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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/5eb9ae4904eb83199746d29679ed33be57bfaecd">5eb9ae49</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-05T18:35:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revert "routine-update: Ready to upload to unstable"
This reverts commit 632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/78a0389ac88f1c7386e855730ef607251aa5ec06">78a0389a</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-05T18:43:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/rules: erased makeblastdb override
should be properly handled by all architectures now.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/b1bfd6c8fab08b96b1335e2d41da7ae6b15b0b29">b1bfd6c8</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-05T18:44:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/tests/run-unit-tests: removed makeblastdb override
this should be properly handled on all architectures, including
mipsel, since ncbi-blast+ 2.10.1-3. Also, the override that was still
present in that file could have been a source of autopkgtest failures.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/4046757bdf037cf458bcd39b3e3d6f1eaf05c04c">4046757b</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-05T18:49:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: bump requirement to ncbi-blast+ 2.10.1-3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/2b9339e183b1d4999bbeaddab1b5d92184594c98">2b9339e1</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-05T19:26:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated d/changelog to reflect changes appropriately
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<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="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc...2b9339e183b1d4999bbeaddab1b5d92184594c98#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;">3</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>
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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;">3</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>
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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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"></span>
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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;">mpisel</span> <span class="n" style="color: #333;">build</span> <span class="n" style="color: #333;">still</span> <span class="n" style="color: #333;">failing</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">buildd</span> <span class="p">(</span><span class="n" style="color: #333;">host</span> <span class="n" style="color: #333;">arch</span> <span class="n" style="color: #333;">mips64el</span><span class="p">,</span> <span class="n" style="color: #333;">schroot</span> <span class="n" style="color: #333;">mipsel</span><span class="p">)</span></span>
</pre>
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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;">overred</span> <span class="n" style="color: #333;">makeblastdb</span> <span class="n" style="color: #333;">memory</span> <span class="n" style="color: #333;">allocation</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">arch</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">build</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">test</span><span class="p">;</span></span>
</pre>
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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;">updated</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">-</span><span class="n" style="color: #333;">unit</span><span class="p">-</span><span class="n" style="color: #333;">test</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">reflect</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">change</span><span class="p">.</span></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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Bumped</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="k" style="font-weight: 600;">version</span> <span class="n" style="color: #333;">requirement</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">2.10.1</span><span class="p">-</span><span class="m" style="color: #099;">3</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;">Made</span> <span class="n" style="color: #333;">sure</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">-</span><span class="n" style="color: #333;">unit</span><span class="p">-</span><span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">did</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">attempt</span> <span class="n" style="color: #333;">memory</span> <span class="n" style="color: #333;">allocation</span> <span class="n" style="color: #333;">override</span></span>
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6
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<td class="diff-line-num new_line" 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">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"></span>
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<td class="diff-line-num new_line old" data-linenumber="6" 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="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;">S<span class="idiff left">un</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">04</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">22</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">45</span></span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" 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;">S<span class="idiff left">at</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">03</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">10</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">34</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff right">12</span></span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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8
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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="mosel"></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="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;">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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"></span>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc...2b9339e183b1d4999bbeaddab1b5d92184594c98#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+ (>= 2.10.1-<span class="idiff left right">2</span>) <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> ncbi-blast+ (>= 2.10.1-<span class="idiff left right">3</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,7 +58,7 @@ Depends: ${python3:Depends},</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> python3-reportlab</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">Recommends: python-biopython-doc (= ${source:Version}),</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> ncbi-blast+ (>= 2.10.<span class="idiff left right">0</span>-3)</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> ncbi-blast+ (>= 2.10.<span class="idiff left right">1</span>-3)</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">Suggests: python3-tk,</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> bwa,</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> clustalo,</span>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc...2b9339e183b1d4999bbeaddab1b5d92184594c98#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">@@ -34,14 +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"># virtualized environment, esp. with schroot, may be too constrained for the</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"># memory allocation required by the test_NCBI_BLAST_tools. See #969608 for</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"># 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 ($(BUILD_ARCH),mipsel)</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> export BLASTDB_LMDB_MAP_SIZE = 3000000000</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="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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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc...2b9339e183b1d4999bbeaddab1b5d92184594c98#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -27,15 +27,6 @@ if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" != "amd64" ]; then</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> test_BWA_tool.py</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># virtualized environment, esp. with schroot, may be too constrained for the</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># memory allocation required by the test_NCBI_BLAST_tools. See #969608 for</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># more details:</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>dpkg-architecture <span class="nt" style="color: #000080;">-qDEB_BUILD_ARCH</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"mipsel"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">BLASTDB_LMDB_MAP_SIZE</span><span class="o" style="font-weight: 600;">=</span>3000000000</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">export </span>BLASTDB_LMDB_MAP_SIZE</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># execute tests</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># in the Debian package dialign it is not needed to set DIALIGN2_DIR but the</span></span>
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