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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/progressivemauve">Debian Med / progressivemauve</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/progressivemauve/commit/f61e0e739a667d01926870ebb2c3acaaaa0730fa">f61e0e73</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-27T08:43:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable building against unversioned libs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/progressivemauve/commit/15f42a183b3fc75847f68e264d39551b8506f9a7">15f42a18</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-27T08:43:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Another spelling fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/progressivemauve/commit/b3ee831e5cbb1a08cbb7bb59795621bd02923cc0">b3ee831e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-27T08:47:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/progressivemauve/commit/c27cc5656250729fb3012198592a3e2407760b29">c27cc565</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-27T08:47:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.5
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/progressivemauve/commit/94a672570408b9ccd16f4d884c80eee5f5588f05">94a67257</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-27T08:54:44+02:00</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/progressivemauve/commit/60171737687fc0fd6811fcce20b02b00ae58b59a">60171737</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-27T08:57:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Silence lintian about version mangling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/progressivemauve/commit/264cad146c48537b35fa8365e9137905785f8a21">264cad14</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-27T09:01:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>7 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="#a787c1b4080ccdf43cc56891b1d4d1011fac4d45">
<span class="new-file">
+
debian/patches/adapt-to-unversioned-libs.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#75b5adc8920765f0c781fef03a85063aa433704e">
debian/patches/do_not_build_static_binaries.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
debian/patches/spelling.patch
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/progressivemauve/compare/06ddc050db8f6e00ce72add59ff2408a35430f3f...264cad146c48537b35fa8365e9137905785f8a21#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
<hr>
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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="plaintext">progressivemauve (1.2.0+4713+dfsg-2) UNRELEASED; urgency=medium</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">progressivemauve (1.2.0+4713+dfsg-3) unstable; urgency=medium</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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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"> * Point Vcs fields to salsa.debian.org</span>
</pre>
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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"> * Standards-Version: 4.1.5</span>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 27 Jul 2018 08:58:00 +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"></span>
</pre>
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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="plaintext">progressivemauve (1.2.0+4713+dfsg-2) unstable; urgency=medium</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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_line" data-linenumber="10" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Adjust Build-Depends to renamed libraries</span>
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<td class="diff-line-num old_line" 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">
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<td class="diff-line-num new_line" data-linenumber="11" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> Closes: #904690</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Enable building against unversioned libs</span>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 27 Jul 2018 0<span class="idiff left right">0:51:34</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 27 Jul 2018 0<span class="idiff left right">6:32:17</span> +0200</span>
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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">progressivemauve (1.2.0+4713+dfsg-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/progressivemauve/compare/06ddc050db8f6e00ce72add59ff2408a35430f3f...264cad146c48537b35fa8365e9137905785f8a21#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -12,10 +12,10 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libboost-iostreams-dev,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libgenome-dev,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libmuscle-dev,</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> libmems-dev</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">3</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/progressivemauve.git</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/progressivemauve.git</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> libmems-dev<span class="idiff left right"> (>= 1.6.0+4725-7~)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">5</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/progressivemauve</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/progressivemauve.git</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: http://darlinglab.org/mauve/user-guide/mauvealigner.html</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Package: progressivemauve</span>
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<li id="a787c1b4080ccdf43cc56891b1d4d1011fac4d45">
<a href="https://salsa.debian.org/med-team/progressivemauve/compare/06ddc050db8f6e00ce72add59ff2408a35430f3f...264cad146c48537b35fa8365e9137905785f8a21#a787c1b4080ccdf43cc56891b1d4d1011fac4d45"><strong>debian/patches/adapt-to-unversioned-libs.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Enable building against unversioned libs</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Last-Updates: Fri, 27 Jul 2018 06:32:17 +0200</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/configure.ac</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/configure.ac</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;">@@ -43,7 +43,7 @@ AC_DEFINE(GETOPT_UNDEFINED,[],"Define th</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ()")</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> )</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;">-PKG_CHECK_MODULES(DEPS, libMems-1.6 >= 1.0.0)</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;">+PKG_CHECK_MODULES(DEPS, libMems >= 1.0.0)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> AC_SUBST(DEPS_CFLAGS)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> AC_SUBST(DEPS_LIBS)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/progressivemauve/compare/06ddc050db8f6e00ce72add59ff2408a35430f3f...264cad146c48537b35fa8365e9137905785f8a21#75b5adc8920765f0c781fef03a85063aa433704e"><strong>debian/patches/do_not_build_static_binaries.patch</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">@@ -4,7 +4,7 @@ Description: Avoid static linking</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> * mauveAlignerStatic fails to build due to a problem linking -lgomp symbols</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> May be these need to be linked right into libGenome to make thos working</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> * Moreover the -static flag is suppressed in general</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> * Once -static is droped progressiveMauveStatic becomes identical to</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> * Once -static is drop<span class="idiff left right">p</span>ed progressiveMauveStatic becomes identical to</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> progressiveMauve and is thus skipped as well</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"></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;">--- a/src/Makefile.am</span></span>
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<a href="https://salsa.debian.org/med-team/progressivemauve/compare/06ddc050db8f6e00ce72add59ff2408a35430f3f...264cad146c48537b35fa8365e9137905785f8a21#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">@@ -2,3 +2,4 @@ fix_build.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">do_not_build_static_binaries.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">spelling.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">use-native-getopt.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">adapt-to-unversioned-libs.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/progressivemauve/compare/06ddc050db8f6e00ce72add59ff2408a35430f3f...264cad146c48537b35fa8365e9137905785f8a21#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</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">@@ -13,3 +13,14 @@ Description: Fix spelling</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> return -1;</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> }</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/repeatoire.cpp</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/repeatoire.cpp</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1776,7 +1776,7 @@ int main( int argc, char* argv[] )</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> }</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> if (vm.count("rmax")) {</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;">- cout << "setting maximimum multiplicity to " </span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cout << "setting maximum multiplicity to " </span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> << rmax << ".\n";</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> } else {</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> cout << "Using default maximum multiplicity (500).\n";</span></pre>
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<a href="https://salsa.debian.org/med-team/progressivemauve/compare/06ddc050db8f6e00ce72add59ff2408a35430f3f...264cad146c48537b35fa8365e9137905785f8a21#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">opts=<span class="idiff left right">dversionmangle=s/.*/0.No-Release/</span> \</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts=<span class="idiff left right">"dversionmangle=s/.*/0.No-Release/;s/\+dfsg//g"</span> \</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"> https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz</span></pre>
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