[med-svn] [bioperl-run] 02/02: Adapt patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository bioperl-run.

commit 93f5097619708265f34d880044dd1e134deedb31
Author: Andreas Tille <tille at 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 <tille at 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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