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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/rapmap">Debian Med / rapmap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/698c04c98a5bcb77c6133286b3f7ace77a56bbff">698c04c9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-01T16:55:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/0ab31fbd676c983990282b87fa9f458448690fbb">0ab31fbd</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-01T16:55:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/cec9e6a77046f5de2ef8dc9bc64f99824cb8a8ca">cec9e6a7</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-01T16:55:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add ppc64el and arm64 alternatives to asm("pause").
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/65441c912d806f466921d31622005a73097838ba">65441c91</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-01T17:54:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Avoid unnecessary linkage to gomp & rt
</pre>
</li>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#c3a07e5594c57567222fe711beb00b807106926a">
<span class="new-file">
+
debian/patches/no_gomp_needed
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<li class="file-stats">
<a href="#0a8d7c289bbb6d9bb3feec5aa0f3e4068bbee285">
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+
debian/patches/portable_pause
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
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+
debian/patches/spelling
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<li class="file-stats">
<a href="#a6163eb70bb3152f3e3422bdd0aad6dc66834cc5">
debian/rapmap.lintian-overrides
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/rapmap/compare/e9da144ea912dc7f029fc4a4b6d361a3868f7984...65441c912d806f466921d31622005a73097838ba#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rapmap (0.12.0+dfsg-3) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * debian/patches/portable_pause: add ppc64el and arm64 alternatives to</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"> asm("pause").</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debian/patches/no_gomp_needed: Avoid unnecessary linkage to gomp.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Tue, 01 Jan 2019 08:09:15 -0800</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">rapmap (0.12.0+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Add further header files to rapmap-dev since these are used in salmon</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/rapmap/compare/e9da144ea912dc7f029fc4a4b6d361a3868f7984...65441c912d806f466921d31622005a73097838ba#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: rapmap</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Michael R. Crusoe <michael.crusoe@gmail.com></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 (>= 11),</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">@@ -15,7 +16,7 @@ Build-Depends: debhelper (>= 11),</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libtclap-dev,</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> pkg-config,</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> python-markdown</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3.0</span></span>
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19
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/rapmap</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/rapmap.git</span>
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21
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Homepage: https://github.com/COMBINE-lab/RapMap</span>
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<a href="https://salsa.debian.org/med-team/rapmap/compare/e9da144ea912dc7f029fc4a4b6d361a3868f7984...65441c912d806f466921d31622005a73097838ba#c3a07e5594c57567222fe711beb00b807106926a"><strong>debian/patches/no_gomp_needed</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Description: Avoid unnecessary linkage to gomp or rt</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -74,7 +74,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> set( BOOST_EXTRA_FLAGS "--layout=tagged" )</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> ## this get's set differently below if we</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ## are on clang & apple</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set (NON_APPLECLANG_LIBS gomp rt)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set (NON_APPLECLANG_LIBS "$ENV{NON_APPLECLANG_LIBS}")</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> set (PTHREAD_LIB)</span>
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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"> ##</span></pre>
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<a href="https://salsa.debian.org/med-team/rapmap/compare/e9da144ea912dc7f029fc4a4b6d361a3868f7984...65441c912d806f466921d31622005a73097838ba#0a8d7c289bbb6d9bb3feec5aa0f3e4068bbee285"><strong>debian/patches/portable_pause</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Subject: Add portable pauses</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/include/FastxParserThreadUtils.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/include/FastxParserThreadUtils.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -18,7 +18,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> static const size_t MAX_BACKOFF_ITERS = 1024;</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"> ALWAYS_INLINE static void cpuRelax() {</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if defined(__aarch64__) || defined(arm64)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ asm volatile("yield" ::: "memory");</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__PPC64__) || defined(PPC64) || defined(__ppc64__)</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;">+ asm("ori 0,0,0");</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> asm("pause");</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> ALWAYS_INLINE void yieldSleep() {</span></pre>
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<a href="https://salsa.debian.org/med-team/rapmap/compare/e9da144ea912dc7f029fc4a4b6d361a3868f7984...65441c912d806f466921d31622005a73097838ba#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use-debian-libs.patch</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use_shared_libs.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">avoid_privacy_breach.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">spelling</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">portable_pause</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">no_gomp_needed</span></pre>
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<a href="https://salsa.debian.org/med-team/rapmap/compare/e9da144ea912dc7f029fc4a4b6d361a3868f7984...65441c912d806f466921d31622005a73097838ba#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Subject: Fix typo: exeption → exception</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/include/spdlog/details/async_log_helper.h</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/include/spdlog/details/async_log_helper.h</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -282,7 +282,7 @@</span></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"> catch(...)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- _err_handler("Unknown exeption in async logger worker loop.");</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ _err_handler("Unknown exception in async logger worker loop.");</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> }</span>
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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"> if (_worker_teardown_cb) _worker_teardown_cb();</span></pre>
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<a href="https://salsa.debian.org/med-team/rapmap/compare/e9da144ea912dc7f029fc4a4b6d361a3868f7984...65441c912d806f466921d31622005a73097838ba#a6163eb70bb3152f3e3422bdd0aad6dc66834cc5"><strong>debian/rapmap.lintian-overrides</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">rapmap: script-with-language-extension usr/bin/RunRapMap.sh</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># False positive</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">rapmap [amd64]: spelling-error-in-binary usr/bin/rapmap YelD Yield</span></pre>
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<a href="https://salsa.debian.org/med-team/rapmap/compare/e9da144ea912dc7f029fc4a4b6d361a3868f7984...65441c912d806f466921d31622005a73097838ba#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">@@ -5,11 +5,18 @@</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">ifneq (,$(filter $(DEB_HOST_ARCH),arm64 ppc64el))</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> export NON_APPLECLANG_LIBS=z</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> # not really z, but we need something innocent here</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> export NON_APPLECLANG_LIBS=rt</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">endif</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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8
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">%:</span>
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9
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> dh $@</span>
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10
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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11
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">override_dh_auto_configure:</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> dh_auto_configure -- -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> dh_auto_configure -- -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true<span class="idiff left right"> $(EXTRA)</span></span>
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13
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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14
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_dh_auto_build:</span>
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15
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh_auto_build</span>
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