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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/clearcut">Debian Med / clearcut</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/clearcut/-/commit/72550355a5b1d5ba6e78980b95c676bdb7cbb8c0">72550355</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-12T09:40:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">clear errno before using it to check failure from atof()
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/clearcut/-/commit/0ab28bbfeff82b63e91b209f0571ce4632aeab5f">0ab28bbf</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-12T09:40:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/clearcut/-/commit/57008fec98e83d4ada0ed94babbd895a6d300199">57008fec</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-12T09:40:50+01:00</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/clearcut/-/commit/03bb96653f34a7fb7c86f187637f6dc18a370ab3">03bb9665</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-12T09:40:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: Trailing whitespace in debian/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/clearcut/-/commit/70721f022cb542639dbaf61ffae415737e942041">70721f02</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-12T09:40:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/clearcut/-/commit/08c20cda4adc17d0a76da9e4fb2afec9ba8c14dc">08c20cda</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-12T11:05:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Propagate CFLAGS to upstream Makefile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/clearcut/-/commit/6a365aed7d4b1f4e574351ab9d116e57e0c8dc45">6a365aed</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-12T11:07:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#7e4d8660bb2ad163070d1a21dd87c2725d3cc694">
<span class="new-file">
+
debian/patches/clear-errno-before-checking.patch
</span>
</a>
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<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
debian/patches/hardening.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/clearcut/-/compare/cb6d5581824b06490e4bf3139eac3cfe115cbe38...6a365aed7d4b1f4e574351ab9d116e57e0c8dc45#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">clearcut (1.0.9-5) 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"> [ Steve Langasek ]</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"> * clear errno before using it to check failure from atof()</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"> Closes: #953675</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="plaintext"></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"> [ Andreas Tille ]</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"> * Standards-Version: 4.5.0 (routine-update)</span>
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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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * debhelper-compat 12 (routine-update)</span>
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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">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Remove trailing whitespace in debian/copyright (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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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"> * Propagate CFLAGS to upstream Makefile</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 12 Mar 2020 11:06:18 +0100</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">clearcut (1.0.9-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> * Team upload.</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/clearcut/-/compare/cb6d5581824b06490e4bf3139eac3cfe115cbe38...6a365aed7d4b1f4e574351ab9d116e57e0c8dc45#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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<a href="https://salsa.debian.org/med-team/clearcut/-/compare/cb6d5581824b06490e4bf3139eac3cfe115cbe38...6a365aed7d4b1f4e574351ab9d116e57e0c8dc45#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">@@ -4,8 +4,8 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,</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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<pre style="margin: 0;">-<span id="LC8" 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="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/clearcut</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/clearcut.git</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Homepage: http://bioinformatics.hungry.com/clearcut/</span>
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<a href="https://salsa.debian.org/med-team/clearcut/-/compare/cb6d5581824b06490e4bf3139eac3cfe115cbe38...6a365aed7d4b1f4e574351ab9d116e57e0c8dc45#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -32,7 +32,7 @@ License: getopt</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Files: prng.*</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Copyright: (C) 1997-2002, Makoto Matsumoto <m-mat@math.sci.hiroshima-u.ac.jp></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> and Takuji Nishimura, All rights reserved.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> and Takuji Nishimura, All rights reserved.</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">License: BSDlike</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">License: BSDlike</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">@@ -47,8 +47,8 @@ License: BSDlike</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer in the</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> documentation and/or other materials provided with the distribution.</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> 3. The names of its contributors may not be used to endorse or promote<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> products derived from this software without specific prior written<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> 3. The names of its contributors may not be used to endorse or promote</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> products derived from this software without specific prior written</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> permission.</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS</span>
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<li id="7e4d8660bb2ad163070d1a21dd87c2725d3cc694">
<a href="https://salsa.debian.org/med-team/clearcut/-/compare/cb6d5581824b06490e4bf3139eac3cfe115cbe38...6a365aed7d4b1f4e574351ab9d116e57e0c8dc45#7e4d8660bb2ad163070d1a21dd87c2725d3cc694"><strong>debian/patches/clear-errno-before-checking.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: clear errno before using it to check failure from atof()</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> The atof() function is not guaranteed to clear errno on success, so if</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> any earlier errors have been set prior to calling atof(), these will</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> result in a spurious failure. On armhf, glibc 2.31 now opportunistically</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> calls a new syscall that may not be supported on older kernels (Linux 4.15),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> resulting in errno == ENOSYS:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> syscall_0x193(0x5, 0xffb2b650, 0xf77b7000, 0, 0x5, 0xffb2b650) = -1 ENOSYS (Function not implemented)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> Therefore we should clear errno before calling atof() to make sure any</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> errors actually originate from this function.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">Author: Steve Langasek <steve.langasek@ubuntu.com></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">Last-Update: 2020-03-11</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/953675</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff">Index: clearcut-1.0.9/dmat.c</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- clearcut-1.0.9.orig/dmat.c</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ clearcut-1.0.9/dmat.c</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -570,6 +570,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> goto XIT_BAD;</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ errno = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> val = atof(token->buf);</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> if(errno) {</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> fprintf(stderr, "Clearcut: Distance value out-of-range.\n");</span></pre>
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<li id="4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<a href="https://salsa.debian.org/med-team/clearcut/-/compare/cb6d5581824b06490e4bf3139eac3cfe115cbe38...6a365aed7d4b1f4e574351ab9d116e57e0c8dc45#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.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">@@ -4,6 +4,15 @@ Description: Propagate hardening options</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/Makefile</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -73,7 +73,7 @@</span> CC = gcc</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ######################## ALL ARCHITECTURES ##################################</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> # DEFAULT GCC OPTIMIZATION CONFIGURATION (ALL ARCHITECTURES)</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS = -O3 -Wall -funroll-loops -fomit-frame-pointer</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS += -O3 -Wall -funroll-loops -fomit-frame-pointer</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> # BASIC OPTIMIZATION</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> #CFLAGS = -O3</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="p">@@ -124,7 +124,7 @@</span> clean:</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> $(CC) -c $(INCDIRS) $(CFLAGS) $(OPTFLAG) $(DEFS) $<</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> </span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/clearcut/-/compare/cb6d5581824b06490e4bf3139eac3cfe115cbe38...6a365aed7d4b1f4e574351ab9d116e57e0c8dc45#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">mothur_trivial_patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">hardening.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">clear-errno-before-checking.patch</span></pre>
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<li id="b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<a href="https://salsa.debian.org/med-team/clearcut/-/compare/cb6d5581824b06490e4bf3139eac3cfe115cbe38...6a365aed7d4b1f4e574351ab9d116e57e0c8dc45#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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