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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libarb">Debian Med / libarb</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libarb/commit/8c48d38a548ed8a0c96ad9ed1cd11ffa1ca19b39">8c48d38a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-06-07T08:17:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build some first packages in pbuilder
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libarb/commit/fc02f12499a21378ebfb93ba31772cd7f3c00721">fc02f124</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-06-07T08:26:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix some issues in packaging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libarb/commit/634979f027dbb211c8496e339592cc412f9e8bba">634979f0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-06-07T08:30:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More sensible location of the lib - if ARB might rely on a lib subdirectory this should be provide as symlink in the arb package
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#0cf9a12b42f853b2f3a953544c986437a39927fc">
debian/libarb-dev.install
</a>
</li>
<li class="file-stats">
<a href="#6f0d8f90ebeb29c75914ce814ee57adfd6b1ef06">
debian/libarb-dev.links
</a>
</li>
<li class="file-stats">
<a href="#7e765ab89dbcf565fc30aca31b6c7172fdf346df">
debian/libarb.install
</a>
</li>
<li class="file-stats">
<a href="#3003ca3cd7e616a0d99b11f7b0c48744659f4ebd">
debian/patches/fix_main_makefile.patch
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<li class="file-stats">
<a href="#dd2cfa9481ed545b7614b498bf55e14aa7f96ec8">
<span class="deleted-file">
−
debian/patches/fix_makefiles.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#7f1c79caf9de411614a532ba33a601d7bb1d6791">
debian/patches/ignore_unneeded_stuff.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libarb/compare/750c0303770c75c853296310866457d19c5b840f...634979f027dbb211c8496e339592cc412f9e8bba#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 +5,9 @@ Uploaders: Andreas Tille <tille@debian.org>,</td>
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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">
5
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<td class="diff-line-num 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">
5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<td class="diff-line-num old_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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 12~),</span>
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<td class="diff-line-num new old_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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<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">
8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> dh-exec,</span>
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<td class="diff-line-num old_line" data-linenumber="8" 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">
8
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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">
9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libglib2.0-dev,</span>
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<td class="diff-line-num new old_line" data-linenumber="9" 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="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> time,</span>
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9
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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">
11
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> valgrind</span>
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10
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12
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Standards-Version: 4.3.0</span>
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<td class="diff-line-num old_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">
11
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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">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/libarb</span>
</pre>
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<br>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/libarb/compare/750c0303770c75c853296310866457d19c5b840f...634979f027dbb211c8496e339592cc412f9e8bba#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="210" 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="210" 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">@@ -210,140 +210,8 @@ License: ARB</td>
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="plaintext"> 9. July 2008</span>
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<td class="diff-line-num old_line" data-linenumber="211" 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="LC211" class="line" lang="plaintext"> Ralf Westram <westram@arb-home.de></span>
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<td class="diff-line-num new_line" data-linenumber="212" 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="LC212" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="213" 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="LC213" class="line" lang="mosel"><span class="s1" style="color: #d14;">Files: GDE/*</span></span>
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<td class="diff-line-num old old_line" data-linenumber="214" 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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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC214" class="line" lang="mosel"><span class="s1" style="color: #d14;">Copyright: 2004-2008 The Board of Trustees of the University of Illinois and by Steven Smith</span></span>
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<td class="diff-line-num old old_line" data-linenumber="215" 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="LC215" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: GDE</span></span>
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<td class="diff-line-num old old_line" data-linenumber="216" 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="LC216" class="line" lang="mosel"><span class="s1" style="color: #d14;"> * The Genetic Data Environment (GDE) software and documentation are not in the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="217" 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="LC217" class="line" lang="mosel"><span class="s1" style="color: #d14;"> public domain. Portions of this code are owned and copyrighted by the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="218" 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="LC218" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The Board of Trustees of the University of Illinois and by Steven Smith.</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="mosel"><span class="s1" style="color: #d14;"> External functions used by GDE are the property of their authors.</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="mosel"><span class="s1" style="color: #d14;"> This release of the GDE program and documentation may not be sold, or</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="mosel"><span class="s1" style="color: #d14;"> incorporated into a commercial product, in whole or in part without the</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="mosel"><span class="s1" style="color: #d14;"> expressed written consent of the University of Illinois and of its author,</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Steven Smith.</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="mosel"><span class="s1" style="color: #d14;"> * All interested parties may redistribute the GDE as long as all copies are</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="mosel"><span class="s1" style="color: #d14;"> accompanied by this documentation, and all copyright notices remain intact.</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Parties interested in redistribution must do so on a non-profit basis,</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="mosel"><span class="s1" style="color: #d14;"> charging only for cost of media. Modifications to the GDE core editor</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="mosel"><span class="s1" style="color: #d14;"> should be forwarded to the author Steven Smith. External programs used</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="mosel"><span class="s1" style="color: #d14;"> by the GDE are copyrighted by, and are the property of their respective</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="mosel"><span class="s1" style="color: #d14;"> authors unless otherwise stated.</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="mosel"><span class="s1" style="color: #d14;">Files: GDE/PHYLIP/*</span></span>
