[med-svn] [Git][med-team/bowtie][master] allow tests to run on s390x

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / bowtie


Commits:
5b82f7d9 by Michael R. Crusoe at 2020-01-08T12:39:43+01:00
allow tests to run on s390x

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/patches/simple-test
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,11 @@
-bowtie (1.2.3+dfsg-3) UNRELEASED; urgency=medium
+bowtie (1.2.3+dfsg-3) unstable; urgency=medium
 
   * Team upload.
   * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
   * `make simple-test` in addition to our own tests
   * Remove obsolete fields Contact from debian/upstream/metadata.
 
- -- Michael R. Crusoe <michael.crusoe at gmail.com>  Tue, 07 Jan 2020 12:11:17 +0100
+ -- Michael R. Crusoe <michael.crusoe at gmail.com>  Wed, 08 Jan 2020 12:39:33 +0100
 
 bowtie (1.2.3+dfsg-2) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -14,7 +14,8 @@ Build-Depends: debhelper-compat (= 12),
                seqan-dev,
                zlib1g-dev,
                libclone-perl,
-               libtest-deep-perl
+               libtest-deep-perl,
+               libsys-info-perl
 Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/bowtie
 Vcs-Git: https://salsa.debian.org/med-team/bowtie.git


=====================================
debian/patches/simple-test
=====================================
@@ -2,27 +2,16 @@ Author: Michael R. Crusoe <michael.crusoe at gmail.com>
 Description: Sys::Info isn't packaged for Debian, so work around it
 --- bowtie.orig/scripts/test/simple_tests.pl
 +++ bowtie/scripts/test/simple_tests.pl
-@@ -14,8 +14,6 @@
- use DNA;
- use Clone qw(clone);
- use Test::Deep;
--use Sys::Info;
--use Sys::Info::Constants qw( :device_cpu );
- 
- my $bowtie = "";
- my $bowtie_build = "";
-@@ -1130,9 +1128,7 @@
- 	while(<FA>) { print $_; }
- 	close(FA);
- 	if($do_build) {
--		my $info = Sys::Info->new;
--		my $cpu = $info->device('CPU');
--		my $nthreads = int(rand($cpu->count || 1)) + 1;
-+		my $nthreads = 2;
+@@ -1135,7 +1135,7 @@
+ 		my $nthreads = int(rand($cpu->count || 1)) + 1;
  		my $build_args = "";
  		$build_args .= " -C " if $color;
- 		my $cmd = "$bowtie_build $idx_type --threads $nthreads --quiet --sanity $build_args $fa .simple_tests.tmp";
-@@ -1285,7 +1281,7 @@
+-		my $cmd = "$bowtie_build $idx_type --threads $nthreads --quiet --sanity $build_args $fa .simple_tests.tmp";
++		my $cmd = "$bowtie_build $idx_type --threads $nthreads --quiet $build_args $fa .simple_tests.tmp";
+ 		print "$cmd\n";
+ 		system($cmd);
+ 		($? == 0) || die "Bad exitlevel from bowtie-build: $?";
+@@ -1285,7 +1285,7 @@
  my $tmpfafn = ".simple_tests.pl.fa";
  my $last_ref = undef;
  foreach my $large_idx (undef,1) {


=====================================
debian/rules
=====================================
@@ -45,7 +45,7 @@ override_dh_auto_clean:
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-	make simple-test
+	unset LD_PRELOAD && make simple-test
 	ln -s debian/tests
 	unset LD_PRELOAD && sh debian/tests/run-unit-test test_at_build_time
 	rm -f tests examples[0-9].out



View it on GitLab: https://salsa.debian.org/med-team/bowtie/commit/5b82f7d929b1fdc7143f529b9dddee9eb470e946

-- 
View it on GitLab: https://salsa.debian.org/med-team/bowtie/commit/5b82f7d929b1fdc7143f529b9dddee9eb470e946
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200108/40000bf2/attachment-0001.html>