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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/febb287152fd95151afd98359b3bc67b765f6363">febb2871</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-07-14T09:55:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: add myself to uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/6e43726384f58ec6ad576a7d046da40e4507573d">6e437263</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-07-14T10:11:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/watch: fix broken link to github & fix mangling
URL scanning and version mangling needed adjustment, compared to
regular github packages, mostly because of the unusual tagging
convention:
release-$MAJOR-$MINOR-$PATCHLEVEL
instead of more common:
v$MAJOR.$MINOR.$PATCHLEVEL
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/fa50a1aa04eb9fb24a877c13c6c601a5223a5731">fa50a1aa</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-07-14T11:14:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add fix-whatis-entries.patch
This patch addresses a couple of bad-whatis-entry lintian warnings.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/2167fc731d80fe5a88e9c45712d87fcc01beefc1">2167fc73</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-07-14T11:22:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adjust lintian override for former script
The script in question is bp_bioperl_application_installer.pl, but it
does not seem to be provided upstream anymore, so the override is now
unjustified.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/f733d45d712aa5f747a489037f802b3187feab5a">f733d45d</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-07-14T11:38:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add unscramble-erpin.patch
This fixes a national-encoding lintian warning, and maybe a couple of
typos in the Perl module documentation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/5a149c51e3884594f66bc890476a15a580941edf">5a149c51</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-07-14T11:55:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix-whatis-entries.patch: dep3 header
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/8c8415411ed6bd33d406be025ac1f495448ecc5c">8c841541</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-07-14T12:16:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add fix-pod-conversion.patch
This patch addresses the lintian warning pod-conversion-message
affecting the module Bio::DB::SoapEUtilities::Result.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/d68f33e89b89c7486fc86a5c8fcbb84398bb521c">d68f33e8</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-07-14T12:18:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#94b3bb3cb1cdde1ec869243a8fc9cbd2fbc9e87d">
debian/bioperl-run.lintian-overrides
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#71c65931d597dbe24ae771740a8ff238e8011de1">
<span class="new-file">
+
debian/patches/fix-pod-conversion.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#1e71d903ee43f08a861dc35e5afa99e694851faf">
<span class="new-file">
+
debian/patches/fix-whatis-entries.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#7ef2369251ea5913b7d8fdb6ebcb8cae0b8ed9b0">
<span class="new-file">
+
debian/patches/unscramble-erpin.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="94b3bb3cb1cdde1ec869243a8fc9cbd2fbc9e87d">
<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d03cd80fba51cd78e9f99768072788ed2b4d08c...d68f33e89b89c7486fc86a5c8fcbb84398bb521c#94b3bb3cb1cdde1ec869243a8fc9cbd2fbc9e87d"><strong>debian/bioperl-run.lintian-overrides</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
</pre>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<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>
</pre>
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<td class="old_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">bioperl-run: script-with-language-extension usr/bin/bp_multi_hmmsearch.pl</span>
</pre>
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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">bioperl-run: script-with-language-extension usr/bin/bp_panalysis.pl</span>
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<td class="old_line diff-line-num" data-linenumber="5" 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="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">bioperl-run: script-with-language-extension usr/bin/bp_papplmaker.pl</span>
</pre>
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</table>
<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d03cd80fba51cd78e9f99768072788ed2b4d08c...d68f33e89b89c7486fc86a5c8fcbb84398bb521c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bioperl-run (1.7.3-7) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * d/watch: fix broken link to github and adjust version mangling to fit</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> upstream's tagging convention (tag "release-x-y-z" for version "x.y.z")</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * adjust lintian override on bp_bioperl_application_installer.pl file</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> extension, which is not provided anymore</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * add fix-whatis-entries.patch; fixes lintian warnings on bad-whatis-entry</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> by providing a convenient description in the NAME field where needed</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * add unscramble-erpin.patch; fixes a kind of typo in ERPIN.pm documentation,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> flagged by lintian warning national-encoding</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * add fix-pod-conversion.patch; address the lintian warning</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> pod-conversion-message affecting Bio::DB::SoapEUtilities::Result.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * d/control: add myself to uploaders</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="LC15" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> Wed, 14 Jul 2021 11:40:03 +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 (1.7.3-6) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d03cd80fba51cd78e9f99768072788ed2b4d08c...d68f33e89b89c7486fc86a5c8fcbb84398bb521c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: bioperl-run</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Charles Plessy <plessy@debian.org>,</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Étienne Mollier <emollier@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-perl</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Priority: optional</span>
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<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d03cd80fba51cd78e9f99768072788ed2b4d08c...d68f33e89b89c7486fc86a5c8fcbb84398bb521c#71c65931d597dbe24ae771740a8ff238e8011de1"><strong>debian/patches/fix-pod-conversion.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix lintian warning about pod-conversion-message</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-07-14</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC6" 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="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/DB/SoapEUtilities/Result.pm</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/DB/SoapEUtilities/Result.pm</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -134,10 +134,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> =back</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"><span class="gd" style="color: #000; background-color: #fdd;">-=over</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> Other methods</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+=over</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;">+</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> =item accessors()</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"> An array of available data accessor names. This</span></pre>
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<li id="1e71d903ee43f08a861dc35e5afa99e694851faf">