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<td class="diff-line-num old old_line" data-linenumber="233" 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="LC233" class="line" lang="mosel"><span class="s1" style="color: #d14;">Copyright: (c) Copyright 1986-1993 by Joseph Felsenstein and the University</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="mosel"><span class="s1" style="color: #d14;"> of Washington.</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: PHYLIP_non-free</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Permission is granted to copy this document provided that</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="mosel"><span class="s1" style="color: #d14;"> no fee is charged for it and that this copyright notice is not removed.</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="mosel"><span class="s1" style="color: #d14;">Comment: Remark from the Debian package maintainer Andreas Tille</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Phylp is not used in the binary package because the Debian</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="mosel"><span class="s1" style="color: #d14;"> package is used which is in the non-free part of Debian.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="241" 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="LC241" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Remark: After heavy discussion with the author of Phylip it</span></span>
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<td class="diff-line-num old old_line" data-linenumber="242" 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="LC242" class="line" lang="mosel"><span class="s1" style="color: #d14;"> was not possible to convince him to use a free license.</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="mosel"><span class="s1" style="color: #d14;">Files: GDE/SUPPORT/CAP2.c</span></span>
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<td class="diff-line-num old old_line" data-linenumber="245" 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">
245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="mosel"><span class="s1" style="color: #d14;">Copyright: (C) 1991 Xiaoqiu Huang</span></span>
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<td class="diff-line-num old old_line" data-linenumber="246" 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">
246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: CAP2_non-free</span></span>
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<td class="diff-line-num old old_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The distribution of the program is granted provided no charge</span></span>
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<td class="diff-line-num old old_line" data-linenumber="248" 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">
248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="mosel"><span class="s1" style="color: #d14;"> is made and the copyright notice is included.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="249" 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">
249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="mosel"><span class="s1" style="color: #d14;">Comment: Remark from the Debian package maintainer Andreas Tille</span></span>
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<td class="diff-line-num old old_line" data-linenumber="250" 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">
250
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC250" class="line" lang="mosel"><span class="s1" style="color: #d14;"> I was unable to find a source URL where this program which is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="251" 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">
251
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC251" class="line" lang="mosel"><span class="s1" style="color: #d14;"> claimed as external can be downloaded.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="252" 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">
252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="253" 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">
253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="mosel"><span class="s1" style="color: #d14;">Files: CONVERTALN/*</span></span>
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<td class="diff-line-num old old_line" data-linenumber="254" 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">
254
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC254" class="line" lang="mosel"><span class="s1" style="color: #d14;">Copyright: (C) 1992 Wen-Min Kuan</span></span>
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<td class="diff-line-num old old_line" data-linenumber="255" 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">
255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: ARP_permissive</span></span>
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<td class="diff-line-num old old_line" data-linenumber="256" 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">
256
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC256" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The files in this directory do not contain an explicite license</span></span>
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<td class="diff-line-num old old_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="mosel"><span class="s1" style="color: #d14;"> statement. It has to be assumed that the license is the same as the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="258" 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">
258
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC258" class="line" lang="mosel"><span class="s1" style="color: #d14;"> general usage and redistribution license for Arb and the authors of</span></span>
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<td class="diff-line-num old old_line" data-linenumber="259" 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">
259
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC259" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Arb got a permission to distribute this code in their product.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="mosel"><span class="s1" style="color: #d14;"> .</span></span>
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<td class="diff-line-num old old_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="mosel"><span class="s1" style="color: #d14;"> This paragraph was just added to the copyright file to mention that</span></span>
