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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/t-coffee">Debian Med / t-coffee</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/t-coffee/commit/c95d597debf91824d5d26bc1a06091a0a79af1cc">c95d597d</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2019-02-04T09:48:44Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">A patch to fix autopkgtest COREDUMP
</pre>
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<strong><a href="https://salsa.debian.org/med-team/t-coffee/commit/8282ba9a71902a1a84e34b1fcf0a6d7fe0bb9773">8282ba9a</a></strong>
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<span>by Liubov Chuprikova</span>
<i>at 2019-02-04T09:50:17Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.3.0
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8b7aede91f63a56963c57c21edec1407bbb19ab9">
<span class="new-file">
+
debian/patches/fix_tempfile_name_sharing.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/t-coffee/compare/b9d1db114cd4f8cc1586d125f577fb55b175ad6f...8282ba9a71902a1a84e34b1fcf0a6d7fe0bb9773#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">t-coffee (12.00.7fb08c2-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Team upload.</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"> * Fix "t-coffee breaks libbio-tools-run-alignment-tcoffee-perl</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> autopkgtest: COREDUMP" fix_tempfile_name_sharing.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> (Closes: #917143)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Standards-Version: 4.3.0</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"> -- Liubov Chuprikova <chuprikovalv@gmail.com> Mon, 04 Feb 2019 10:37:01 +0100</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">t-coffee (12.00.7fb08c2-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * New upstream version</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/t-coffee/compare/b9d1db114cd4f8cc1586d125f577fb55b175ad6f...8282ba9a71902a1a84e34b1fcf0a6d7fe0bb9773#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ Uploaders: Steffen Moeller <moeller@debian.org>,</td>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Section</span><span class="p">:</span> <span class="n" style="color: #333;">science</span></span>
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6
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<td class="diff-line-num new_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">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">Priority</span><span class="p">:</span> <span class="n" style="color: #333;">optional</span></span>
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7
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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">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">Build</span><span class="p">-</span><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="n" style="color: #333;">debhelper</span> <span class="p">(>=</span> <span class="m" style="color: #099;">11</span><span class="p">~)</span></span>
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8
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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.<span class="idiff left right">2.1</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.<span class="idiff left right">3.0</span></span></span>
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<td class="diff-line-num new_line" data-linenumber="9" 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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Browser</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">t</span><span class="p">-</span><span class="n" style="color: #333;">coffee</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Git</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">t</span><span class="p">-</span><span class="n" style="color: #333;">coffee</span><span class="p">.</span><span class="n" style="color: #333;">git</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"><span class="n" style="color: #333;">Homepage</span><span class="p">:</span> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">tcoffee</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">Projects_home_page</span><span class="p">/</span><span class="n" style="color: #333;">t_coffee_home_page</span><span class="p">.</span><span class="n" style="color: #333;">html</span></span>
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<li id="8b7aede91f63a56963c57c21edec1407bbb19ab9">
<a href="https://salsa.debian.org/med-team/t-coffee/compare/b9d1db114cd4f8cc1586d125f577fb55b175ad6f...8282ba9a71902a1a84e34b1fcf0a6d7fe0bb9773#8b7aede91f63a56963c57c21edec1407bbb19ab9"><strong>debian/patches/fix_tempfile_name_sharing.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Liubov Chuprikova <chuprikovalv@gmail.com> </span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/917143</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Last-Update: Sun, 03 Feb 2019 23:42:41 +0100</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Description: Delete static for tempfile names so that </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">different processes do not use the same file.</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"></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/t_coffee_source/util_lib/reformat.c</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;">+++ b/t_coffee_source/util_lib/reformat.c</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1524,8 +1524,8 @@</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"> else if (format && (strm(format, "saga_aln" ) ||strm(format, "clustal_aln")||strm(format, "t_coffee_aln" ) || strm (format, "msf_aln")))</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> {</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;">- static char*tmp_name1=vtmpnam (NULL);</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- static char*tmp_name2=vtmpnam (NULL);</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;">+ char*tmp_name1=vtmpnam (NULL);</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;">+ char*tmp_name2=vtmpnam (NULL);</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> printf_system ( "seq2name_seq.pl %s > %s",name, tmp_name1);</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> printf_system ( "nameseq2fasta.pl %s > %s",tmp_name1, tmp_name2);</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1534,6 +1534,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> A=seq2aln (S, A, 0);</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> //read_aln ( name, A);</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ vfree(tmp_name1);</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ vfree(tmp_name2);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> else if (format && strm (format, "conc_aln"))A=input_conc_aln (name,NULL);</span></pre>
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<a href="https://salsa.debian.org/med-team/t-coffee/compare/b9d1db114cd4f8cc1586d125f577fb55b175ad6f...8282ba9a71902a1a84e34b1fcf0a6d7fe0bb9773#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">@@ -6,3 +6,4 @@ set_proper_dir_permissions.patch</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">mayhem.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">stable-linking-inputs.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">clustalw2.patch</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">fix_tempfile_name_sharing.patch</span></pre>
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