollier at 2024-11-20T22:41:04+01:00 d/control: remove redundant control relation. Gbp-Dch: ignore - - - - - 60f0c2f7 by Étienne Mollier at 2024-11-20T22:41:55+01:00 d/changelog: ready for upload to unstable. - - - - - 4 changed files: - debian/changelog - debian/control - debian/patches/series - − debian/patches/skip_tests_for_ncbi-blast+.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,14 @@ +bioperl-run (1.7.3-12) unstable; urgency=medium + + * d/control: remove build dependency on ncbi-blast+-legacy. + This skips the failing test reported in bug #1077454. + * skip_tests_for_ncbi-blast+.patch: remove. + The workaround in this patch gets to interfere with the test run once + ncbi-blast+-legacy is not available anymore. + * d/control: declare compliance to standards version 4.7.0. + + -- Étienne Mollier <[email protected]> Wed, 20 Nov 2024 22:41:27 +0100 + bioperl-run (1.7.3-11) unstable; urgency=medium * d/control: restrict emboss build-dependency. ===================================== debian/control ===================================== @@ -32,7 +32,17 @@ Build-Depends-Indep: perl, # failures in bioperl-run, so the package is excluded on !amd64 for now. bedtools [any-amd64], bedtools-test, - ncbi-blast+-legacy, +# 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, + libbio-perl-perl, clustalw [any-amd64], emboss [any-amd64 arm64 mips64el ppc64el riscv64], exonerate, @@ -60,7 +70,7 @@ Build-Depends-Indep: perl, pftools [any-amd64], # Needed for the network tests: libwww-perl -Standards-Version: 4.6.2 +Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/bioperl-run Vcs-Git: https://salsa.debian.org/med-team/bioperl-run.git Homepage: https://metacpan.org/release/BioPerl-Run ===================================== debian/patches/series ===================================== @@ -7,7 +7,6 @@ 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 ===================================== debian/patches/skip_tests_for_ncbi-blast+.patch deleted ===================================== @@ -1,26 +0,0 @@ -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"; View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/16f1a768366cc95e31c9582108f1811781127b76...60f0c2f7f2eac5438f879d4c6d13dc111400848d -- View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/16f1a768366cc95e31c9582108f1811781127b76...60f0c2f7f2eac5438f879d4c6d13dc111400848d You're receiving this email because of your account on salsa.debian.org.
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