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<td class="diff-line-num old old_line" data-linenumber="262" 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">
262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="mosel"><span class="s1" style="color: #d14;"> there is some copyrighted work which was not mentioned above.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="mosel"><span class="s1" style="color: #d14;">Comment: convert_aln -- an alignment(or sequence) converter written</span></span>
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<td class="diff-line-num old old_line" data-linenumber="264" 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">
264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="mosel"><span class="s1" style="color: #d14;"> by Wen-Min Kuan for the Ribsomal Database Project(RDP), April 28, 1992.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="mosel"><span class="s1" style="color: #d14;"> .</span></span>
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<td class="diff-line-num old old_line" data-linenumber="266" 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">
266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Remark from the Debian package maintainer Andreas Tille:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="267" 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">
267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="mosel"><span class="s1" style="color: #d14;"> I was unable to find a source URL where this program which is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="268" 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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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC268" class="line" lang="mosel"><span class="s1" style="color: #d14;"> claimed as external can be downloaded.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="269" 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="LC269" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="mosel"><span class="s1" style="color: #d14;">Files: GDE/FASTDNAML/*</span></span>
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<td class="diff-line-num old old_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="mosel"><span class="s1" style="color: #d14;">Copyright: (C) 1998, 1999, 2000 by Gary J. Olsen,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="272" 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">
272
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC272" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 1986 - 1990 by the University of Washington and Joseph Felsenstein.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="273" 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">
273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: GPL</span></span>
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<td class="diff-line-num old old_line" data-linenumber="274" 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">
274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="mosel"><span class="s1" style="color: #d14;">Comment: Remark from the Debian package maintainer Andreas Tille:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="275" 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">
275
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC275" class="line" lang="mosel"><span class="s1" style="color: #d14;"> This is not used in the binary package because it is available as</span></span>
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<td class="diff-line-num old old_line" data-linenumber="276" 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">
276
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC276" class="line" lang="mosel"><span class="s1" style="color: #d14;"> official Debian package and has a free license (see this package).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="277" 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">
277
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC277" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="mosel"><span class="s1" style="color: #d14;">Files: GDE/RAxML/a*</span></span>
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<td class="diff-line-num old old_line" data-linenumber="279" 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">
279
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC279" class="line" lang="mosel"><span class="s1" style="color: #d14;">Copyright: (C) 2004-2008 Alexandros Stamatakis, Michael Ott, Thomas Ludwig</span></span>
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<td class="diff-line-num old old_line" data-linenumber="280" 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">
280
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC280" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: GPL</span></span>
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<td class="diff-line-num old old_line" data-linenumber="281" 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">
281
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC281" class="line" lang="mosel"><span class="s1" style="color: #d14;">Comment: There is also a file GDE/RAxML/softwaredisclaimer in this directory</span></span>
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<td class="diff-line-num old old_line" data-linenumber="282" 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">
282
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC282" class="line" lang="mosel"><span class="s1" style="color: #d14;"> which contains some license text which might be provided in a private</span></span>
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<td class="diff-line-num old old_line" data-linenumber="283" 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">
283
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC283" class="line" lang="mosel"><span class="s1" style="color: #d14;"> mail or whatever from the RAxML authors to the Arb authors. The relevance</span></span>
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<td class="diff-line-num old old_line" data-linenumber="284" 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">
284
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC284" class="line" lang="mosel"><span class="s1" style="color: #d14;"> of this file is completely unclear because RAxML as it can be obtained from</span></span>
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<td class="diff-line-num old old_line" data-linenumber="285" 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">
285
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC285" class="line" lang="mosel"><span class="s1" style="color: #d14;"> http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm is GPLed and the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="286" 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">
286
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC286" class="line" lang="mosel"><span class="s1" style="color: #d14;"> remaining files in this directory are neither copyrighted by the RAxML</span></span>
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<td class="diff-line-num old old_line" data-linenumber="287" 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">
287
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC287" class="line" lang="mosel"><span class="s1" style="color: #d14;"> authors nor do they feature a similar license statement. This file is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="288" 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">
288
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC288" class="line" lang="mosel"><span class="s1" style="color: #d14;"> subject for clarification by the Arb authors.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="289" 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">
