[med-svn] [Git][med-team/bioperl-run][master] 5 commits: d/control: remove build dependency on ncbi-blast+-legacy.

[Étienne Mollier (@emollier)]

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 <emollier at debian.org>  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 <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";



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
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