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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mptp">Debian Med / mptp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b">9c16f116</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-29T08:54:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.2.4</pre>
</li>
</ul>
<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#458e1d0f85716e3c7c27857fb05bfd41d637ba7c">
ChangeLog.md
</a>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
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<li class="file-stats">
<a href="#0e766443d2ebc74860970a223861f9bc7b7c049f">
man/mptp.1
</a>
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<li class="file-stats">
<a href="#67e794015a01b8816bd16290e5f8538236da8245">
src/Makefile.am
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<li class="file-stats">
<a href="#7bd7f552051f121b1d3c559bd85474d6ac25ed5d">
src/aic.c
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<li class="file-stats">
<a href="#d4680ab5b75426bc629f111b7048e43970a06112">
src/arch.c
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</li>
<li class="file-stats">
<a href="#7442ac311dbfd89059322cc1ea0b6ab7ac8d6493">
src/auto.c
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<li class="file-stats">
<a href="#081af4c1121861433cb353b9119324fd66a95171">
src/dp.c
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<li class="file-stats">
<a href="#9f173d5aaed86988a2509a3e6308e29d6abcd717">
src/mptp.c
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<li class="file-stats">
<a href="#91197b4433b6a20331e46f63a38dfda8981df1c1">
src/mptp.h
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<li class="file-stats">
<a href="#c071ca59b5fdd284648c9b06098ae9faa464f921">
src/multirun.c
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<li class="file-stats">
<a href="#b76ede0b033220303429258462504f67f8e221ea">
src/random.c
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<li class="file-stats">
<a href="#a84dd12c0a2a7a35be02ff3fb545cdba7ab7c61b">
src/rtree.c
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<li class="file-stats">
<a href="#67c319180cbcafb0d1d073f70f07d14aff317006">
src/util.c
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</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="na" style="color: teal;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">c</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: teal;">compiler</span><span class="pi">:</span></span>
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc</span></span>
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: teal;">matrix</span><span class="pi">:</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: teal;">include</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">]</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">gcc-4.6'</span><span class="pi">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=gcc-4.6</span></span>
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6
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"></span>
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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC7" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">./autogen.sh && ./configure && make && make check</span></span></pre>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">gcc-4.7'</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=gcc-4.7</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">gcc-4.8'</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=gcc-4.8</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">gcc-4.9'</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=gcc-4.9</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">gcc-5'</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=gcc-5</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">]</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">gcc-6'</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=gcc-6</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">clang</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">,</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">llvm-toolchain-precise-3.5'</span><span class="pi">]</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">clang-3.5'</span><span class="pi">]</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=clang-3.5</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="yaml"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">clang</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">,</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">llvm-toolchain-precise-3.6'</span><span class="pi">]</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">clang-3.6'</span><span class="pi">]</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=clang-3.6</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="yaml"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">clang</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">,</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">llvm-toolchain-precise-3.7'</span><span class="pi">]</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">clang-3.7'</span><span class="pi">]</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=clang-3.7</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">clang</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">,</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">llvm-toolchain-precise-3.8'</span><span class="pi">]</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">clang-3.8'</span><span class="pi">]</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=clang-3.8</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="yaml"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="yaml"> <span class="na" style="color: teal;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">clang</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">,</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">llvm-toolchain-trusty-3.9'</span><span class="pi">]</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">clang-3.9'</span><span class="pi">]</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=clang-3.9</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="yaml"></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: teal;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="yaml"> <span class="na" style="color: teal;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="yaml"> <span class="na" style="color: teal;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">clang</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="yaml"> <span class="na" style="color: teal;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="yaml"> <span class="na" style="color: teal;">apt</span><span class="pi">:</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="yaml"> <span class="na" style="color: teal;">sources</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ubuntu-toolchain-r-test'</span><span class="pi">,</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">llvm-toolchain-trusty-4.0'</span><span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="yaml"> <span class="na" style="color: teal;">packages</span><span class="pi">:</span> <span class="pi">[</span><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">clang-4.0'</span><span class="pi">]</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="yaml"> <span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">COMPILER=clang-4.0</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">./autogen.sh && CC=$COMPILER ./configure && make && make check</span></span></pre>
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<li id="458e1d0f85716e3c7c27857fb05bfd41d637ba7c">
