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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/snap">Debian Med / snap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snap/commit/4f06b07aba4f09ce9a57ba03305c9c5bf835495a">4f06b07a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-08T07:39:41+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Forwarded patches upstream
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#10484c46723d67acd9ad2013186cc74d9a8743a0">
debian/patches/build-with-gcc-6.patch
</a>
</li>
<li class="file-stats">
<a href="#e5ca805e5f6423db22f740b282b3bd9c143749f2">
debian/patches/fix_missing_braces_in_if_statements.patch
</a>
</li>
<li class="file-stats">
<a href="#34d8991cbaaf5cecf9a0dd6947c32426754e1a8e">
debian/patches/gcc-8.patch
</a>
</li>
<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
debian/patches/hardening.patch
</a>
</li>
<li class="file-stats">
<a href="#b6d185566548cafbc08fe64d398928ddf91cc9c5">
debian/patches/replace_itoa_with_broken_indentation.patch
</a>
</li>
<li class="file-stats">
<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
debian/patches/spelling.patch
</a>
</li>
<li class="file-stats">
<a href="#cd0744ea22cd1d571c40b85951aa47416ea5cabd">
debian/patches/unused-but-set-variable.patch
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</li>
<li class="file-stats">
<a href="#13f37995f507dd8223b4debac916678fa48d6b8d">
debian/patches/use-CC.patch
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<h4>Changes:</h4>
<li id="10484c46723d67acd9ad2013186cc74d9a8743a0">
<a href="https://salsa.debian.org/med-team/snap/commit/4f06b07aba4f09ce9a57ba03305c9c5bf835495a#10484c46723d67acd9ad2013186cc74d9a8743a0"><strong>debian/patches/build-with-gcc-6.patch</strong></a>
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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="LC1" class="line" lang="diff">Author: Sascha Steinbiss <satta@tetrinetsucht.de></span>
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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="LC2" class="line" lang="diff">Last-Update: Sat, 30 Apr 2016 17:48:14 +0100</span>
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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="LC3" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/812011</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3</span>
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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="LC5" class="line" lang="diff">Description: changing the (likely buggy) behaviour of the zoeHSPCmpQuery and</span>
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<td class="diff-line-num old_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">
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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="LC6" class="line" lang="diff"> zoeHSPCmpSbjct functions to do the correct comparisons. This fixes:</span>
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<td class="diff-line-num old_line" data-linenumber="6" 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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<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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> error: self-comparison always evaluates to false [-Werror=tautological-compare]</span>
</pre>
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<br>
</li>
<li id="e5ca805e5f6423db22f740b282b3bd9c143749f2">
<a href="https://salsa.debian.org/med-team/snap/commit/4f06b07aba4f09ce9a57ba03305c9c5bf835495a#e5ca805e5f6423db22f740b282b3bd9c143749f2"><strong>debian/patches/fix_missing_braces_in_if_statements.patch</strong></a>
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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="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
</pre>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Last-Update: Wed, 24 Aug 2016 10:43:36 +0200</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/835283</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">Description: add missing braces</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/exonpairs.c</span></span>
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<li id="34d8991cbaaf5cecf9a0dd6947c32426754e1a8e">
<a href="https://salsa.debian.org/med-team/snap/commit/4f06b07aba4f09ce9a57ba03305c9c5bf835495a#34d8991cbaaf5cecf9a0dd6947c32426754e1a8e"><strong>debian/patches/gcc-8.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff">Description: Enlarge too short target string for sprintf</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/897864</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">Last-Update: Mon, 07 May 2018 23:38:54 +0200</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<li id="4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<a href="https://salsa.debian.org/med-team/snap/commit/4f06b07aba4f09ce9a57ba03305c9c5bf835495a#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">LastChanged: Fri, 25 Oct 2013 16:39:26 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">Description: Propagate Hardening options</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<li id="b6d185566548cafbc08fe64d398928ddf91cc9c5">
<a href="https://salsa.debian.org/med-team/snap/commit/4f06b07aba4f09ce9a57ba03305c9c5bf835495a#b6d185566548cafbc08fe64d398928ddf91cc9c5"><strong>debian/patches/replace_itoa_with_broken_indentation.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Last-Update: Wed, 24 Aug 2016 10:43:36 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">Description: itoa implementation had broken indentation - use</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> sprintf instead</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
</pre>
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<li id="45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
<a href="https://salsa.debian.org/med-team/snap/commit/4f06b07aba4f09ce9a57ba03305c9c5bf835495a#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff">Description: Fix spelling</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">Last-Update: Mon, 07 May 2018 23:38:54 +0200</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Zoe/zoePhasePref.c</span></span>
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<li id="cd0744ea22cd1d571c40b85951aa47416ea5cabd">
<a href="https://salsa.debian.org/med-team/snap/commit/4f06b07aba4f09ce9a57ba03305c9c5bf835495a#cd0744ea22cd1d571c40b85951aa47416ea5cabd"><strong>debian/patches/unused-but-set-variable.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Date: Tue, 07 Oct 2014 13:31:52 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">Description: When enabling hardening flags by</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> using debhelper 9 unsused variables should not be assigned.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> This patch comments those variables.</span>
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<li id="13f37995f507dd8223b4debac916678fa48d6b8d">
<a href="https://salsa.debian.org/med-team/snap/commit/4f06b07aba4f09ce9a57ba03305c9c5bf835495a#13f37995f507dd8223b4debac916678fa48d6b8d"><strong>debian/patches/use-CC.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">@@ -2,6 +2,7 @@ Author: Sascha Steinbiss <satta@tetrinetsucht.de>,</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> Helmut Grohne <helmut@subdivi.de></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff">Last-Update: Fri, 8 Dec 2017 22:32:22 +0100</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/883891</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">Description: Do not force gcc explicitly but use $(CC) instead</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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Zoe/Makefile</span></span>
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