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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/prime-phylo">Debian Med / prime-phylo</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/prime-phylo/commit/d125b9327cbb9f33b3c364788bc9ac1a40945894">d125b932</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T13:47:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Suggests: s/python-biopython/python3-biopython/
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prime-phylo/commit/316cc2923092851b9e3a675bba14bb5f5ca08589">316cc292</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T13:48:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prime-phylo/commit/9a21439bd92c286e5aaa776b7ed902c81f053d59">9a21439b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T13:48:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prime-phylo/commit/95dcdadbfe3a5ee68f6af2bdf39871d24b340a3b">95dcdadb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T13:48:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prime-phylo/commit/a622999aa7595ed89cf6fbd438e4158fca9c96e3">a622999a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T13:49:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete field Contact from debian/upstream/metadata.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prime-phylo/commit/2af05ca3d949aa7e740d6cfc9303720bec2c73cc">2af05ca3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T13:55:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/prime-phylo/compare/8fbdf1b1e07b6ee03deb4ed0c316072fa96b1937...2af05ca3d949aa7e740d6cfc9303720bec2c73cc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">prime-phylo (1.0.11-8) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Suggests: s/python-biopython/python3-biopython/</span>
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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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debhelper-compat 12</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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Trim trailing whitespace.</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"> * Remove obsolete field Contact from debian/upstream/metadata.</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" 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> Wed, 11 Dec 2019 14:49:07 +0100</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext">prime-phylo (1.0.11-7) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> [ Giovanni Mascellani ]</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/prime-phylo/compare/8fbdf1b1e07b6ee03deb4ed0c316072fa96b1937...2af05ca3d949aa7e740d6cfc9303720bec2c73cc#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/prime-phylo/compare/8fbdf1b1e07b6ee03deb4ed0c316072fa96b1937...2af05ca3d949aa7e740d6cfc9303720bec2c73cc#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Uploaders: Erik Sjolund <erik.sjolund@gmail.com>,</td>
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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">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> gengetopt,</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> cmake,</span>
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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"> libblas-dev,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@ Build-Depends: debhelper (>= 11~),</td>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> libboost-mpi-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="19" 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">
19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libboost-serialization-dev,</span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> zlib1g-dev</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2</span>.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.1</span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/prime-phylo</span>
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<td class="diff-line-num old_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/prime-phylo.git</span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Homepage: http://prime.sbc.su.se</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,7 +33,7 @@ Suggests: njplot,</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> muscle,</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> probalign,</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> mafft,</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> python-biopython,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-biopython,</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> mrbayes,</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> phyml,</span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> raxml</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/prime-phylo/compare/8fbdf1b1e07b6ee03deb4ed0c316072fa96b1937...2af05ca3d949aa7e740d6cfc9303720bec2c73cc#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">@@ -24,5 +24,3 @@ override_dh_auto_configure:</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">override_dh_makeshlibs:</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> dh_makeshlibs -pprime-phylo -Xprime-phylo.so -Xprime-phylo-sfile.so</span></pre>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/prime-phylo/compare/8fbdf1b1e07b6ee03deb4ed0c316072fa96b1937...2af05ca3d949aa7e740d6cfc9303720bec2c73cc#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Contact: Lars Arvestad <arve@csc.kth.se></span>
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2
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Author: Åkerborg, Ö. and Sennblad, B. and Arvestad, L. and Lagergren, J.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Simultaneous Bayesian gene tree reconstruction and reconciliation analysis</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Journal: Proceedings of the National Academy of Sciences</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Year: 2009</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Volume: 106</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Number: 14</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> Pages: 5714-5719</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> DOI: 10.1073/pnas.0806251106</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> PMID: 19299507</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667006/</span>
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<td class="diff-line-num old old_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> eprint: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667006/pdf/zpq5714.pdf</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> <span class="idiff left right"> </span>Author: Åkerborg, Ö. and Sennblad, B. and Arvestad, L. and Lagergren, J.</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right"> </span>Title: ></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <span class="idiff left right"> </span>Simultaneous Bayesian gene tree reconstruction and reconciliation analysis</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <span class="idiff left right"> </span>Journal: Proceedings of the National Academy of Sciences</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right"> </span>Year: 2009</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right"> </span>Volume: 106</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> <span class="idiff left right"> </span>Number: 14</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right"> </span>Pages: 5714-5719</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right"> </span>DOI: 10.1073/pnas.0806251106</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right"> </span>PMID: 19299507</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> <span class="idiff left right"> </span>URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667006/</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <span class="idiff left right"> </span>eprint: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667006/pdf/zpq5714.pdf</span>
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15
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Registry:</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: OMICtools</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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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: OMICS_29591</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: bio.tools</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="plaintext"> <span class="idiff left right"> </span>Entry: PrIME</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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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: SciCrunch</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: NA</span></pre>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">- Name: OMICtools</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Entry: OMICS_29591</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">- Name: bio.tools</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> Entry: PrIME</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">- Name: SciCrunch</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Entry: NA</span></pre>
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