[med-svn] [bowtie2] 01/01: remove non-free build-dep, skip 'sim' tests

[Sascha Steinbiss]

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

satta pushed a commit to branch master
in repository bowtie2.

commit 84c7efeaabd6245f7222f01a8946e7f03c6148e4
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Wed Jan 25 15:51:58 2017 +0100

    remove non-free build-dep, skip 'sim' tests
---
 debian/changelog                                        | 17 +++++++++++++++++
 debian/control                                          |  3 +--
 ...ip_test_requiring_non-free_libmath-random-perl.patch | 15 ++++++++++-----
 3 files changed, 28 insertions(+), 7 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 17f95ee..4557b84 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,20 @@
+bowtie2 (2.3.0-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+
+  [ Sascha Steinbiss ]
+  * Skip tests involving simulated reads to avoid use of non-free build-dep
+    libmath-random-perl again.
+    Closes: #852546
+
+  [ Alexandre Mestiashvili ]
+  * Add patch suppressing -Wmisleading-indentation warnings.
+
+  [ Steffen Moeller ]
+  * Adjust EDAM annotations.
+
+ -- Sascha Steinbiss <satta at debian.org>  Wed, 25 Jan 2017 14:28:58 +0100
+
 bowtie2 (2.3.0-1) unstable; urgency=medium
 
   * Team upload.
diff --git a/debian/control b/debian/control
index a6beb02..7859b98 100644
--- a/debian/control
+++ b/debian/control
@@ -10,8 +10,7 @@ Build-Depends: debhelper (>= 10),
                libtbb-dev,
                python,
                liblocal-lib-perl,
-               libtest-deep-perl,
-               libmath-random-perl
+               libtest-deep-perl
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bowtie2.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/bowtie2.git
diff --git a/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch b/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
index 1500440..feec033 100644
--- a/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
+++ b/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
@@ -15,7 +15,7 @@ Description: Math::Random is in package libmath-random-perl which is
  use Getopt::Long;
  use List::Util qw(max min);
  
-@@ -105,7 +104,6 @@ $rdlen_min = $rdlen_min || 40;    # min
+@@ -105,7 +104,6 @@
  $frag_av   = $frag_av   || 250;   # mean fragment len
  $frag_sd   = $frag_sd   || 45;    # s.d. when drawing frag len from normal dist
  my @fraglens  = ();     # fragment lengths (for paired)
@@ -23,7 +23,7 @@ Description: Math::Random is in package libmath-random-perl which is
  
  if($long) {
  	$nreads = 6000;
-@@ -134,77 +132,15 @@ for(0..length($rf)-1) {
+@@ -134,77 +132,15 @@
  }
  
  print STDERR "Adding microindels...\n";
@@ -101,7 +101,7 @@ Description: Math::Random is in package libmath-random-perl which is
  sub rand_quals($) {
  	my $ret = "";
  	my $upper = (rand() < 0.2 ? 11 : 40);
-@@ -259,61 +195,10 @@ if($paired) {
+@@ -259,61 +195,10 @@
  		}
  		# Possibly reverse complement
  		$fstr = revcomp($fstr) if (int(rand(2)) == 0);
@@ -165,7 +165,7 @@ Description: Math::Random is in package libmath-random-perl which is
  print STDERR "DONE\n";
 --- a/Makefile
 +++ b/Makefile
-@@ -483,13 +483,13 @@ install: all
+@@ -483,13 +483,13 @@
  		cp -f $$file $(DESTDIR)$(bindir) ; \
  	done
  
@@ -183,7 +183,7 @@ Description: Math::Random is in package libmath-random-perl which is
  	eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
  	sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
  
-@@ -500,7 +500,6 @@ perl-deps:
+@@ -500,11 +500,10 @@
  		mkdir .perllib.tmp ; \
  		$$DL http://cpanmin.us | perl - -l $(CURDIR)/.perllib.tmp App::cpanminus local::lib ; \
  		eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
@@ -191,3 +191,8 @@ Description: Math::Random is in package libmath-random-perl which is
  	fi
  
  .PHONY: test
+-test: simple-test random-test
++test: simple-test #random-test
+ 
+ .PHONY: clean
+ clean:

-- 
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