[med-svn] [Git][med-team/bioperl-run][master] 9 commits: Only 6 tests for Hyphy
Andreas Tille
gitlab at salsa.debian.org
Fri Sep 14 19:37:53 BST 2018
Andreas Tille pushed to branch master at Debian Med / bioperl-run
Commits:
324f940b by Andreas Tille at 2018-09-14T17:23:20Z
Only 6 tests for Hyphy
- - - - -
9ec02d72 by Andreas Tille at 2018-09-14T17:25:25Z
debhelper 11
- - - - -
1fc7b6f4 by Andreas Tille at 2018-09-14T17:25:28Z
Point Vcs fields to salsa.debian.org
- - - - -
a28463ac by Andreas Tille at 2018-09-14T17:25:28Z
Standards-Version: 4.2.1
- - - - -
aeea3ff7 by Andreas Tille at 2018-09-14T17:30:40Z
skip phyml test at all
- - - - -
def8d921 by Andreas Tille at 2018-09-14T17:57:20Z
Fix Homepage
- - - - -
f7497cd6 by Andreas Tille at 2018-09-14T18:07:30Z
Cleanup patches
- - - - -
5d3bb778 by Andreas Tille at 2018-09-14T18:32:56Z
Lintian-override for script-with-language-extension
- - - - -
cf6bb849 by Andreas Tille at 2018-09-14T18:34:49Z
Upload to unstable
- - - - -
9 changed files:
- + debian/bioperl-run.lintian-overrides
- debian/changelog
- debian/compat
- debian/control
- − debian/patches/adjust_bowtie_tests.patch
- debian/patches/hyphy.patch
- debian/patches/skip_tests_for_phyml.patch
- − debian/patches/skip_tests_for_samtools.patch
- debian/rules
Changes:
=====================================
debian/bioperl-run.lintian-overrides
=====================================
@@ -0,0 +1,7 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+bioperl-run: script-with-language-extension usr/bin/bp_bioperl_application_installer.pl
+bioperl-run: script-with-language-extension usr/bin/bp_multi_hmmsearch.pl
+bioperl-run: script-with-language-extension usr/bin/bp_panalysis.pl
+bioperl-run: script-with-language-extension usr/bin/bp_papplmaker.pl
+bioperl-run: script-with-language-extension usr/bin/bp_run_neighbor.pl
+bioperl-run: script-with-language-extension usr/bin/bp_run_protdist.pl
=====================================
debian/changelog
=====================================
@@ -1,12 +1,18 @@
-bioperl-run (1.7.2-4) UNRELEASED; urgency=medium
+bioperl-run (1.7.2-4) unstable; urgency=medium
* (Build-)Depends: ncoils
* do not run tests parallel to get sensibly sorted output
* Allow MPI oversubscription (as in phyml build since phyml caused
problems inside build time tests)
+ This is also not reliable - skip phyml test at all
Closes: #906337
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.2.1
+ * Fix Homepage
+ * Lintian-override for script-with-language-extension
- -- Andreas Tille <tille at debian.org> Fri, 14 Sep 2018 13:22:55 +0200
+ -- Andreas Tille <tille at debian.org> Fri, 14 Sep 2018 20:10:08 +0200
bioperl-run (1.7.2-3) unstable; urgency=medium
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Charles Plessy <plessy at debian.org>,
Section: science
Testsuite: autopkgtest-pkg-perl
Priority: optional
-Build-Depends: debhelper (>= 10)
+Build-Depends: debhelper (>= 11~)
Build-Depends-Indep: perl,
libmodule-build-perl,
bioperl,
@@ -48,10 +48,10 @@ Build-Depends-Indep: perl,
wise,
# Needed for the network tests:
libwww-perl
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/git/debian-med/bioperl-run.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/bioperl-run.git
-Homepage: http://search.cpan.org/dist/BioPerl-Run/
+Standards-Version: 4.2.1
+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
Package: bioperl-run
Architecture: all
=====================================
debian/patches/adjust_bowtie_tests.patch deleted
=====================================
@@ -1,22 +0,0 @@
-Description: adjust expected test output, bowtie-1.2.1+ returns 2000 processed
-reads instead of 1000
-From: Alex Mestiashvili <mailatgoogl at gmail.com>
---- bioperl-run.orig/t/Bowtie.t
-+++ bioperl-run/t/Bowtie.t
-@@ -185,14 +185,14 @@
- ok $bowtiefac->_run( -ind => $refseq,
- -seq => $rda1, -seq2 => $rda2 ), "read paired fasta sequence";
-
-- like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success");
-+ like($bowtiefac->stderr, qr/reads processed: 2000/, "bowtie success");
-
- $bowtiefac->reset_parameters( -fasta => 0 );
- $bowtiefac->set_parameters( -fastq => 1 );
- ok $bowtiefac->_run( -ind => $refseq,
- -seq => $rdq1, -seq2 => $rdq2 ), "read paired fastq sequence";
-
-- like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success");
-+ like($bowtiefac->stderr, qr/reads processed: 2000/, "bowtie success");
-
-
- # test single
=====================================
debian/patches/hyphy.patch
=====================================
@@ -17,7 +17,7 @@ Description: Hyphy
BEGIN {
use Bio::Root::Test;
- test_begin(-tests => 10,
-+ test_begin(-tests => 9,
++ test_begin(-tests => 6,
-requires_module =>'IO::String');
use_ok('Bio::Tools::Run::Phylo::Hyphy::SLAC');
=====================================
debian/patches/skip_tests_for_phyml.patch
=====================================
@@ -35,7 +35,7 @@ Description: Somehow there are issues to initialise openmpi, but beside these wa
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
- [hostname:2001] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
+ [hostname:2001] Local abort before MPI_INIT completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
.
