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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-biopython">Debian Med / python-biopython</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/8ea33aeba927fcedd13d5fadeefbb467cd4eb01d">8ea33aeb</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-20T18:55:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Sides of #969608 have been addressed
The work around is removed in favor of using the ncbi-blast+ 2.10.1-1
or later.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/13965712a0ac3bc7dc5fd931aab2a4fe669cc203">13965712</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-20T19:31:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated d/changelog accordingly
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/3e9ded594ee9ddf11ba495a349b25f36e4a443a7">3e9ded59</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-20T19:47:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add python3-biopython.lintian-overrides
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/44b723551393105926d04cc3256ca6c50d934fb5">44b72355</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-23T20:39:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: build-dep on ncbi-blast+ >= 2.10.1-2
This version addresses FTBFS on mipsel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/8db760753d61bda00b56e9d6fce04f6a79487f25">8db76075</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-02T23:16:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/changelog a bit more comprehensive, hopefully
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/63ba5cc15fdf74f88bd71ebbfafcbcd3f49e0b50">63ba5cc1</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-02T23:23:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#4f54ae2ba427341e16fce8429f01ffdfa30a8314">
<span class="new-file">
+
debian/python3-biopython.lintian-overrides
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/f4f41aebd08313023b535681e6a1a283b8f9d788...63ba5cc15fdf74f88bd71ebbfafcbcd3f49e0b50#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="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.78</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;"><span class="idiff left right">UNRELEASED</span></span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
</pre>
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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">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.78</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;"><span class="idiff left right">unstable</span></span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
</pre>
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2
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<td class="diff-line-num new_line" data-linenumber="2" 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">
2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="3" 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">
3
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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">DEP3</span> <span class="n" style="color: #333;">description</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">blastdbv4</span><span class="p">-</span><span class="n" style="color: #333;">tests</span><span class="p">-</span><span class="n" style="color: #333;">filter</span><span class="p">-</span><span class="n" style="color: #333;">archs</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">.</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4" 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">
4
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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Removed</span><span class="p">,</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">last</span><span class="p">,</span> <span class="n" style="color: #333;">patch</span> <span class="n" style="color: #333;">working</span> <span class="n" style="color: #333;">around</span> <span class="n" style="color: #333;">makeblastd</span> <span class="n" style="color: #333;">bug</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v5</span><span class="p">.</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5" 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">
5
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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Reviewed</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">forwarded</span> <span class="n" style="color: #333;">patches</span> <span class="n" style="color: #333;">upstream</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">applicable</span><span class="p">.</span></span>
</pre>
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<td class="diff-line-num new old_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="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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Bumped</span> <span class="n" style="color: #333;">build</span> <span class="n" style="color: #333;">requirement</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">ncbi</span><span class="p">-</span><span class="n" style="color: #333;">blast</span><span class="p">+</span> <span class="m" style="color: #099;">2.10.1</span><span class="p">-</span><span class="m" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">greater</span><span class="p">:</span></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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="p">-</span> <span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">building</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">mipsel</span><span class="p">;</span></span>
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<td class="diff-line-num new old_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="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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">-</span> <span class="n" style="color: #333;">removed</span> <span class="n" style="color: #333;">patch</span> <span class="n" style="color: #333;">working</span> <span class="n" style="color: #333;">around</span> <span class="n" style="color: #333;">makeblastdb</span> <span class="n" style="color: #333;">bug</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v5</span><span class="p">,</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">unnecessary</span><span class="p">.</span></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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Cleaned</span> <span class="n" style="color: #333;">up</span> <span class="n" style="color: #333;">patches</span><span class="p">:</span></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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"> <span class="p">-</span> <span class="n" style="color: #333;">added</span> <span class="n" style="color: #333;">DEP3</span> <span class="n" style="color: #333;">description</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">blastdbv4</span><span class="p">-</span><span class="n" style="color: #333;">tests</span><span class="p">-</span><span class="n" style="color: #333;">filter</span><span class="p">-</span><span class="n" style="color: #333;">archs</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">;</span></span>
</pre>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"> <span class="p">-</span> <span class="n" style="color: #333;">reviewed</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">forwarded</span> <span class="n" style="color: #333;">patches</span> <span class="n" style="color: #333;">upstream</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">applicable</span><span class="p">.</span></span>
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6
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="mosel"> <span class="p">--</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">É</span><span class="n" style="color: #333;">tienne</span> <span class="n" style="color: #333;">Mollier</span> <span class="p"><</span><span class="n" style="color: #333;">etienne</span><span class="p">.</span><span class="n" style="color: #333;">mollier</span><span class="p">@</span><span class="n" style="color: #333;">mailoo</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;"><span class="idiff left">Mon</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">14</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Sep</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2020</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">21</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">28</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff right">54</span></span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="p">--</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">É</span><span class="n" style="color: #333;">tienne</span> <span class="n" style="color: #333;">Mollier</span> <span class="p"><</span><span class="n" style="color: #333;">etienne</span><span class="p">.</span><span class="n" style="color: #333;">mollier</span><span class="p">@</span><span class="n" style="color: #333;">mailoo</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;"><span class="idiff left">Fri</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">02</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Oct</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2020</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">23</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">18</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff right">07</span></span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.78</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/f4f41aebd08313023b535681e6a1a283b8f9d788...63ba5cc15fdf74f88bd71ebbfafcbcd3f49e0b50#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">@@ -24,7 +24,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> fasttree <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> mafft <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> muscle <!nocheck>,</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> ncbi-blast+ (>= 2.10.<span class="idiff left right">0-3</span>) <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> ncbi-blast+ (>= 2.10.<span class="idiff left right">1-2</span>) <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> phylip <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> phyml [any-amd64 any-i386] <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> prank <!nocheck>,</span>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/f4f41aebd08313023b535681e6a1a283b8f9d788...63ba5cc15fdf74f88bd71ebbfafcbcd3f49e0b50#4f54ae2ba427341e16fce8429f01ffdfa30a8314"><strong>debian/python3-biopython.lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># This link has been introduced with the resolution of #672407 and might not</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># be as much a concern as if it were an architecture dependent shared object.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">breakout-link usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd -> usr/share/xml/schema/w3c/mathml/dtd/mathml2.dtd</span></pre>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/f4f41aebd08313023b535681e6a1a283b8f9d788...63ba5cc15fdf74f88bd71ebbfafcbcd3f49e0b50#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">@@ -34,15 +34,6 @@ else</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> EXCLUDEARCHamd64=raxml_tool</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"># arm64 virtualized environment, esp. with schroot, may be too constrained for</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"># the memory allocation required by the test_NCBI_BLAST_tools. See #969608</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"># following for more details:</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"># https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">ifeq ($(BUILDARCH),arm64)</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> export BLASTDB_LMDB_MAP_SIZE=20000000000</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"># avoid tests requiring data base connections if no server is running while we are doing the build</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"># This would not trigger a failure but bloats the build log with irrelevant noise</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2</span>
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