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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/emmax">Debian Med / emmax</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/emmax/commit/f31edd57f279dcc92aab4f03e1b74217a46dee16">f31edd57</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-03-20T20:36:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/emmax/commit/da7cdba6f01933d620e61aad79df3e0d93c4709a">da7cdba6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-03-20T20:37:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/emmax/commit/57adf98ffb56469fd2a4140eb821e281bbad9539">57adf98f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-03-20T20:49:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try to force hardening but no success to get rid of the lintian issue
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/emmax/commit/deb4abd0220c1014a903f22930dbc21dc80bc35a">deb4abd0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-03-20T20:51:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to new
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#06c4eccb42cf4d3e7718310bfc1c2e1dd83325d7">
debian/patches/aborts.patch
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</li>
<li class="file-stats">
<a href="#99eca758bc7496e6ef16983eafdce2b26e162e27">
debian/patches/clean.patch
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<li class="file-stats">
<a href="#991d0467e39400683bf9829ffb1736472e0c16db">
debian/patches/dynamic.patch
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<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<span class="new-file">
+
debian/patches/hardening.patch
</span>
</a>
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<li class="file-stats">
<a href="#8ffad69b5a1013cd9a89d5344abc42d97fe70154">
debian/patches/install.patch
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</li>
<li class="file-stats">
<a href="#b1de8025b28a12221d61b892198cd3fceb8ee4b0">
debian/patches/logfile.patch
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<li class="file-stats">
<a href="#40797e92d7d6ff15696c3b6c810138c63cdf84a4">
debian/patches/paths.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">emmax (0~beta.20100307-1) <span class="idiff left right">UNRELEASED</span>; urgency=low</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">emmax (0~beta.20100307-1) <span class="idiff left right">unstable</span>; urgency=low</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<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"> * Initial release <span class="idiff left right">pending, not uploaded because of unknown license.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release <span class="idiff left right">(Closes: #925158)</span></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 20 Mar 2019 1<span class="idiff left right">3:55:07</span> +0100</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 20 Mar 2019 1<span class="idiff left right">8:28:20</span> +0100</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" 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">@@ -25,6 +25,6 @@ Description: genetic mapping considering population structure</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> association mapping accounting for the sample structure. In addition</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> to the computational efficiency obtained by EMMA algorithm, EMMAX takes</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> advantage of the fact that each locus explains only a small fraction of</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> complex traits, which allows to avoid repetitive variance component</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> complex traits, which allows <span class="idiff left right">one </span>to avoid repetitive variance component</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> estimation procedure, resulting in a significant amount of increase in</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> computational time of association mapping using mixed model.</span></pre>
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<li id="06c4eccb42cf4d3e7718310bfc1c2e1dd83325d7">
<a href="https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a#06c4eccb42cf4d3e7718310bfc1c2e1dd83325d7"><strong>debian/patches/aborts.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Steffen Moeller</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: 2013-06-11 09:09:19 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Clean exit when no options are given</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">Index: emmax-0~beta.20100307/emmax-kin.c</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- emmax-0~beta.20100307.orig/emmax-kin.c</span></span>
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<a href="https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a#99eca758bc7496e6ef16983eafdce2b26e162e27"><strong>debian/patches/clean.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Steffen Moeller</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: 2013-06-11 09:09:19 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Proper cleaning</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">Index: emmax-0~beta.20100307/makefile</span></span>
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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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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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">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- emmax-0~beta.20100307.orig/makefile</span></span>
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<li id="991d0467e39400683bf9829ffb1736472e0c16db">
<a href="https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a#991d0467e39400683bf9829ffb1736472e0c16db"><strong>debian/patches/dynamic.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Steffen Moeller</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: 2013-06-11 09:09:19 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Dynamic linking</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">Index: emmax-0~beta.20100307/makefile</span></span>
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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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- emmax-0~beta.20100307.orig/makefile</span></span>
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<li id="4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<a href="https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Wed, 20 Mar 2019 18:28:20 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Propagate hardening options (unfortunately this does not help)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/makefile</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -5,9 +5,9 @@ PREFIX=/usr</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> INCFLAGS = </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> LIBFLAGS = -Wall</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-COMPFLAGS = ${INCFLAGS} -O2 -Wall -g</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;">+COMPFLAGS = ${INCFLAGS} -O2 -Wall -g $(CFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> CC = gcc</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;">-CLIBS = -L/usr/lib/atlas-base -L/usr/lib/lapack/ -llapack_atlas -llapack -lcblas -lblas -latlas -lcblas -lm -lz</span></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;">+CLIBS = -L/usr/lib/atlas-base -L/usr/lib/lapack/ -llapack_atlas -llapack -lcblas -lblas -latlas -lcblas -lm -lz $(LDFLAGS)</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"> all: emmax emmax-kin</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span></pre>
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<li id="8ffad69b5a1013cd9a89d5344abc42d97fe70154">
<a href="https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a#8ffad69b5a1013cd9a89d5344abc42d97fe70154"><strong>debian/patches/install.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Steffen Moeller</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: 2013-06-11 09:09:19 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Proper install target</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">Index: emmax-0~beta.20100307/makefile</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- emmax-0~beta.20100307.orig/makefile</span></span>
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<a href="https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a#b1de8025b28a12221d61b892198cd3fceb8ee4b0"><strong>debian/patches/logfile.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Steffen Moeller</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: 2013-06-11 09:09:19 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Log only if file pointer exists</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">Index: emmax-0~beta.20100307/emmax.c</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- emmax-0~beta.20100307.orig/emmax.c</span></span>
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<li id="40797e92d7d6ff15696c3b6c810138c63cdf84a4">
<a href="https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a#40797e92d7d6ff15696c3b6c810138c63cdf84a4"><strong>debian/patches/paths.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Steffen Moeller</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: 2013-06-11 09:09:19 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Fix header path of clapack.h</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">Index: emmax-0~beta.20100307/emmax.c</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- emmax-0~beta.20100307.orig/emmax.c</span></span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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>
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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">@@ -5,3 +5,4 @@ install.patch</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">clean.patch</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">logfile.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">atlas.patch</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">hardening.patch</span></pre>
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