--- a/t/Phyml.t
=====================================
debian/patches/skip_tests_for_samtools.patch deleted
=====================================
@@ -1,65 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 16 Dec 2016 09:17:37 +0100
-Description: May be this is just a result of samtools incompatibilities
- ------------- EXCEPTION -------------
-MSG: /usr/bin/samtools call crashed: There was a problem running /usr/bin/samtools : [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
-Usage: samtools sort [options...] [in.bam]
-Options:
- -l INT Set compression level, from 0 (uncompressed) to 9 (best)
- -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
- -n Sort by read name
- -o FILE Write final output to FILE rather than standard output
- -T PREFIX Write temporary files to PREFIX.nnnn.bam
- -@, --threads INT
- Set number of sorting and compression threads [1]
- --input-fmt-option OPT[=VAL]
- Specify a single input file format option in the form
- of OPTION or OPTION=VALUE
- -O, --output-fmt FORMAT[,OPT[=VAL]]...
- Specify output format (SAM, BAM, CRAM)
- --output-fmt-option OPT[=VAL]
- Specify a single output file format option in the form
- of OPTION or OPTION=VALUE
- --reference FILE
- Reference sequence FASTA FILE [null]
-
-STACK Bio::Tools::Run::WrapperBase::_run /build/bioperl-run-1.6.9/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:1033
-STACK Bio::Tools::Run::Samtools::run /build/bioperl-run-1.6.9/blib/lib/Bio/Tools/Run/Samtools.pm:176
-STACK toplevel t/Samtools.t:103
- -------------------------------------
-
---- a/t/Samtools.t
-+++ b/t/Samtools.t
-@@ -10,7 +10,7 @@ BEGIN {
- # '..' for debugging from .t file
- unshift @INC, $home;
- use Bio::Root::Test;
-- test_begin(-tests => 40,
-+ test_begin(-tests => 37,
- -requires_modules => [qw(IPC::Run Bio::Tools::Run::Samtools)]);
- }
-
-@@ -65,8 +65,8 @@ is_deeply( $samt->{_options}->{_prefixes
- is_deeply( $samt->{_options}->{_params},
- [qw( command refseq map_qcap ref_list site_list theta n_haplos exp_hap_diff indel_prob )],
- "commands filtered by prefix");
--is( join(' ', @{$samt->_translate_params}),
-- "pileup -T 0.05 -f my.fas", "translate params" );
-+#is( join(' ', @{$samt->_translate_params}),
-+# "pileup -T 0.05 -f my.fas", "translate params" ); # should not be tested - result are simply swapped parameters: 'pileup -f my.fas -T 0.05'
-
- my $new_bam = Bio::Tools::Run::Samtools->new(
- -command => 'merge',
-@@ -100,10 +100,10 @@ SKIP : {
- ok -B $tmpfiles{rtbamfile}, "bam file present and binary";
-
- ok $samt = Bio::Tools::Run::Samtools->new( -command => 'sort' ), 'bam sort factory';
-- ok $samt->run( -bam => $tmpfiles{rtbamfile}, -pfx => 'sorted_bam'), 'sort bam file';
-+ # ok $samt->run( -bam => $tmpfiles{rtbamfile}, -pfx => 'sorted_bam'), 'sort bam file'; # Probably changed samtools interface
-
- ok $samt = Bio::Tools::Run::Samtools->new( -command => 'index' ), 'bam index factory';
-- ok $samt->run( -bam => 'sorted_bam', -out => $tmpfiles{bai}), 'make bam index';
-+ # ok $samt->run( -bam => 'sorted_bam', -out => $tmpfiles{bai}), 'make bam index'; # samtools index: failed to open "sorted_bam": No such file or directory
- ok -B $tmpfiles{bai}, 'bai file present and binary';
-
- unlink('sorted_bam');
=====================================
debian/rules
=====================================
@@ -10,8 +10,11 @@ NOT_SUPPORTED_TESTS=Blat \
Eponine \
Glimmer2 \
Gumby \
- RepeatMasker
+ RepeatMasker \
+ Phyml \
+ Hyphy
+# fpr exclusion of Phyml and Hyphy tests see bug #906337
# Cap3 - some sensible tests seem to run despite this is not packaged
# The following tests should work but are missing to be packaged BioPerl modules
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/compare/6cb42cfaddea09d2bd906ed1e9f6928d7df609e8...cf6bb84982d2ab0258bec07eea6c0f954ce556d1
--
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/compare/6cb42cfaddea09d2bd906ed1e9f6928d7df609e8...cf6bb84982d2ab0258bec07eea6c0f954ce556d1
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