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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/bioperl-run">Debian Med / bioperl-run</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/db05db97ac6d974e0a99fd342114c22f2292a84c">db05db97</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-06T22:28:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: restrict build-deps architectures
hmmer, pftools and infernal are only available on a subset of
architectures, this prevents proper execution of autodep8 autopkgtest
on unsupported architectures. As these components are not mandatory
for execution of bioperl-run, they can be skipped on unsupported
architectures.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/2516d7a62875d10ed8925f15e74e4e1a5ed5f340">2516d7a6</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-06T22:36:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added skip-test-for-kalign.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/2691c904e1798dc1c49467edb94cac633b286054">2691c904</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-06T22:37:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/7d03cd80fba51cd78e9f99768072788ed2b4d08c">7d03cd80</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-01-06T22:46:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#55587278125c83c74b6973aa366a96a213a5a48d">
<span class="new-file">
+
debian/patches/skip-test-for-kalign.patch
</span>
</a>
</li>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/e0217b4d2474d08cdcf70d335f493fdfd0c25659...7d03cd80fba51cd78e9f99768072788ed2b4d08c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bioperl-run (1.7.3-6) unstable; 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"> * d/control: restrict build-dependencies to their supported architectures.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * added skip-test-for-kalign.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org> Wed, 06 Jan 2021 22:38:23 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">bioperl-run (1.7.3-5) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload.</span>
</pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/e0217b4d2474d08cdcf70d335f493fdfd0c25659...7d03cd80fba51cd78e9f99768072788ed2b4d08c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" 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">@@ -33,9 +33,9 @@ Build-Depends-Indep: perl,</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> clustalw,</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> emboss,</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> exonerate,</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> hmmer,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> hmmer<span class="idiff left right"> [any-amd64 any-i386 powerpc ppc64]</span>,</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> hyphy-pt | hyphy-mpi,</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> infernal,</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> infernal<span class="idiff left right"> [any-amd64 any-i386]</span>,</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> kalign,</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> mafft,</span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> muscle,</span>
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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">@@ -54,7 +54,7 @@ Build-Depends-Indep: perl,</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> lagan,</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> pal2nal,</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"># probalign, # too old?</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> pftools,</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> pftools<span class="idiff left right"> [any-amd64]</span>,</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"># Needed for the network tests:</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> libwww-perl</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/e0217b4d2474d08cdcf70d335f493fdfd0c25659...7d03cd80fba51cd78e9f99768072788ed2b4d08c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -14,3 +14,4 @@ remove_tests_for_ensembl.patch</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">skip_tests_for_soap.patch</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">get-overlap.patch</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">alternate-data.patch</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">skip-test-for-kalign.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/e0217b4d2474d08cdcf70d335f493fdfd0c25659...7d03cd80fba51cd78e9f99768072788ed2b4d08c#55587278125c83c74b6973aa366a96a213a5a48d"><strong>debian/patches/skip-test-for-kalign.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: skip last Kalign test</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> This test fails on armhf and ppc64el and prevents migration of bioperl-run to</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> testing. This is either a Kalign bug on these architectures, or a side effect</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> of working with qemu-user-static. Skipping that test buys us some time to</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> investigate further, temporary hopefully.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Last-Update: 2021-01-06</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/t/Kalign.t</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/t/Kalign.t</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -4,7 +4,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> use strict;</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> BEGIN {</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> use Bio::Root::Test;</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- test_begin(-tests => 8);</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ test_begin(-tests => 7);</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> use_ok('Bio::Tools::Run::Alignment::Kalign');</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> use_ok('Bio::AlignIO');</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> use_ok('Bio::SeqIO'); </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">@@ -38,6 +38,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> $aln = $factory->align($seq_array_ref);</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> is $aln->num_sequences, 7;</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> my $s1_perid = $aln->average_percentage_identity;</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- is(int($s1_perid), 42);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #is(int($s1_perid), 42);</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span></pre>
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