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<h3>
Alexandre Mestiashvili pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie2">Debian Med / bowtie2</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/62d5e31b6d3d85ad1031ce1d6a6b25baba8856ba">62d5e31b</a></strong>
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<span>by Alexandre Mestiashvili</span>
<i>at 2020-04-19T11:10:30+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch fixing ftbfs with gcc10, thanks to Jun Aruga
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<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/faabd9d8e0d57c67a9dd147cae90faba86b2457b">faabd9d8</a></strong>
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<span>by Alexandre Mestiashvili</span>
<i>at 2020-04-19T11:12:46+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
Gbp-Dch: Ignore
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#3ee0030ede7a48b8f10e35e7f10d0f74b240b097">
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debian/patches/gcc10_ftbfs_invalid_dquote_char.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bowtie2/-/compare/c801da14953540bafd3005114d045776db47eb70...faabd9d8e0d57c67a9dd147cae90faba86b2457b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bowtie2 (2.4.1-2) unstable; 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"> * Add patch fixing FTBFS with gcc10, thanks to Jun Aruga</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #957054</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Alexandre Mestiashvili <mestia@debian.org> Sun, 19 Apr 2020 11:11:42 +0200</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">bowtie2 (2.4.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team upload.</span>
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<li id="3ee0030ede7a48b8f10e35e7f10d0f74b240b097">
<a href="https://salsa.debian.org/med-team/bowtie2/-/compare/c801da14953540bafd3005114d045776db47eb70...faabd9d8e0d57c67a9dd147cae90faba86b2457b#3ee0030ede7a48b8f10e35e7f10d0f74b240b097"><strong>debian/patches/gcc10_ftbfs_invalid_dquote_char.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: mestia@debian.org</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Use proper double quotes, see</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">https://github.com/BenLangmead/bowtie2/issues/278</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie2.orig/processor_support.h</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie2/processor_support.h</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -49,7 +49,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> #elif defined(USING_GCC_COMPILER)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> __get_cpuid(0x1, ®s.EAX, ®s.EBX, ®s.ECX, ®s.EDX);</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #else</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std::cerr << “ERROR: please define __cpuid() for this build.\n”; </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;">+ std::cerr << "ERROR: please define __cpuid() for this build.\n"; </span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> assert(0);</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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> #endif</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;</span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/compare/c801da14953540bafd3005114d045776db47eb70...faabd9d8e0d57c67a9dd147cae90faba86b2457b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gcc10_ftbfs_invalid_dquote_char.patch</span>
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1
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">drop-not-needed-js-from-manual.patch</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">wrong-interpreter-path.patch</span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">hardening.patch</span>
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