<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#458e1d0f85716e3c7c27857fb05bfd41d637ba7c"><strong>ChangeLog.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,12 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown">All notable changes to <span class="sb" style="color: #d14;">`mptp`</span> will be documented in this file.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown">This project adheres to <span class="p">[</span><span class="nv" style="color: teal;">Semantic Versioning</span><span class="p">](</span><span class="sx" style="color: #d14;">http://semver.org/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.2.4] - 2018-05-14</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p"> -</span> If we do not manage to generate a random starting delimitation with the</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"> wanted number of species (randomly chosen), we use the currently generated</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"> delimitation instead.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.2.3] - 2017-07-25</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p"> -</span> Replaced hsearch which was causing problems on APPLE with custom hashtable</span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -78,9 +78,9 @@ where `DIR` is the directory where bash autocompletion is stored. You can use</td>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown">and the documentation, use the following commands:</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown">wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.<span class="idiff left right">2/mptp-src-0.2.2</span>.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>zxvf mptp-src-0.2.<span class="idiff left right">2</span>.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>mptp-src-0.2.<span class="idiff left right">2</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown">wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.<span class="idiff left right">4/mptp-src-0.2.4</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>zxvf mptp-src-0.2.<span class="idiff left right">4</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>mptp-src-0.2.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown">./configure</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown">make</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown">make <span class="nb" style="color: #0086b3;">install</span> <span class="c" style="color: #998; font-style: italic;"># as root, or run sudo make install</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,12 +110,12 @@ To use the pre-compiled binary, download the appropriate executable for your</td>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown">system using the following commands if you are using a Linux system:</span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="markdown">wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.<span class="idiff left right">2/mptp-0.2.2</span>-linux-x86_64.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>zxvf mptp-0.2.<span class="idiff left right">2</span>-linux-x86_64.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown">wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.<span class="idiff left right">4/mptp-0.2.4</span>-linux-x86_64.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>zxvf mptp-0.2.<span class="idiff left right">4</span>-linux-x86_64.tar.gz</span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown">You will now have the binary distribution in a folder called</span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="markdown"><span class="sb" style="color: #d14;">`mptp-0.2.<span class="idiff left right">2</span>-linux-x86_64`</span> in which you will find three subfolders <span class="sb" style="color: #d14;">`bin`</span>, <span class="sb" style="color: #d14;">`man`</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"><span class="sb" style="color: #d14;">`mptp-0.2.<span class="idiff left right">4</span>-linux-x86_64`</span> in which you will find three subfolders <span class="sb" style="color: #d14;">`bin`</span>, <span class="sb" style="color: #d14;">`man`</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown">and <span class="sb" style="color: #d14;">`doc`</span>. We recommend making a copy or a symbolic link to the mptp binary</span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"><span class="sb" style="color: #d14;">`bin/mptp`</span> in a folder included in your <span class="sb" style="color: #d14;">`$PATH`</span>, and a copy or a symbolic link</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown">to the mptp man page <span class="sb" style="color: #d14;">`man/mptp.1`</span> in a folder included in your <span class="sb" style="color: #d14;">`$MANPATH`</span>. The</span>
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<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,13 +2,15 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># Process this file with autoconf to produce a configure script.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_PREREQ([2.63])</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">AC_INIT([mptp], [0.2.<span class="idiff left right">3], [Tomas.Flouri@h-its.org</span>])</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">AC_INIT([mptp], [0.2.<span class="idiff left right">4], [t.flouris@ucl.ac.uk</span>])</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">AM_INIT_AUTOMAKE([subdir-objects])</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">AC_LANG([C])</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">AC_CONFIG_SRCDIR([src/mptp.c])</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">AC_CONFIG_HEADERS([config.h])</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">AC_CANONICAL_HOST</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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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">${CFLAGS=""}</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"># Checks for programs.</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">AC_PROG_CC</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">AC_PROG_RANLIB</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">@@ -72,6 +74,18 @@ AS_IF([test "x$enable_pdfman" != "xno"], [</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> fi</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">])</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"># Various OS-related dependencies</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">case "${host_os}" in</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> linux*)</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> ;;</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> cygwin*|mingw*)</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> AC_CHECK_LIB([psapi],[GetProcessMemoryInfo])</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> ;;</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> darwin*)</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> ;;</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">esac</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">AM_CONDITIONAL(HAVE_PS2PDF, test "x${have_ps2pdf}" = "xyes")</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">AM_PROG_CC_C_O</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"></span>
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<li id="0e766443d2ebc74860970a223861f9bc7b7c049f">
<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#0e766443d2ebc74860970a223861f9bc7b7c049f"><strong>man/mptp.1</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.\" ============================================================================</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">.TH mptp 1 "<span class="idiff left right">January 31, 2017" "mptp 0.2.2</span>" "USER COMMANDS"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.TH mptp 1 "<span class="idiff left right">May 14, 2018" "mptp 0.2.4</span>" "USER COMMANDS"</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.\" ============================================================================</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH NAME</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">mptp \(em single-locus species delimitation</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="354" 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="354" 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">@@ -354,5 +354,10 @@ incorrectly formatted trees.</td>