289
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC289" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="290" 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">
290
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC290" class="line" lang="mosel"><span class="s1" style="color: #d14;">Files: GDE/RAxML/c* GDE/RAxML/p*</span></span>
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<td class="diff-line-num old old_line" data-linenumber="291" 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">
291
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC291" class="line" lang="mosel"><span class="s1" style="color: #d14;">Copyright: (C) 1993-2002 by the University of Washington.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="292" 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">
292
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC292" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Written by Joseph Felsenstein, Hisashi Horino, and others</span></span>
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<td class="diff-line-num old old_line" data-linenumber="293" 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">
293
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC293" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: RAxML_non-free</span></span>
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<td class="diff-line-num old old_line" data-linenumber="294" 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">
294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Permission is granted to copy and use this program provided no</span></span>
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<td class="diff-line-num old old_line" data-linenumber="295" 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">
295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="mosel"><span class="s1" style="color: #d14;"> fee is charged for it and provided that this copyright notice is not</span></span>
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<td class="diff-line-num old old_line" data-linenumber="296" 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">
296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="mosel"><span class="s1" style="color: #d14;"> removed.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="298" 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">
298
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC298" class="line" lang="mosel"><span class="s1" style="color: #d14;">Files: GDE/RAxML/g*</span></span>
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<td class="diff-line-num old old_line" data-linenumber="299" 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">
299
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC299" class="line" lang="mosel"><span class="s1" style="color: #d14;">Copyright: (C) 1987, 1993, 1994</span></span>
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<td class="diff-line-num old old_line" data-linenumber="300" 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">
300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The Regents of the University of California. All rights reserved.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="301" 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">
301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: BSD-3-clause</span></span>
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<td class="diff-line-num old old_line" data-linenumber="302" 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">
302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Copyright (c) The Regents of the University of California.</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="mosel"><span class="s1" style="color: #d14;"> All rights reserved.</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="mosel"><span class="s1" style="color: #d14;"> .</span></span>
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<td class="diff-line-num old old_line" data-linenumber="305" 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">
305
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC305" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Redistribution and use in source and binary forms, with or without</span></span>
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<td class="diff-line-num old old_line" data-linenumber="306" 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">
306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="mosel"><span class="s1" style="color: #d14;"> modification, are permitted provided that the following conditions</span></span>
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<td class="diff-line-num old old_line" data-linenumber="307" 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">
307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="mosel"><span class="s1" style="color: #d14;"> are met:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="308" 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">
308
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC308" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 1. Redistributions of source code must retain the above copyright</span></span>
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<td class="diff-line-num old old_line" data-linenumber="309" 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">
309
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<td class="diff-line-num new_line old" data-linenumber="213" 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="LC309" class="line" lang="mosel"><span class="s1" style="color: #d14;"> notice, this list of conditions and the following disclaimer.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="310" 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">
310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 2. Redistributions in binary form must reproduce the above copyright</span></span>
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<td class="diff-line-num old old_line" data-linenumber="311" 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">
311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="mosel"><span class="s1" style="color: #d14;"> notice, this list of conditions and the following disclaimer in the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="312" 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">
312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="mosel"><span class="s1" style="color: #d14;"> documentation and/or other materials provided with the distribution.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="313" 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">
313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="mosel"><span class="s1" style="color: #d14;"> 3. Neither the name of the University nor the names of its contributors</span></span>
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<td class="diff-line-num old old_line" data-linenumber="314" 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">
314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="mosel"><span class="s1" style="color: #d14;"> may be used to endorse or promote products derived from this software</span></span>
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<td class="diff-line-num old old_line" data-linenumber="315" 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">
315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="mosel"><span class="s1" style="color: #d14;"> without specific prior written permission.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="316" 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">
316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="mosel"><span class="s1" style="color: #d14;"> .</span></span>
