[med-svn] [roary] 01/02: Merge tag 'debian/3.6.8+dfsg-2' into debian/jessie-backports

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch debian/jessie-backports
in repository roary.

commit aac360f4938df1bb5a0b605c9ea27fe84943a5cc
Merge: 04e79e8 6805d50
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Aug 22 00:08:51 2016 -0700

    Merge tag 'debian/3.6.8+dfsg-2' into debian/jessie-backports
    
    roary Debian release 3.6.8+dfsg-2

 .travis.yml                                        |   14 +-
 Dockerfile                                         |   19 +
 README.md                                          |   11 +-
 debian/changelog                                   |   32 +
 debian/tests/control                               |    1 +
 dist.ini                                           |    2 +-
 install_dependencies.sh                            |   12 +-
 lib/Bio/Roary/ExtractProteomeFromGFF.pm            |   27 +-
 lib/Bio/Roary/GeneNamesFromGFF.pm                  |    8 +
 lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm |   58 +-
 lib/Bio/Roary/ParseGFFAnnotationRole.pm            |    2 +-
 lib/Bio/Roary/SplitGroups.pm                       |    4 +
 t/Bio/Roary/AnnotateGroups.t                       |   17 +
 t/Bio/Roary/CommandLine/Roary.t                    |  174 +-
 t/Bio/Roary/ExtractProteomeFromGFFs.t              |   38 +
 t/data/allow_no_fasta_delimiter/annotation_1.gff   |  173 +
 .../annotation_1.gff.proteome.faa.expected         |   36 +
 t/data/allow_no_fasta_delimiter/annotation_2.gff   |  173 +
 .../annotation_2.gff.proteome.faa.expected         |   36 +
 t/data/example_annotation_no_fasta_line.gff        |  270 ++
 t/data/expected_core_60_summary_statistics.txt     |    4 +-
 ...xpected_mafft_real_data_core_gene_alignment.aln |  924 ++---
 t/data/expected_real_data_core_gene_alignment.aln  | 4074 ++++++++++----------
 t/data/gene_name_field/annotation_1.gff            |  173 +
 t/data/gene_name_field/annotation_2.gff            |  173 +
 .../expected_reannotated_groups_file               |    8 +
 t/data/gene_name_field/groups                      |    8 +
 27 files changed, 3784 insertions(+), 2687 deletions(-)

diff --cc debian/changelog
index ad04833,6b0f6f9..4cb2e67
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,35 +1,41 @@@
+ roary (3.6.8+dfsg-2) unstable; urgency=medium
+ 
+   * d/tests/control: Add 'allow-stderr' restriction.
+     libfile-slurper-perl update to 0.009-1 introduced a new warning,
+     otherwise breaking the test.
+ 
+  -- Sascha Steinbiss <satta at debian.org>  Sat, 13 Aug 2016 20:30:58 +0000
+ 
+ roary (3.6.8+dfsg-1) unstable; urgency=medium
+ 
+   * New upstream release.
+ 
+  -- Sascha Steinbiss <satta at debian.org>  Wed, 03 Aug 2016 08:55:05 +0000
+ 
+ roary (3.6.6+dfsg-1) unstable; urgency=medium
+ 
+   * New upstream release.
+ 
+  -- Sascha Steinbiss <satta at debian.org>  Tue, 26 Jul 2016 09:02:02 +0000
+ 
+ roary (3.6.5+dfsg-1) unstable; urgency=medium
+ 
+   * New upstream release.
+ 
+  -- Sascha Steinbiss <satta at debian.org>  Fri, 22 Jul 2016 08:32:03 +0000
+ 
+ roary (3.6.4+dfsg-1) unstable; urgency=medium
+ 
+   * New upstream release.
+ 
+  -- Sascha Steinbiss <satta at debian.org>  Sun, 10 Jul 2016 17:17:39 +0000
+ 
 +roary (3.6.3+dfsg-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Afif Elghraoui <afif at debian.org>  Sat, 09 Jul 2016 14:35:50 -0700
 +
  roary (3.6.3+dfsg-1) unstable; urgency=medium
  
    * New upstream release.

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roary.git