<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d03cd80fba51cd78e9f99768072788ed2b4d08c...d68f33e89b89c7486fc86a5c8fcbb84398bb521c#1e71d903ee43f08a861dc35e5afa99e694851faf"><strong>debian/patches/fix-whatis-entries.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix whatis entries in multiple Bio Perl modules</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-07-14</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC6" 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="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/Tools/Run/Alignment/Blat.pm</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/Tools/Run/Alignment/Blat.pm</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> =head1 NAME</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"><span class="gd" style="color: #000; background-color: #fdd;">-Bio::Tools::Run::Alignment::Blat </span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Bio::Tools::Run::Alignment::Blat - wrapper modules for the Blat program</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> =head1 SYNOPSIS</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;">--- bioperl-run.orig/lib/Bio/Tools/Run/Alignment/Exonerate.pm</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;">+++ bioperl-run/lib/Bio/Tools/Run/Alignment/Exonerate.pm</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> =head1 NAME</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Bio::Tools::Run::Alignment::Exonerate</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Bio::Tools::Run::Alignment::Exonerate - wrapper for the exonerate alignment program</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> =head1 SYNOPSIS</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 class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/Tools/Run/Phylo/FastTree.pm</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/Tools/Run/Phylo/FastTree.pm</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> =head1 NAME</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Bio::Tools::Run::Phylo::FastTree</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Bio::Tools::Run::Phylo::FastTree - Bio::Tree getter from DNA alignment</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> =head1 SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="p">@@ -10,7 +10,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> =head1 NAME</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;">-Bio::Tools::Run::Phylo::Phylip::PhylipConf</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Bio::Tools::Run::Phylo::Phylip::PhylipConf - manage Phylip menu configuration</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> =head1 SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/Tools/Run/Phylo/Raxml.pm</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/Tools/Run/Phylo/Raxml.pm</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> =head1 NAME</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;">-Bio::Tools::Run::Phylo::Raxml</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;">+Bio::Tools::Run::Phylo::Raxml - Bio::Tree getter from DNA alignment through raxml</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> =head1 SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/Tools/Run/Primate.pm</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/Tools/Run/Primate.pm</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -11,8 +11,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> =head1 NAME</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Wrapper for Primate, Guy Slater's near exact match finder for short sequence</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-tags.</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Bio::Tools::Run::Primate - wrapper for Primate, Guy Slater's near exact match</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+finder for short sequence tags.</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> =head1 SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/Tools/Run/Prints.pm</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/Tools/Run/Prints.pm</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> =head1 NAME</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Bio::Tools::Run::Prints </span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Bio::Tools::Run::Prints - PRINTS fingerprint identification algorithm</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> =head1 SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/Tools/Run/Profile.pm</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/Tools/Run/Profile.pm</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> =head1 NAME</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Bio::Tools::Run::Profile</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Bio::Tools::Run::Profile - wrapper for the pfscan program</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> =head1 SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/Tools/Run/Signalp.pm</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/Tools/Run/Signalp.pm</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="p">@@ -9,7 +9,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> =head1 NAME</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Bio::Tools::Run::Signalp</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Bio::Tools::Run::Signalp - wrapper for the Signalp program</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> =head1 SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/Tools/Run/TribeMCL.pm</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/Tools/Run/TribeMCL.pm</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="p">@@ -12,7 +12,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> =head1 NAME</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Bio::Tools::Run::TribeMCL</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Bio::Tools::Run::TribeMCL - Markov method for CLustering proteins</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> =head1 SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bioperl-run.orig/lib/Bio/Tools/Run/Vista.pm</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bioperl-run/lib/Bio/Tools/Run/Vista.pm</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="p">@@ -10,9 +10,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> =head1 NAME</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Bio::Tools::Run::Vista</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Wrapper for Vista</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Bio::Tools::Run::Vista - Wrapper for Vista</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> =head1 SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d03cd80fba51cd78e9f99768072788ed2b4d08c...d68f33e89b89c7486fc86a5c8fcbb84398bb521c#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">@@ -15,3 +15,6 @@ skip_tests_for_soap.patch</td>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">get-overlap.patch</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">alternate-data.patch</span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">skip-test-for-kalign.patch</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">fix-whatis-entries.patch</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">unscramble-erpin.patch</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">fix-pod-conversion.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d03cd80fba51cd78e9f99768072788ed2b4d08c...d68f33e89b89c7486fc86a5c8fcbb84398bb521c#7ef2369251ea5913b7d8fdb6ebcb8cae0b8ed9b0"><strong>debian/patches/unscramble-erpin.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: replace exotic character by seemingly correct plain old dash '-'</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> A couple of ISO-8859 characters trigger the lintian warning national-encoding.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> Looking into details, it seems that a plain old dash '-' got replaced by a</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> more exotic character 'Ð'. This patch brings the '-' in the description of</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> the affected Perl module ERPIN.pm.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Last-Update: 2021-07-14</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/lib/Bio/Tools/Run/ERPIN.pm</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/lib/Bio/Tools/Run/ERPIN.pm</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -31,7 +31,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> 'cutoff' => [0, 10, 15, 20]</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> ]</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> # or use a simple string...</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;">- #strategy => 'umask 4 add 5 -nomask -cutoff 0 10 15',</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;">+ #strategy => '-umask 4 -add 5 -nomask -cutoff 0 10 15',</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> pcw => 100</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></pre>
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<a href="https://salsa.debian.org/med-team/bioperl-run/-/compare/7d03cd80fba51cd78e9f99768072788ed2b4d08c...d68f33e89b89c7486fc86a5c8fcbb84398bb521c#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">opts="uversionmangle=s/[-_]/./g" \</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">https://github.com/bioperl/bioperl-run/releases .*/archive/release-(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)$</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">opts="uversionmangle=s/^release-\(.*\)$/\1/;s/[-_]/./g" \</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> https://github.com/bioperl/bioperl-run/tags \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> (?:.*?/)?release-v?(\d[\d-]*)\.tar\.gz debian uupdate</span>
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4
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"># http://search.cpan.org/dist/BioPerl-Run/ .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$</span></pre>
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