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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/rnahybrid">Debian Med / rnahybrid</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/rnahybrid/commit/19a4d12e523175878ac15ed1f8c1eee1716d3ae5">19a4d12e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T09:35:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rnahybrid/commit/7a7fcf30a271ea9b6c529b3ed594c268123f64ca">7a7fcf30</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T09:36:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rnahybrid/commit/dfc52fb80d4fd8c27a8a0dc735ccc9d4c75c0044">dfc52fb8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T09:36:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rnahybrid/commit/e5d6651118f5793e08392b6648ae22b892bc5db4">e5d66511</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T09:36:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Secure URI in copyright format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rnahybrid/commit/7bf0e2211e961da42c36b9033f7d96f5b5290bf2">7bf0e221</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T09:38:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rnahybrid/commit/c90af2c65c569cda97f6aee0e8fd8cd03378f0d1">c90af2c6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T09:38:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rnahybrid/commit/f23930dd7635f5257acf5b667e83de41c4dd4edf">f23930dd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T09:38:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rnahybrid/commit/e155c1cc1bb2f2d0f086ae0b926a55477dc9bd5a">e155c1cc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T10:29:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rnahybrid/commit/6a2870d358b2b380f8b20106423eb59f1cbf4bfa">6a2870d3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T10:32:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#a74a2f301bd0ed2dd19f507912e8c006702841c9">
debian/patches/fix_loop_index.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/rnahybrid/compare/d7ce6c32eb76f093fff9125d40ceb48c7c5d2e16...6a2870d358b2b380f8b20106423eb59f1cbf4bfa#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
<hr>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rnahybrid (2.1.2-5) unstable; urgency=medium</span>
</pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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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="plaintext">  * debhelper 11</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
 
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<td class="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * Point Vcs fields to salsa.debian.org</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
 
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<td class="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Standards-Version: 4.2.1</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
 
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<td class="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">
6
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Secure URI in copyright format</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
 
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<td class="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">
7
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target</span>
</pre>
</td>
</tr>
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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">
8
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">  * Remove trailing whitespace in debian/changelog</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
 
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  * Remove trailing whitespace in debian/copyright</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
 
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<td class="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
</pre>
</td>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Tue, 30 Oct 2018 11:29:39 +0100</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1" 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">
1
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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">rnahybrid (2.1.2-4) unstable; urgency=medium</span>
</pre>
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2
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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"></span>
</pre>
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3
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">  * Exclude armel from Architectures</span>
</pre>
</td>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" 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">@@ -46,7 +58,7 @@ rnahybrid (2.1.2-1) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">rnahybrid (2.1.1-2) unstable; urgency=low</span>
</pre>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">  * debian/upstream: Make author field BibTeX compliant</span>
</pre>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">  * debian/control:<span class="idiff left right"> </span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">  * debian/control:</span>
</pre>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">     - cme fix dpkg-control</span>
</pre>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">     - use anonscm in VCS fields</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="52" 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="LC64" class="line" lang="plaintext">  * debian/patches/gcc-4.8.patch: Fix build error with gcc-4.8 by adding</span>
</pre>
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</table>
<br>
</li>
<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/rnahybrid/compare/d7ce6c32eb76f093fff9125d40ceb48c7c5d2e16...6a2870d358b2b380f8b20106423eb59f1cbf4bfa#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
<hr>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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</table>
<br>
</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/rnahybrid/compare/d7ce6c32eb76f093fff9125d40ceb48c7c5d2e16...6a2870d358b2b380f8b20106423eb59f1cbf4bfa#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
<hr>
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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">@@ -4,11 +4,11 @@ Uploaders: Charles Plessy <plessy@debian.org>,</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">           Andreas Tille <tille@debian.org></span>
</pre>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
</pre>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
</pre>
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<td class="diff-line-num new_line old" data-linenumber="7" 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="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">0</span>),</span>
</pre>
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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">Build-Depends: debhelper (>= 1<span class="idiff left right">1~</span>),</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">               libg2-dev</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="9" 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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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.2</span></span>
</pre>
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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC10" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/rnahybrid.git</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/rnahybrid.git</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/rnahybrid</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/rnahybrid.git</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Package: rnahybrid</span>
</pre>
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</li>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/rnahybrid/compare/d7ce6c32eb76f093fff9125d40ceb48c7c5d2e16...6a2870d358b2b380f8b20106423eb59f1cbf4bfa#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Upstream-Name: RNAhybrid<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: RNAhybrid</span>
</pre>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Contact: Marc Rehmsmeier <marc@techfak.uni-bielefeld.de></span>
</pre>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">                  Peter Steffen <psteffen@techfak.uni-bielefeld.de></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">                  Matthias Hoechsmann <mhoechsm@techfak.uni-bielefeld.de></span>
</pre>
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<br>
</li>
<li id="a74a2f301bd0ed2dd19f507912e8c006702841c9">
<a href="https://salsa.debian.org/med-team/rnahybrid/compare/d7ce6c32eb76f093fff9125d40ceb48c7c5d2e16...6a2870d358b2b380f8b20106423eb59f1cbf4bfa#a74a2f301bd0ed2dd19f507912e8c006702841c9"><strong>debian/patches/fix_loop_index.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ Description: Fix issues that are becoming visible on arm but might be</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> energy.c:539:53: note: within this loop</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff">   for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<=ALPHASIZE;k++) dr_dangle_dg_ar[i][j][k] = 0;</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"> Perhaps that <span class="idiff left right">that </span>k<= in the k loop should be < like in the i and j loops so it doesn't go beyond the end of the array.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> Perhaps that k<= in the k loop should be < like in the i and j loops so it doesn't go beyond the end of the array.</span>
</pre>
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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"> ALPHASIZE is 6, so the k loop would try go one too far.  Every array allocated with ALPHASIZE certainly don't add one anywhere, so any look going from 0 to ALPHASIZE must use < not <= so there are two places in the file that are wrong.</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"></span>
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<br>
</li>
<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/rnahybrid/compare/d7ce6c32eb76f093fff9125d40ceb48c7c5d2e16...6a2870d358b2b380f8b20106423eb59f1cbf4bfa#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make">  dh <span class="nv" style="color: teal;">$@</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"><span class="nl">override_dh_auto_test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="16" 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="LC16" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(,$(filter</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">nocheck,$(DEB_BUILD_OPTIONS)))</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/RNAhybrid</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-s</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">3utr_worm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-t</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/cel-hbl-1.fasta</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-q</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/cel-let-7.fasta</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/RNAcalibrate</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-d</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/3UTR_worm.freq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-k</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">50</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-l</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">50,30</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-q</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/cel-let-7.fasta</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/RNAhybrid</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-d</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1.9,0.28</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-t</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/cel-hbl-1.fasta</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-q</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/cel-let-7.fasta</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" 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="21" 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">@@ -20,3 +21,4 @@ override_dh_auto_test:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/RNAcalibrate</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-f</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2,7</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-d</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/3UTR_worm.freq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-k</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">50</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-l</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">50,30</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-q</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/cel-let-7.fasta</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/RNAhybrid</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-s</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">3utr_worm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-t</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/cbr-hbl-1.fasta</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-q</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/cel-let-7.fasta</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">-src/RNAeffective</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-k</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">30</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-s</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-t</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/hbl-1.fasta</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-q</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">examples/cel-let-7.fasta</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span></pre>
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