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tille pushed a commit to branch master
in repository bioperl-run.
commit 93f5097619708265f34d880044dd1e134deedb31
Author: Andreas Tille <ti...@debian.org>
Date: Sat Sep 16 21:34:59 2017 +0200
Adapt patches
---
debian/patches/series | 1 -
debian/patches/skip_tests_for_phylip.patch | 4 ++--
debian/patches/skip_tests_for_t-coffee.patch | 33 ----------------------------
3 files changed, 2 insertions(+), 36 deletions(-)
diff --git a/debian/patches/series b/debian/patches/series
index 328387c..c5dbb50 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,7 +1,6 @@
skip_tests_for_wise.patch
skip_tests_for_phylip.patch
skip_tests_for_phyml.patch
-skip_tests_for_t-coffee.patch
skip_tests_for_bowtie.patch
skip_tests_for_infernal.patch
skip_tests_for_muscle.patch
diff --git a/debian/patches/skip_tests_for_phylip.patch
b/debian/patches/skip_tests_for_phylip.patch
index 0a9ba7e..9c6b48d 100644
--- a/debian/patches/skip_tests_for_phylip.patch
+++ b/debian/patches/skip_tests_for_phylip.patch
@@ -11,9 +11,9 @@ Description: No idea why the number of tests is 8 instead of 9
- test_begin(-tests => 11);
+ test_begin(-tests => 9);
use_ok('Bio::Tools::Run::Phylo::Phylip::ProtPars');
- use_ok('Bio::Tools::Run::Alignment::Clustalw');
}
-@@ -78,10 +78,10 @@ SKIP: {
+
+@@ -79,10 +79,10 @@ SKIP: {
@nodes = sort { $a->id cmp $b->id } $tree2->get_nodes();
is (scalar(@nodes),27,
"creating tree by protpars");
diff --git a/debian/patches/skip_tests_for_t-coffee.patch
b/debian/patches/skip_tests_for_t-coffee.patch
deleted file mode 100644
index 06b72ad..0000000
--- a/debian/patches/skip_tests_for_t-coffee.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-Author: Andreas Tille <ti...@debian.org>
-Last-Update: Fri, 16 Dec 2016 09:17:37 +0100
-Description: Ignore a broken version comparison
-
---- a/t/TCoffee.t
-+++ b/t/TCoffee.t
-@@ -5,7 +5,7 @@
- use strict;
- BEGIN {
- use Bio::Root::Test;
-- test_begin(-tests => 27);
-+ test_begin(-tests => 25);
- use_ok('Bio::Tools::Run::Alignment::TCoffee');
- use_ok('Bio::SimpleAlign');
- use_ok('Bio::AlignIO');
-@@ -42,7 +42,7 @@ SKIP: {
- test_skip(-requires_executable => $factory,
- -tests => 20);
- my $version = $factory->version;
-- cmp_ok ($version, '>=', 1.22, "Code tested only on t_coffee versions >
1.22" );
-+ # cmp_ok ($version, '>=', 1.22, "Code tested only on t_coffee versions
> 1.22" ); # Argument "11.00.8" isn't numeric in numeric ge (>=) at (eval
in cmp_ok) t/TCoffee.t
- $aln = $factory->align($inputfilename);
- ok($aln);
- is( $aln->num_sequences, 7);
-@@ -67,7 +67,7 @@ SKIP: {
-
- # convert any warnings about program to an actual exception
- $factory->verbose(2);
-- lives_ok {$aln = $factory->profile_align($profile1,$profile2)};
-+ # lives_ok {$aln = $factory->profile_align($profile1,$profile2)};
# FIXME: this failure should be verified since t_coffee crashed
- skip("T-COFFEE error, skipping tests", 15) if $@;
- is $aln->num_sequences, 7;
-
--
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