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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie">Debian Med / bowtie</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/bowtie/commit/5b82f7d929b1fdc7143f529b9dddee9eb470e946">5b82f7d9</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-01-08T12:39:43+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow tests to run on s390x
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#0a860cdba9fc7bcf6b28c442b89b1e1f2c4add92">
debian/patches/simple-test
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bowtie/commit/5b82f7d929b1fdc7143f529b9dddee9eb470e946#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">bowtie (1.2.3+dfsg-3) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bowtie (1.2.3+dfsg-3) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * `make simple-test` in addition to our own tests</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Remove obsolete fields Contact from debian/upstream/metadata.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> <span class="idiff left right">Tue, 07 Jan 2020 12:11:17</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> <span class="idiff left right">Wed, 08 Jan 2020 12:39:33</span> +0100</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">bowtie (1.2.3+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bowtie/commit/5b82f7d929b1fdc7143f529b9dddee9eb470e946#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +14,8 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> seqan-dev,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libclone-perl,</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> libtest-deep-perl</span>
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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> libtest-deep-perl,</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> libsys-info-perl</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Standards-Version: 4.4.0</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bowtie</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bowtie.git</span>
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<li id="0a860cdba9fc7bcf6b28c442b89b1e1f2c4add92">
<a href="https://salsa.debian.org/med-team/bowtie/commit/5b82f7d929b1fdc7143f529b9dddee9eb470e946#0a860cdba9fc7bcf6b28c442b89b1e1f2c4add92"><strong>debian/patches/simple-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,27 +2,16 @@ Author: Michael R. Crusoe <michael.crusoe@gmail.com></td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: Sys::Info isn't packaged for Debian, so work around it</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie.orig/scripts/test/simple_tests.pl</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie/scripts/test/simple_tests.pl</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -14,8 +14,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> use DNA;</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> use Clone qw(clone);</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> use Test::Deep;</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-use Sys::Info;</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-use Sys::Info::Constants qw( :device_cpu );</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> my $bowtie = "";</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> my $bowtie_build = "";</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -1130,9 +1128,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> while(<FA>) { print $_; }</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> close(FA);</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> if($do_build) {</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my $info = Sys::Info->new;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my $cpu = $info->device('CPU');</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my $nthreads = int(rand($cpu->count || 1)) + 1;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ my $nthreads = 2;</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -1135,7 +1135,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> my $nthreads = int(rand($cpu->count || 1)) + 1;</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> my $build_args = "";</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> $build_args .= " -C " if $color;</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> my $cmd = "$bowtie_build $idx_type --threads $nthreads --quiet --sanity $build_args $fa .simple_tests.tmp";</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="p">@@ -1285,7 +1281,7 @@</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my $cmd = "$bowtie_build $idx_type --threads $nthreads --quiet --sanity $build_args $fa .simple_tests.tmp";</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ my $cmd = "$bowtie_build $idx_type --threads $nthreads --quiet $build_args $fa .simple_tests.tmp";</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> print "$cmd\n";</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> system($cmd);</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> ($? == 0) || die "Bad exitlevel from bowtie-build: $?";</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -1285,7 +1285,7 @@</span></span>
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26
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> my $tmpfafn = ".simple_tests.pl.fa";</span>
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27
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> my $last_ref = undef;</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> foreach my $large_idx (undef,1) {</span>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/5b82f7d929b1fdc7143f529b9dddee9eb470e946#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,7 +45,7 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> make simple-test</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> <span class="idiff left right">unset LD_PRELOAD && </span>make simple-test</span>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> ln -s debian/tests</span>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> unset LD_PRELOAD && sh debian/tests/run-unit-test test_at_build_time</span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> rm -f tests examples[0-9].out</span>
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