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<h3>
Andreas Tille 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/324f940b21e71c37be68fed3976906c5f4734c37">324f940b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-14T17:23:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Only 6 tests for Hyphy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/commit/9ec02d7276beb8750240be59f24ae4eb2d8eda63">9ec02d72</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-14T17:25:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/commit/1fc7b6f4ac99f384370299883cc7401db41f6db2">1fc7b6f4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-14T17:25:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/commit/a28463accab2f407a83b3229b8cf833c7eaedde9">a28463ac</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-14T17:25:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/commit/aeea3ff7ca24aedfe09e39ff1113158d9ab6f624">aeea3ff7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-14T17:30:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">skip phyml test at all
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/commit/def8d9213925d21668e7a7d32266c47b176a2556">def8d921</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-14T17:57:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix Homepage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/commit/f7497cd6a3eaba5aa5e1b62fac68d09ff41ef829">f7497cd6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-14T18:07:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/commit/5d3bb7787a78539fc186efbae15742c2eedfb00f">5d3bb778</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-14T18:32:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Lintian-override for script-with-language-extension
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/commit/cf6bb84982d2ab0258bec07eea6c0f954ce556d1">cf6bb849</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-14T18:34:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#94b3bb3cb1cdde1ec869243a8fc9cbd2fbc9e87d">
<span class="new-file">
+
debian/bioperl-run.lintian-overrides
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#2fe82977bfb005c69ac844f159323fbb3c1634a3">
<span class="deleted-file">
−
debian/patches/adjust_bowtie_tests.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#c11bb3787b73deb58b86299e579e1a6352f43b07">
debian/patches/hyphy.patch
</a>
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<li class="file-stats">
<a href="#24e36b085f4ea642c8ae59bb011c7e8f2b64805b">
debian/patches/skip_tests_for_phyml.patch
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</li>
<li class="file-stats">
<a href="#aa73105d9073dccc64c5e475f16540de3a1b7c1e">
<span class="deleted-file">
−
debian/patches/skip_tests_for_samtools.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="94b3bb3cb1cdde1ec869243a8fc9cbd2fbc9e87d">
<a href="https://salsa.debian.org/med-team/bioperl-run/compare/6cb42cfaddea09d2bd906ed1e9f6928d7df609e8...cf6bb84982d2ab0258bec07eea6c0f954ce556d1#94b3bb3cb1cdde1ec869243a8fc9cbd2fbc9e87d"><strong>debian/bioperl-run.lintian-overrides</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">bioperl-run: script-with-language-extension usr/bin/bp_bioperl_application_installer.pl</span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">bioperl-run: script-with-language-extension usr/bin/bp_multi_hmmsearch.pl</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">bioperl-run: script-with-language-extension usr/bin/bp_panalysis.pl</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">bioperl-run: script-with-language-extension usr/bin/bp_papplmaker.pl</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">bioperl-run: script-with-language-extension usr/bin/bp_run_neighbor.pl</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">bioperl-run: script-with-language-extension usr/bin/bp_run_protdist.pl</span></pre>
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</table>
<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bioperl-run/compare/6cb42cfaddea09d2bd906ed1e9f6928d7df609e8...cf6bb84982d2ab0258bec07eea6c0f954ce556d1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">bioperl-run (1.7.2-4) <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">bioperl-run (1.7.2-4) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="3" 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">
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<td class="diff-line-num new_line" data-linenumber="3" 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * (Build-)Depends: ncoils</span>
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<td class="diff-line-num old_line" data-linenumber="4" 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">
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<td class="diff-line-num new_line" data-linenumber="4" 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">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * do not run tests parallel to get sensibly sorted output</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Allow MPI oversubscription (as in phyml build since phyml caused</span>
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<td class="diff-line-num old_line" data-linenumber="6" 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">
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<td class="diff-line-num new_line" data-linenumber="6" 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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> problems inside build time tests)</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> This is also not reliable - skip phyml test at all</span>
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<td class="diff-line-num new_line" data-linenumber="8" 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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> Closes: #906337</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * debhelper 11</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Fix Homepage</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Lintian-override for script-with-language-extension</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 14 Sep 2018 <span class="idiff left right">13:22:55</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 14 Sep 2018 <span class="idiff left right">20:10:08</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">bioperl-run (1.7.2-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/bioperl-run/compare/6cb42cfaddea09d2bd906ed1e9f6928d7df609e8...cf6bb84982d2ab0258bec07eea6c0f954ce556d1#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bioperl-run/compare/6cb42cfaddea09d2bd906ed1e9f6928d7df609e8...cf6bb84982d2ab0258bec07eea6c0f954ce556d1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -5,7 +5,7 @@ Uploaders: Charles Plessy <plessy@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-perl</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">0</span>)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1~</span>)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Build-Depends-Indep: perl,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libmodule-build-perl,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> bioperl,</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">@@ -48,10 +48,10 @@ Build-Depends-Indep: perl,</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> wise,</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"># Needed for the network tests:</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> libwww-perl</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.3</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/git/debian-med/bioperl-run.git</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/bioperl-run.git</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">Homepage: http<span class="idiff left right">://search.cpan.org/dist/BioPerl-Run/</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/bioperl-run</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/bioperl-run.git</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Homepage: http<span class="idiff left right">s://metacpan.org/release/BioPerl-Run</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Package: bioperl-run</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">Architecture: all</span>
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<li id="2fe82977bfb005c69ac844f159323fbb3c1634a3">
<a href="https://salsa.debian.org/med-team/bioperl-run/compare/6cb42cfaddea09d2bd906ed1e9f6928d7df609e8...cf6bb84982d2ab0258bec07eea6c0f954ce556d1#2fe82977bfb005c69ac844f159323fbb3c1634a3"><strong>debian/patches/adjust_bowtie_tests.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: adjust expected test output, bowtie-1.2.1+ returns 2000 processed</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">reads instead of 1000</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">From: Alex Mestiashvili <mailatgoogl@gmail.com></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/t/Bowtie.t</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/t/Bowtie.t</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -185,14 +185,14 @@</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> ok $bowtiefac->_run( -ind => $refseq,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> -seq => $rda1, -seq2 => $rda2 ), "read paired fasta sequence";</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success");</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ like($bowtiefac->stderr, qr/reads processed: 2000/, "bowtie success");</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> $bowtiefac->reset_parameters( -fasta => 0 );</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> $bowtiefac->set_parameters( -fastq => 1 );</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> ok $bowtiefac->_run( -ind => $refseq,</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> -seq => $rdq1, -seq2 => $rdq2 ), "read paired fastq sequence";</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success");</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ like($bowtiefac->stderr, qr/reads processed: 2000/, "bowtie success");</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> # test single</span></pre>
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<a href="https://salsa.debian.org/med-team/bioperl-run/compare/6cb42cfaddea09d2bd906ed1e9f6928d7df609e8...cf6bb84982d2ab0258bec07eea6c0f954ce556d1#c11bb3787b73deb58b86299e579e1a6352f43b07"><strong>debian/patches/hyphy.patch</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">@@ -17,7 +17,7 @@ Description: Hyphy</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> BEGIN {</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> use Bio::Root::Test;</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- test_begin(-tests => 10,</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ test_begin(-tests => <span class="idiff left right">9</span>,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ test_begin(-tests => <span class="idiff left right">6</span>,</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> -requires_module =>'IO::String');</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> use_ok('Bio::Tools::Run::Phylo::Hyphy::SLAC');</span>
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<a href="https://salsa.debian.org/med-team/bioperl-run/compare/6cb42cfaddea09d2bd906ed1e9f6928d7df609e8...cf6bb84982d2ab0258bec07eea6c0f954ce556d1#24e36b085f4ea642c8ae59bb011c7e8f2b64805b"><strong>debian/patches/skip_tests_for_phyml.patch</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">@@ -35,7 +35,7 @@ Description: Somehow there are issues to initialise openmpi, but beside these wa</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> *** on a NULL communicator</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> *** and potentially your MPI job)</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> [hostname:2001] Local abort before MPI_INIT completed <span class="idiff left right">completed </span>successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> [hostname:2001] Local abort before MPI_INIT completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> .</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/t/Phyml.t</span></span>
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<li id="aa73105d9073dccc64c5e475f16540de3a1b7c1e">
<a href="https://salsa.debian.org/med-team/bioperl-run/compare/6cb42cfaddea09d2bd906ed1e9f6928d7df609e8...cf6bb84982d2ab0258bec07eea6c0f954ce556d1#aa73105d9073dccc64c5e475f16540de3a1b7c1e"><strong>debian/patches/skip_tests_for_samtools.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Last-Update: Fri, 16 Dec 2016 09:17:37 +0100</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Description: May be this is just a result of samtools incompatibilities</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> ------------- EXCEPTION -------------</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">MSG: /usr/bin/samtools call crashed: There was a problem running /usr/bin/samtools : [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">Usage: samtools sort [options...] [in.bam]</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">Options:</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> -l INT Set compression level, from 0 (uncompressed) to 9 (best)</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> -n Sort by read name</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> -o FILE Write final output to FILE rather than standard output</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> -T PREFIX Write temporary files to PREFIX.nnnn.bam</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> -@, --threads INT</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> Set number of sorting and compression threads [1]</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> --input-fmt-option OPT[=VAL]</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> Specify a single input file format option in the form</span>