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354
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="plaintext">.TP</span>
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355
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="plaintext">.BR v0.2.3\~ "released July 25th, 2017"</span>
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356
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="plaintext">Replaced hsearch() with custom hashtable. Fixed minor output error messages.</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext">.BR v0.2.4\~ "released May 14th, 2018"</span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext">If we do not manage to generate a random starting delimitation with the wanted</span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext">number of species (randomly chosen), we use the currently generated</span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext">delimitation instead.</span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="plaintext">.RE</span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="plaintext">.LP</span></pre>
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<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#67e794015a01b8816bd16290e5f8538236da8245"><strong>src/Makefile.am</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,8 +4,7 @@ libparse_utree_a_SOURCES = parse_utree.y lex_utree.l</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="nv" style="color: teal;">libparse_rtree_a_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> parse_rtree.y lex_rtree.l</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nv" style="color: teal;">noinst_LIBRARIES</span> <span class="o" style="font-weight: 600;">=</span> libparse_utree.a libparse_rtree.a</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="make"><span class="nv" style="color: teal;">AM_CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: navy;">-I</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">srcdir</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-mtune</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-Wsign-compare</span> <span class="nt" style="color: navy;">-g</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">LIBS</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="nv" style="color: teal;">AM_CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: navy;">-I</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">srcdir</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-mtune</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-Wsign-compare</span> <span class="nt" style="color: navy;">-g</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="nv" style="color: teal;">AM_YFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-d</span> <span class="nt" style="color: navy;">-p</span> <span class="sb" style="color: #d14;">`</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SED</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-n</span> <span class="s1" style="color: #d14;">'s/.*_\(.*\)/\1_/p'</span> <span class="o" style="font-weight: 600;"><<<</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nv" style="color: teal;">AM_LFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-o</span> lex.yy.c</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#7bd7f552051f121b1d3c559bd85474d6ac25ed5d"><strong>src/aic.c</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">@@ -258,7 +258,7 @@ static void mcmc_finalize(rtree_t * root,</td>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">densities</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">dp_recurse</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span> <span class="n" style="color: #333;">method</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">dp_recurse</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">long</span></span> <span class="n" style="color: #333;">method</span><span class="p">)</span></span>
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="c"><span class="p">{</span></span>
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263
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c"></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">@@ -830,7 +830,7 @@ void aic_mcmc(rtree_t * tree,</td>
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830
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="c"></span>
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831
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* throw a coin to decide whether to convert a coalescent root to a</span></span>
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832
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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> speciation or the other way round */</span></span>
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833
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="c"> <span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">erand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="c"> <span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">mptp_</span>erand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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834
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834
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">speciation</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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835
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="c"></span>
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836
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836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">speciation</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">crnodes_count</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">snodes_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></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">@@ -844,7 +844,7 @@ void aic_mcmc(rtree_t * tree,</td>
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844
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844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="c"></span>
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845
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845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="c"></span>
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846
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846
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* select a coalescent root, split it into two coalescent nodes */</span></span>
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847
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="c"> <span class="n" style="color: #333;">rand_long</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nrand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="c"> <span class="n" style="color: #333;">rand_long</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">mptp_</span>nrand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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848
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848
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rand_long</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">crnodes_count</span><span class="p">;</span></span>
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849
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849
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="c"> <span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">crnodes</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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850
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="c"></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">@@ -923,7 +923,7 @@ void aic_mcmc(rtree_t * tree,</td>
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* decide whether to accept or reject proposal */</span></span>
