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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<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>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add gcc11.patch to fix ftbfs with gcc 11

Closes: #984043
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ea-utils/-/commit/c66b17062823b4c4123f1ad5d4a77b259e602cc5">c66b1706</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-17T21:41:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ready to upload to unstable
</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#f38d99f8398b7290799cca649a21e6f07a117391">
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+
debian/patches/gcc11.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
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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>
</pre>
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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>
</pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
</pre>
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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>
</pre>
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</li>
<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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<td class="new_line diff-line-num new" data-linenumber="15" 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="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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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff">                  case 'w': window = atoi(optarg); break;</span>
</pre>
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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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<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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<td class="new_line diff-line-num new" data-linenumber="21" 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="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                 case 'b': brkdown_outfile = optarg; ++brkdown; break;</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="22" 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="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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<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>
</pre>
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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>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="25" 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="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                 case 'b': brkdown_outfile = optarg; brkdown=1; break;</span></span>
</pre>
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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>
</pre>
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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>
</pre>
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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>
</pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff">                                    if (!optopt) {</span>
</pre>
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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>
</pre>
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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>
</pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -226,7 +226,7 @@</span></span>
</pre>
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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>
</pre>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff">                 switch (c) {</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="36" 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="LC36" class="line" lang="diff">                 case 'd': ++debug; break;                                       // increment debug level</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="37" 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="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                case 'D': ++trackdup; break;</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="38" 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">
38
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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>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="39" 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="LC39" class="line" lang="diff">                 case 'B': inbam=1; break;</span>
</pre>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff">                 case 'A': max_chr=1000000; break;                               // max chrom</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff">                 case 'R': rnafile=optarg;                                       // pass through</span></pre>
</td>
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<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/e3bf006d01905e2be8a4c2f69af7ad3f5ba37791...c66b17062823b4c4123f1ad5d4a77b259e602cc5#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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">...</td>
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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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<td class="old_line diff-line-num" data-linenumber="3" 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">
3
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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>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="4" 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">
4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">cross.patch</span>
</pre>
</td>
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<td class="old_line diff-line-num" 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">
5
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<td class="new_line diff-line-num" 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">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">arm64.patch</span>
</pre>
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<td class="old_line diff-line-num new" 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">
 
</td>
<td class="new_line diff-line-num new" 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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">gcc11.patch</span></pre>
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