Commit f0a273ea authored by Andreas Tille's avatar Andreas Tille

New upstream version

parent 8234880f
bioperl-run (1.6.9-4) UNRELEASED; urgency=medium
bioperl-run (1.7.1-1) UNRELEASED; urgency=medium
* New upstream version
* Testsuite: autopkgtest-pkg-perl
* cme fix dpkg-control
* Enable lots of tests
......@@ -7,6 +8,9 @@ bioperl-run (1.6.9-4) UNRELEASED; urgency=medium
bioperl-run in commit acd57a7d14112c5fd2cd979005b072efdaf57679 which is
taken over in quilt patch
* Fix homepage
* d/watch:
- version=4
- Fix versionmangling
-- Andreas Tille <tille@debian.org> Fri, 16 Dec 2016 09:17:37 +0100
......
This diff is collapsed.
Forwarded: https://redmine.open-bio.org/issues/3255
From 8d4322bea521c457029a00155fe292ef7ef177d4 Mon Sep 17 00:00:00 2001
From: Charles Plessy <plessy@debian.org>
Date: Sat, 18 Jun 2011 12:58:08 +0900
Subject: [PATCH] Use system's Perl.
---
scripts/bioperl_application_installer.PLS | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
--- a/scripts/bioperl_application_installer.PLS
+++ b/scripts/bioperl_application_installer.PLS
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# BioPerl script for Bio::Installer
#
# Cared for by Albert Vilella
Forwarded: https://redmine.open-bio.org/issues/3254
From 4d1fe98b390c67170d0d23325de5ccd8fdc6ea1a Mon Sep 17 00:00:00 2001
From: Charles Plessy <plessy@debian.org>
Date: Sat, 18 Jun 2011 12:43:21 +0900
Subject: [PATCH] New --install_scripts option to request script installation non-interactively.
---
Build.PL | 5 +++--
1 files changed, 3 insertions(+), 2 deletions(-)
--- a/Build.PL
+++ b/Build.PL
@@ -27,7 +27,8 @@ my $build = Module::Build->new(
},
get_options => {
accept => { },
- network => { }
+ network => { },
+ install_scripts => { }
},
auto_features => {
Network => {
@@ -42,7 +43,7 @@ my $build = Module::Build->new(
my $accept = $build->args->{accept};
# Optionally have script files installed.
-if ($accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
+if ($build->args('install_scripts') or $accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
my $files = $build->_find_file_by_type('PLS', 'scripts');
my $script_build = File::Spec->catdir($build->blib, 'script');
This source diff could not be displayed because it is too large. You can view the blob instead.
install-scripts.patch
Use-system-s-Perl.patch
Some-spellchecking.patch
move-StandAloneBlast-and-WrapperBase-from-root-Bio.-.patch
skip_tests_for_wise.patch
skip_tests_for_muscle.patch
# skip_tests_for_bowtie.patch
# skip_tests_for_muscle.patch # does not apply in 1.7.1
# skip_tests_for_bowtie.patch # skip whole patch in 1.6.9
skip_tests_for_phylip.patch
# skip_tests_for_infernal.patch
# skip_tests_for_infernal.patch # skip whole patch in 1.6.9
skip_tests_for_phyml.patch
skip_tests_for_ncbi-blast+.patch
skip_tests_for_samtools.patch
# skip_tests_for_ncbi-blast+.patch # does not apply in 1.7.1
# skip_tests_for_samtools.patch # does not apply in 1.7.1
skip_tests_for_t-coffee.patch
skip_tests_for_maq.patch
# skip_tests_for_maq.patch # does not apply in 1.7.1
......@@ -2,40 +2,9 @@ Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 16 Dec 2016 09:17:37 +0100
Description: No idea why the number of tests is 8 instead of 9
--- a/t/Consense.t
+++ b/t/Consense.t
@@ -6,7 +6,7 @@ use strict;
BEGIN {
use Bio::Root::Test;
- test_begin(-tests => 9,
+ test_begin(-tests => 8,
-requires_module => 'IO::String');