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<pre style="margin: 0;">-<span id="LC926" class="line" lang="c"> <span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">erand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="c"> <span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">mptp_</span>erand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* accept */</span></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">@@ -987,7 +987,7 @@ void aic_mcmc(rtree_t * tree,</td>
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<pre style="margin: 0;"> <span id="LC987" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> / \ / \</span></span>
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<pre style="margin: 0;"> <span id="LC988" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> CR * * CR C * * C */</span></span>
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<pre style="margin: 0;"> <span id="LC989" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC990" class="line" lang="c"> <span class="n" style="color: #333;">rand_long</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nrand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="c"> <span class="n" style="color: #333;">rand_long</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">mptp_</span>nrand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC991" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rand_long</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">snodes_count</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="c"> <span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snodes</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC993" class="line" lang="c"></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">@@ -1063,7 +1063,7 @@ void aic_mcmc(rtree_t * tree,</td>
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* decide whether to accept or reject proposal */</span></span>
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<pre style="margin: 0;">-<span id="LC1066" class="line" lang="c"> <span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">erand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="c"> <span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">mptp_</span>erand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1067" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1068" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* accept */</span></span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#d4680ab5b75426bc629f111b7048e43970a06112"><strong>src/arch.c</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">@@ -23,47 +23,56 @@</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">arch_get_memused</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _WIN32</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">PROCESS_MEMORY_COUNTERS</span> <span class="n" style="color: #333;">pmc</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"> <span class="n" style="color: #333;">GetProcessMemoryInfo</span><span class="p">(</span><span class="n" style="color: #333;">GetCurrentProcess</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pmc</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">PROCESS_MEMORY_COUNTERS</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pmc</span><span class="p">.</span><span class="n" style="color: #333;">PeakWorkingSetSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">rusage</span> <span class="n" style="color: #333;">r_usage</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">getrusage</span><span class="p">(</span><span class="n" style="color: #333;">RUSAGE_SELF</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">r_usage</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#<span class="idiff left right">if defined</span> __APPLE__</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#<span class="idiff left right"> ifdef</span> __APPLE__</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Mac: ru_maxrss gives the size in bytes */</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p"><span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">r_usage</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ru_maxrss</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">r_usage</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ru_maxrss</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#<span class="idiff left right"> </span>else</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Linux: ru_maxrss gives the size in kilobytes */</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_maxrss</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_maxrss</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">arch_get_memtotal</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if defined(_SC_PHYS_PAGES) && defined(_SC_PAGESIZE)</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">phys_pages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="n" style="color: #333;">_SC_PHYS_PAGES</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pagesize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="n" style="color: #333;">_SC_PAGESIZE</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _WIN32</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">phys_pages</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">pagesize</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot determine amount of RAM"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// sysconf(3) notes that pagesize * phys_pages can overflow, such as</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// when long is 32-bits and there's more than 4GB RAM. Since vsearch</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// apparently targets LP64 systems like x86_64 linux, this will not</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// arise in practice on the intended platform.</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pagesize</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">LONG_MAX</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">phys_pages</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">LONG_MAX</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">pagesize</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">phys_pages</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">MEMORYSTATUSEX</span> <span class="n" style="color: #333;">ms</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">ms</span><span class="p">.</span><span class="n" style="color: #333;">dwLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">MEMORYSTATUSEX</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">GlobalMemoryStatusEx</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ms</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ms</span><span class="p">.</span><span class="n" style="color: #333;">ullTotalPhys</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#elif defined(__APPLE__)</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mib</span> <span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="n" style="color: #333;">CTL_HW</span><span class="p">,</span> <span class="n" style="color: #333;">HW_MEMSIZE</span> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int64_t</span></span> <span class="n" style="color: #333;">ram</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">long</span></span> <span class="n" style="color: #333;">ram</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">ram</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sysctl</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mib</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">ram</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">sysctl</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mib</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">ram</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot determine amount of RAM"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ram</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGESIZE)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">phys_pages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="n" style="color: #333;">_SC_PHYS_PAGES</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pagesize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="n" style="color: #333;">_SC_PAGESIZE</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">phys_pages</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">pagesize</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot determine amount of RAM"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pagesize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">phys_pages</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">sysinfo</span> <span class="n" style="color: #333;">si</span><span class="p">;</span></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">@@ -73,3 +82,76 @@ unsigned long arch_get_memtotal()</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">arch_get_cores</span><span class="p">()</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"><span class="p">{</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _WIN32</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">SYSTEM_INFO</span> <span class="n" style="color: #333;">si</span><span class="p">;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">GetSystemInfo</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">si</span><span class="p">);</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">si</span><span class="p">.</span><span class="n" style="color: #333;">dwNumberOfProcessors</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="n" style="color: #333;">_SC_NPROCESSORS_ONLN</span><span class="p">);</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"><span class="p">}</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">arch_get_user_system_time</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">user_time</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">system_time</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">user_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">system_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _WIN32</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="n" style="color: #333;">HANDLE</span> <span class="n" style="color: #333;">hProcess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetCurrentProcess</span><span class="p">();</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">FILETIME</span> <span class="n" style="color: #333;">ftCreation</span><span class="p">,</span> <span class="n" style="color: #333;">ftExit</span><span class="p">,</span> <span class="n" style="color: #333;">ftKernel</span><span class="p">,</span> <span class="n" style="color: #333;">ftUser</span><span class="p">;</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">ULARGE_INTEGER</span> <span class="n" style="color: #333;">ul</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">GetProcessTimes</span><span class="p">(</span><span class="n" style="color: #333;">hProcess</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ftCreation</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ftExit</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ftKernel</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ftUser</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">ul</span><span class="p">.</span><span class="n" style="color: #333;">u</span><span class="p">.</span><span class="n" style="color: #333;">HighPart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftUser</span><span class="p">.</span><span class="n" style="color: #333;">dwHighDateTime</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="n" style="color: #333;">ul</span><span class="p">.</span><span class="n" style="color: #333;">u</span><span class="p">.</span><span class="n" style="color: #333;">LowPart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftUser</span><span class="p">.</span><span class="n" style="color: #333;">dwLowDateTime</span><span class="p">;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">user_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ul</span><span class="p">.</span><span class="n" style="color: #333;">QuadPart</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">100.0e-9</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">ul</span><span class="p">.</span><span class="n" style="color: #333;">u</span><span class="p">.</span><span class="n" style="color: #333;">HighPart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftKernel</span><span class="p">.</span><span class="n" style="color: #333;">dwHighDateTime</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">ul</span><span class="p">.</span><span class="n" style="color: #333;">u</span><span class="p">.</span><span class="n" style="color: #333;">LowPart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftKernel</span><span class="p">.</span><span class="n" style="color: #333;">dwLowDateTime</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">system_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ul</span><span class="p">.</span><span class="n" style="color: #333;">QuadPart</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">100.0e-9</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">rusage</span> <span class="n" style="color: #333;">r_usage</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">getrusage</span><span class="p">(</span><span class="n" style="color: #333;">RUSAGE_SELF</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">r_usage</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">user_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_utime</span><span class="p">.</span><span class="n" style="color: #333;">tv_sec</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_utime</span><span class="p">.</span><span class="n" style="color: #333;">tv_usec</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.0e-6</span><span class="p">;</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">system_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_stime</span><span class="p">.</span><span class="n" style="color: #333;">tv_sec</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_stime</span><span class="p">.</span><span class="n" style="color: #333;">tv_usec</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.0e-6</span><span class="p">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"><span class="p">}</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">arch_srandom</span><span class="p">()</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"><span class="p">{</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* initialize pseudo-random number generator */</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_seed</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seed</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"> <span class="p">{</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _WIN32</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">srand</span><span class="p">(</span><span class="n" style="color: #333;">GetTickCount</span><span class="p">());</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="131" 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">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"/dev/urandom"</span><span class="p">,</span> <span class="n" style="color: #333;">O_RDONLY</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fd</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" 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">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to open /dev/urandom"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" 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">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">fd</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seed</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">seed</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">fatal</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to read from /dev/urandom"</span><span class="p">);</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">close</span><span class="p">(</span><span class="n" style="color: #333;">fd</span><span class="p">);</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">srandom</span><span class="p">(</span><span class="n" style="color: #333;">seed</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="p">}</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="p">{</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _WIN32</span></span>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="n" style="color: #333;">srand</span><span class="p">(</span><span class="n" style="color: #333;">seed</span><span class="p">);</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">srandom</span><span class="p">(</span><span class="n" style="color: #333;">seed</span><span class="p">);</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"> <span class="p">}</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"><span class="p">}</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">arch_random</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"><span class="p">{</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _WIN32</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rand</span><span class="p">();</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">random</span><span class="p">();</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#7442ac311dbfd89059322cc1ea0b6ab7ac8d6493"><strong>src/auto.