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<td class="diff-line-num old old_line" data-linenumber="317" 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">
317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="mosel"><span class="s1" style="color: #d14;"> THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND</span></span>
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<td class="diff-line-num old old_line" data-linenumber="318" 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">
318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></span>
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<td class="diff-line-num old old_line" data-linenumber="319" 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">
319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="mosel"><span class="s1" style="color: #d14;"> IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="mosel"><span class="s1" style="color: #d14;"> FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="mosel"><span class="s1" style="color: #d14;"> DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="mosel"><span class="s1" style="color: #d14;"> OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)</span></span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="mosel"><span class="s1" style="color: #d14;"> HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT</span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="mosel"><span class="s1" style="color: #d14;"> LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY</span></span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="mosel"><span class="s1" style="color: #d14;"> OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="mosel"><span class="s1" style="color: #d14;"> SUCH DAMAGE.</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="mosel"></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="mosel"><span class="s1" style="color: #d14;">Files: GDE/TREEPUZZLE/*</span></span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="mosel"><span class="s1" style="color: #d14;">Copyright: (C) 1995-1999 Korbinian Strimmer and Arndt von Haeseler</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="mosel"><span class="s1" style="color: #d14;"> (C) 1999-2001 Heiko A. Schmidt, Korbinian Strimmer,Martin Vingron,</span></span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Arndt von Haeseler</span></span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: GPL</span></span>
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334
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="mosel"><span class="s1" style="color: #d14;">Comment: This code is not used in the binary package because it is available</span></span>
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<td class="diff-line-num old old_line" data-linenumber="335" 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">
335
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="mosel"><span class="s1" style="color: #d14;"> as official Debian package and has a free license (see this package).</span></span>
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336
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="mosel"></span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="mosel"><span class="s1" style="color: #d14;">Files: READSEQ/*</span></span>
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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="mosel"><span class="s1" style="color: #d14;">Copyright: 1990-1993 D. Gilbert <gilbertd@bio.indiana.edu></span></span>
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<td class="diff-line-num old old_line" data-linenumber="339" 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">
339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: PD</span></span>
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<td class="diff-line-num old old_line" data-linenumber="340" 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">
340
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="mosel"><span class="s1" style="color: #d14;"> readseq is public domain software</span></span>
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<td class="diff-line-num old old_line" data-linenumber="341" 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">
341
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="mosel"><span class="s1" style="color: #d14;">Comment: This code is not used in the binary package because it is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="342" 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">
342
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="mosel"><span class="s1" style="color: #d14;"> available as official Debian package and has a free license (see this</span></span>
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<td class="diff-line-num old old_line" data-linenumber="343" 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">
343
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="mosel"><span class="s1" style="color: #d14;"> package).</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="mosel"><span class="s1" style="color: #d14;">Copyright: (C) 2008-201<span class="idiff left right">3</span> Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">Copyright: (C) 2008-201<span class="idiff left right">9</span> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="plaintext">License: GPL</span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext">License: GPL</span>
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<a href="https://salsa.debian.org/med-team/libarb/compare/750c0303770c75c853296310866457d19c5b840f...634979f027dbb211c8496e339592cc412f9e8bba#0cf9a12b42f853b2f3a953544c986437a39927fc"><strong>debian/libarb-dev.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">-</span><span class="nx">dev</span><span class="o" style="font-weight: 600;">/</span><span class="nx">INCLUDE</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">arb</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">-</span><span class="nx">dev</span><span class="o" style="font-weight: 600;">/*</span><span class="nx">_COM</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">arb</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">-</span><span class="nx">dev</span><span class="o" style="font-weight: 600;">/</span><span class="nx">SL</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">arb</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="php"></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/dh-exec</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">SL</span><span class="o" style="font-weight: 600;">/*/*.</span><span class="nx">a</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="nx">DEB_HOST_MULTIARCH</span><span class="p">}</span><span class="o" style="font-weight: 600;">/</span><span class="nx">arb</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libarb/compare/750c0303770c75c853296310866457d19c5b840f...634979f027dbb211c8496e339592cc412f9e8bba#6f0d8f90ebeb29c75914ce814ee57adfd6b1ef06"><strong>debian/libarb-dev.links</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/include/arb usr/lib/arb/INCLUDE</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># This is probably not needed any more - if at all it should probably be usr/lib/${DEB_HOST_MULTIARCH}/arb/INCLUDE</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># usr/include/arb usr/lib/arb/INCLUDE</span></pre>