use_ok('Bio::Tools::Run::Phylo::Phylip::Consense');
use_ok('Bio::AlignIO');
--- a/t/Neighbor.t
+++ b/t/Neighbor.t
@@ -103,10 +103,10 @@ SKIP: {
@nodes = sort { defined $a->id &&
defined $b->id &&
$a->id cmp $b->id } $tree->get_nodes();
- is ($nodes[12]->id, 'S01',"failed to assign serial names");
- foreach my $nd (@nodes){
- $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
- }
- is ($nodes[12]->id, 'Spar_21273',"failed to restore original names");
+ #is ($nodes[12]->id, 'S01',"failed to assign serial names"); # Got undef in these tests! FIXME
+ #foreach my $nd (@nodes){
+ # $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
+ #}
+ #is ($nodes[12]->id, 'Spar_21273',"failed to restore original names");
-}
\ No newline at end of file
+}
--- a/t/ProtPars.t
+++ b/t/ProtPars.t
@@ -8,7 +8,7 @@ $DEBUG = test_debug();
@@ -7,7 +7,7 @@ $DEBUG = test_debug();
use strict;
BEGIN {
use Bio::Root::Test;
......@@ -44,8 +13,8 @@ Description: No idea why the number of tests is 8 instead of 9
use_ok('Bio::Tools::Run::Phylo::Phylip::ProtPars');
use_ok('Bio::Tools::Run::Alignment::Clustalw');
}
@@ -81,10 +81,10 @@ SKIP: {
@nodes = sort { $a->id cmp $b->id } $tree->get_nodes();
@@ -78,10 +78,10 @@ SKIP: {
@nodes = sort { $a->id cmp $b->id } $tree2->get_nodes();
is (scalar(@nodes),27,
"creating tree by protpars");
- is ($nodes[12]->id, 'S01',"assign serial names");
......
......@@ -40,25 +40,7 @@ Description: Somehow there are issues to initialise openmpi, but beside these wa
--- a/t/Phyml.t
+++ b/t/Phyml.t
@@ -5,7 +5,7 @@ use strict;
BEGIN {
use Bio::Root::Test;
- test_begin(-tests => 47);
+ test_begin(-tests => 42);
use_ok('Bio::Tools::Run::Phylo::Phyml');
use_ok('Bio::AlignIO');
}
@@ -88,7 +88,7 @@ SKIP: {
is ($factory->data_type('dna'), '0', 'data_type, dna');
is ($factory->data_type('protein'), '1', 'data_type, protein');
- is ($factory->model, 'JTT', 'model, default');
+ # is ($factory->model, 'JTT', 'model, default'); # got: 'WAG' - expected: 'JTT'
is ($factory->opt_topology, 'y', 'opt_topology, default');
@@ -106,18 +106,17 @@ SKIP: {
@@ -103,18 +103,17 @@ SKIP: {
# $factory->tempdir($workdir);
# using filename input
......@@ -87,7 +69,7 @@ Description: Somehow there are issues to initialise openmpi, but beside these wa
# using AlignIO on a DNA MSA
@@ -148,8 +147,8 @@ SKIP: {
@@ -145,7 +144,7 @@ SKIP: {
$factory = Bio::Tools::Run::Phylo::Phyml->new(%args);
$factory->save_tempfiles(1);
......@@ -98,4 +80,3 @@ Description: Somehow there are issues to initialise openmpi, but beside these wa
+ #@leaves = $tree->get_leaf_nodes;
+ #is (@leaves, 5, 'Result tree from DNA SimpleAlign input had correct number of leaves');
}
......@@ -7,19 +7,16 @@ endif
# The following programs are not packaged for Debian and thus
# the test is not supported
NOT_SUPPORTED_TESTS=Blat \
Bowtie \
Eponine \
Glimmer2 \
Gumby \
Infernal \
RepeatMasker
# 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
FAILING_TESTS_FOR_DUE_TO_MISSING_MODULES=BWA \
MCS \
Match
MCS
%:
dh $@
......
version=3
opts="uversionmangle=s/_/./g" \
version=4
opts="uversionmangle=s/[-_]/./g" \
https://github.com/bioperl/bioperl-run/releases .*/archive/release-(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)$
# http://search.cpan.org/dist/BioPerl-Run/ .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
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