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" 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="193" 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">@@ -193,7 +193,7 @@ static void link_sequences(rtree_t * root, char ** headers, char ** sequence, lo</td>
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193
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"> <span class="n" style="color: #333;">rtree_query_tipnodes</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">tipnodes</span><span class="p">);</span></span>
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194
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c"></span>
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195
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* create a libc hash table of size tip_count */</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashtable_create</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">root</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">leaves</span></span><span class="p">);</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashtable_create</span><span class="p">(<span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">root</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">leaves</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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197
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="c"></span>
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198
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* populate a libc hash table with tree tip labels */</span></span>
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199
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#081af4c1121861433cb353b9119324fd66a95171"><strong>src/dp.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="186" 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="186" 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">@@ -186,7 +186,6 @@ void dp_ptp(rtree_t * tree, long method)</td>
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="c"> <span class="n" style="color: #333;">dp_vector_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">vector</span><span class="p">;</span></span>
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187
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PTP_METHOD_MULTI</span><span class="p">)</span></span>
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188
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="c"> <span class="p">{</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="c"> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vec</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">score_multi</span><span class="p">;</span></span>
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190
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">min_aic_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aic</span><span class="p">(</span><span class="n" style="color: #333;">vec</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">score_multi</span><span class="p">,</span> <span class="n" style="color: #333;">vec</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">species_count</span><span class="p">,</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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191
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">edge_count</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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192
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="201" 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="200" 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">@@ -201,6 +200,7 @@ void dp_ptp(rtree_t * tree, long method)</td>
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201
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="p">}</span></span>
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202
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c"> <span class="p">}</span></span>
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203
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c"> <span class="p">}</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vec</span><span class="p">[</span><span class="n" style="color: #333;">best_index</span><span class="p">].</span><span class="n" style="color: #333;">score_multi</span><span class="p">;</span></span>
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204
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"> <span class="p">}</span></span>
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205
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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206
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="223" 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="223" 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">@@ -223,10 +223,12 @@ void dp_ptp(rtree_t * tree, long method)</td>
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223
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">edge_count</span><span class="p">,</span></span>
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224
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="c"> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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225
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Score Null Model: %.6f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">coal_logl</span><span class="p">);</span></span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"Best score for single coalescent rate: %.6f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">vec</span><span class="p">[</span><span class="n" style="color: #333;">best_index</span><span class="p">].</span><span class="n" style="color: #333;">score_single</span><span class="p">);</span></span>
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228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"Best score for multi coalescent rate: %.6f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c"> <span class="n" style="color: #333;">vec</span><span class="p">[</span><span class="n" style="color: #333;">best_index</span><span class="p">].</span><span class="n" style="color: #333;">score_multi</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PTP_METHOD_SINGLE</span><span class="p">)</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"Best score for single coalescent rate: %.6f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="c"> <span class="n" style="color: #333;">vec</span><span class="p">[</span><span class="n" style="color: #333;">best_index</span><span class="p">].</span><span class="n" style="color: #333;">score_single</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"Best score for multi coalescent rate: %.6f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="c"> <span class="n" style="color: #333;">vec</span><span class="p">[</span><span class="n" style="color: #333;">best_index</span><span class="p">].</span><span class="n" style="color: #333;">score_multi</span><span class="p">);</span></span>
