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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/ea-utils">Debian Med / ea-utils</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/ea-utils/-/commit/a4fee74e2081d480cf3b58096cb3472e201fa27e">a4fee74e</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-17T21:24:34+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add gcc11.patch to fix ftbfs with gcc 11
Closes: #984043
</pre>
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<strong><a href="https://salsa.debian.org/med-team/ea-utils/-/commit/c66b17062823b4c4123f1ad5d4a77b259e602cc5">c66b1706</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2021-10-17T21:41:52+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ready to upload to unstable
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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+
debian/patches/gcc11.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/e3bf006d01905e2be8a4c2f69af7ad3f5ba37791...c66b17062823b4c4123f1ad5d4a77b259e602cc5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ea-utils (1.1.2+dfsg-9) 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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add gcc11.patch to fix ftbfs with gcc 11. (Closes: #984043)</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"> -- Étienne Mollier <emollier@debian.org> Sun, 17 Oct 2021 21:37:07 +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">ea-utils (1.1.2+dfsg-8) 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="f38d99f8398b7290799cca649a21e6f07a117391">
<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/e3bf006d01905e2be8a4c2f69af7ad3f5ba37791...c66b17062823b4c4123f1ad5d4a77b259e602cc5#f38d99f8398b7290799cca649a21e6f07a117391"><strong>debian/patches/gcc11.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix failure to build from source with gcc 11</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984043</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2021-10-17</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></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;">--- ea-utils.orig/fastq-stats.cpp</span></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;">+++ ea-utils/fastq-stats.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -180,14 +180,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> while ( (c = getopt (argc, argv, "?DdL:g:x:b:c:w:s:h")) != -1) {</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> switch (c) {</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> case 'c': cyclemax = atoi(optarg); break;</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case 'D': ++nodup; break;</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case 'd': ++debug; break;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case 'D': nodup=1; break;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case 'd': debug=1; break;</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> case 'w': window = atoi(optarg); break;</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> case 's': show_max = atoi(optarg); break;</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case 'x': fastx_outfile = optarg; ++fastx; break;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case 'b': brkdown_outfile = optarg; ++brkdown; break;</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case 'L': ++len_hist; lenhist_outfile = optarg; break;</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case 'g': gc_outfile = optarg; ++gc; break;</span></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;">+ case 'x': fastx_outfile = optarg; fastx=1; break;</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case 'b': brkdown_outfile = optarg; brkdown=1; break;</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case 'L': len_hist=1; lenhist_outfile = optarg; break;</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case 'g': gc_outfile = optarg; gc=1; break;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> case 'h': usage(stdout); return 0;</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> case '?':</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> if (!optopt) {</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ea-utils.orig/sam-stats.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ea-utils/sam-stats.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -226,7 +226,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> while ( (c = getopt_long(argc, argv, "?BzArR:Ddx:MhS:", long_options, &long_index)) != -1) {</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> switch (c) {</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> case 'd': ++debug; break; // increment debug level</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case 'D': ++trackdup; break;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case 'D': trackdup=1; break;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> case 'B': inbam=1; break;</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> case 'A': max_chr=1000000; break; // max chrom</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> case 'R': rnafile=optarg; // pass through</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/e3bf006d01905e2be8a4c2f69af7ad3f5ba37791...c66b17062823b4c4123f1ad5d4a77b259e602cc5#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -3,3 +3,4 @@ hardening.patch</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">name-space-conflict.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">cross.patch</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">arm64.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">gcc11.patch</span></pre>
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