Verified Commit 5b82f7d9 authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

allow tests to run on s390x

parent ca149dd0

debian/changelog

+2 −2
Original line number Diff line number Diff line 
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@gmail.com>  Tue, 07 Jan 2020 12:11:17 +0100

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 08 Jan 2020 12:39:33 +0100



bowtie (1.2.3+dfsg-2) unstable; urgency=medium

debian/control

+2 −1
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@@ -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

+8 −19
Original line number Diff line number Diff line
@@ -2,27 +2,16 @@ Author: Michael R. Crusoe <michael.crusoe@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

+1 −1
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@@ -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