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<a href="https://salsa.debian.org/med-team/libarb/compare/750c0303770c75c853296310866457d19c5b840f...634979f027dbb211c8496e339592cc412f9e8bba#7e765ab89dbcf565fc30aca31b6c7172fdf346df"><strong>debian/libarb.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">so</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">arb</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/dh-exec</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">lib</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">so</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="nx">DEB_HOST_MULTIARCH</span><span class="p">}</span><span class="o" style="font-weight: 600;">/</span><span class="nx">arb</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libarb/compare/750c0303770c75c853296310866457d19c5b840f...634979f027dbb211c8496e339592cc412f9e8bba#3003ca3cd7e616a0d99b11f7b0c48744659f4ebd"><strong>debian/patches/fix_main_makefile.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Wed, 05 Jun 2019 15:03:30 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Strip everything from ARB Makefiles that's not contained in the</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> free library parts.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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1
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -201,8 +201,8 @@ ifeq ($(DEBUG),0)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> endif</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"> ifeq ($(DEBIAN),1)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- lflags += -rpath=/usr/lib/arb/lib -z relro</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ lflags += -z relro</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ clflags += -Wl,-z,relro</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> ifeq ($(DEBUG),1)</span>
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3
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -705,7 +705,7 @@ ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),</span></span>
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4
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> @echo '$(ARBHOME)/$@:1: has been generated.'</span>
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5
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> @echo 'Please edit $@ to configure your system!'</span>
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<li id="dd2cfa9481ed545b7614b498bf55e14aa7f96ec8">
<a href="https://salsa.debian.org/med-team/libarb/compare/750c0303770c75c853296310866457d19c5b840f...634979f027dbb211c8496e339592cc412f9e8bba#dd2cfa9481ed545b7614b498bf55e14aa7f96ec8"><strong>debian/patches/fix_makefiles.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CORE/Makefile</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CORE/Makefile</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12,6 +12,13 @@ GENERATED_HEADERS= \</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> arb_diff.h \</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> arb_match.h \</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 class="gi" style="color: #000; background-color: #dfd;">+ARBHOME=..</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+A_CXX=$(CXX)</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;">+shared_cflags= -fPIC -I../INCLUDE -I. -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include/ -DDEBUG</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SHARED_LIB_SUFFIX=so</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LINK_SHARED_LIB := $(A_CXX) $(clflags) -shared $(GCOVFLAGS) -o# link shared lib</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAIN=libCORE.a</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> LIB_SHARED=../lib/$(MAIN:.a=).$(SHARED_LIB_SUFFIX)</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> # MAIN contains .a (instead of wanted .so). Translate via do_...-target</span></pre>
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<a href="https://salsa.debian.org/med-team/libarb/compare/750c0303770c75c853296310866457d19c5b840f...634979f027dbb211c8496e339592cc412f9e8bba#7f1c79caf9de411614a532ba33a601d7bb1d6791"><strong>debian/patches/ignore_unneeded_stuff.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, 05 Jun 2019 15:03:30 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Some scripts are referencing things that are not available in</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> the stripped down free library part. Just patch this out.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/SOURCE_TOOLS/generate_all_links.sh</span></span>
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2
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/SOURCE_TOOLS/generate_all_links.sh</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,7 @@</span></span>
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<a href="https://salsa.debian.org/med-team/libarb/compare/750c0303770c75c853296310866457d19c5b840f...634979f027dbb211c8496e339592cc412f9e8bba#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -7,6 +7,7 @@</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</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">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">libdevel=$(DEB_SOURCE)-dev</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">ARBHOME=$(CURDIR)</span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -63,6 +64,12 @@ override_dh_auto_clean: config.makefile</td>
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63
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> find -name \*.log -a ! -name phyml-manual.log -print0 | xargs -0 rm -f</span>
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64
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> rm -f TEMPLATES/arb_build.h</span>
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65
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">override_dh_install:</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> dh_install</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> mkdir -p debian/$(libdevel)/usr/include/arb</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> install INCLUDE/*.h INCLUDE/*.hxx debian/$(libdevel)/usr/include/arb</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> rm -rf debian/$(libdevel)/usr/include/arb/valgrind.h</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></span>
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66
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext">override_dh_strip:</span>
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67
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> # Fix rpath issue (once libarb is installed)</span>
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68
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"> if [ -e debian/libarb/usr/lib/arb/lib/ARB.so ] ; then \</span>
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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">@@ -73,10 +80,3 @@ override_dh_strip:</td>
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73
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"></span>
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74
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">override_dh_installchangelogs:</span>
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75
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> dh_installchangelogs arb_CHANGES.txt</span></pre>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">override_dh_shlibdeps:</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> dh_shlibdeps -a -l debian/libarb/usr/lib</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">override_dh_fixperms:</span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> dh_fixperms</span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> chmod 0644 debian/libarb-dev/usr/include/arb/xml.hxx</span></pre>
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