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<td class="diff-line-num old old_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> of OPTION or OPTION=VALUE</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> -O, --output-fmt FORMAT[,OPT[=VAL]]...</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">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> Specify output format (SAM, BAM, CRAM)</span>
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<td class="diff-line-num old old_line" data-linenumber="20" 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">
20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> --output-fmt-option OPT[=VAL]</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> Specify a single output file format option in the form</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> of OPTION or OPTION=VALUE</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> --reference FILE</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> Reference sequence FASTA FILE [null]</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">STACK Bio::Tools::Run::WrapperBase::_run /build/bioperl-run-1.6.9/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:1033</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff">STACK Bio::Tools::Run::Samtools::run /build/bioperl-run-1.6.9/blib/lib/Bio/Tools/Run/Samtools.pm:176</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff">STACK toplevel t/Samtools.t:103</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> -------------------------------------</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/t/Samtools.t</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/t/Samtools.t</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,7 +10,7 @@ BEGIN {</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> # '..' for debugging from .t file</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> unshift @INC, $home;</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> use Bio::Root::Test;</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- test_begin(-tests => 40,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ test_begin(-tests => 37,</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> -requires_modules => [qw(IPC::Run Bio::Tools::Run::Samtools)]);</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -65,8 +65,8 @@ is_deeply( $samt->{_options}->{_prefixes</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"> is_deeply( $samt->{_options}->{_params}, </span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> [qw( command refseq map_qcap ref_list site_list theta n_haplos exp_hap_diff indel_prob )],</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> "commands filtered by prefix");</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-is( join(' ', @{$samt->_translate_params}),</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "pileup -T 0.05 -f my.fas", "translate params" );</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#is( join(' ', @{$samt->_translate_params}),</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# "pileup -T 0.05 -f my.fas", "translate params" ); # should not be tested - result are simply swapped parameters: 'pileup -f my.fas -T 0.05'</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"> my $new_bam = Bio::Tools::Run::Samtools->new(</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> -command => 'merge',</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -100,10 +100,10 @@ SKIP : {</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> ok -B $tmpfiles{rtbamfile}, "bam file present and binary";</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> ok $samt = Bio::Tools::Run::Samtools->new( -command => 'sort' ), 'bam sort factory';</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ok $samt->run( -bam => $tmpfiles{rtbamfile}, -pfx => 'sorted_bam'), 'sort bam file';</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # ok $samt->run( -bam => $tmpfiles{rtbamfile}, -pfx => 'sorted_bam'), 'sort bam file'; # Probably changed samtools interface</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"> ok $samt = Bio::Tools::Run::Samtools->new( -command => 'index' ), 'bam index factory';</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ok $samt->run( -bam => 'sorted_bam', -out => $tmpfiles{bai}), 'make bam index';</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # ok $samt->run( -bam => 'sorted_bam', -out => $tmpfiles{bai}), 'make bam index'; # samtools index: failed to open "sorted_bam": No such file or directory</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> ok -B $tmpfiles{bai}, 'bai file present and binary';</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"> unlink('sorted_bam');</span></pre>
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<a href="https://salsa.debian.org/med-team/bioperl-run/compare/6cb42cfaddea09d2bd906ed1e9f6928d7df609e8...cf6bb84982d2ab0258bec07eea6c0f954ce556d1#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">@@ -10,8 +10,11 @@ NOT_SUPPORTED_TESTS=Blat \</td>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> Eponine \</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> Glimmer2 \</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> Gumby \</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> RepeatMasker</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> RepeatMasker \</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Phyml \</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Hyphy</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"># fpr exclusion of Phyml and Hyphy tests see bug #906337</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># Cap3 - some sensible tests seem to run despite this is not packaged</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># The following tests should work but are missing to be packaged BioPerl modules</span>
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