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="c"> <span class="p">}</span></span>
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="c"></span>
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* do a Likelihood Ratio Test (lrt) and return the computed p-value */</span></span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#9f173d5aaed86988a2509a3e6308e29d6abcd717"><strong>src/mptp.c</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">@@ -582,7 +582,7 @@ void fillheader()</td>
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="c"> <span class="s" style="color: #d14;">"%s %s_%s, %1.fGB RAM, %ld cores"</span><span class="p">,</span></span>
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583
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="c"> <span class="n" style="color: #333;">PROG_NAME</span><span class="p">,</span> <span class="n" style="color: #333;">PROG_VERSION</span><span class="p">,</span> <span class="n" style="color: #333;">PROG_ARCH</span><span class="p">,</span></span>
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584
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584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="c"> <span class="n" style="color: #333;">arch_get_memtotal</span><span class="p">()</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">sysconf</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">_SC_NPROCESSORS_ONLN</span></span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">arch_get_cores</span></span><span class="p"><span class="idiff right">(</span>));</span></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">show_header</span><span class="p">()</span></span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#91197b4433b6a20331e46f63a38dfda8981df1c1"><strong>src/mptp.h</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">@@ -22,7 +22,8 @@</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _GNU_SOURCE</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <assert.h></span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <search.h></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <ctype.h></span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <fcntl.h></span></span>
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26
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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27
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdarg.h></span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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="34" 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">@@ -33,10 +34,11 @@</td>
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33
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <limits.h></span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <locale.h></span></span>
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35
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/stat.h></span></span>
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36
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/time.h></span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/resource.h></span></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <unistd.h></span></span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdbool.h></span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <time.h></span></span>
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" 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="53" 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">@@ -51,12 +53,40 @@</td>
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51
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_NAME PACKAGE</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_VERSION PACKAGE_VERSION</span></span>
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __APPLE__</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_ARCH "macosx_x86_64"</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __PPC__</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __LITTLE_ENDIAN__</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_CPU "ppc64le"</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#error "Big endian ppc64 CPUs not supported"</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"></span>
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56
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_ARCH "linux_x86_64"</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_CPU "x86_64"</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"></span>
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58
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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59
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __APPLE__</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_OS "osx"</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/resource.h></span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/sysctl.h></span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __linux__</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_OS "linux"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/resource.h></span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/sysinfo.h></span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"></span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _WIN32</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_OS "win"</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <windows.h></span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <psapi.h></span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_ARCH PROG_OS "_" PROG_CPU</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"></span>
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60
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PLL_FAILURE 0</span></span>
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61
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PLL_SUCCESS 1</span></span>
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62
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PLL_LINEALLOC 2048</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="206" 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="236" 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">@@ -206,7 +236,7 @@ typedef struct hashtable_s</td>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">pair_s</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">label</span><span class="p">;</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">in</span>t</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size_</span>t</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">pair_t</span><span class="p">;</span></span>
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211
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c"></span>
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212
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* macros */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="289" 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="319" 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">@@ -289,9 +319,10 @@ char * xstrchrnul(char *s, int c);</td>
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289
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xstrdup</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xstrndup</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">getusec</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">show_rusage</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mode</span><span class="p">);</span></span>
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294
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">random_init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rstate</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">seedval</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mptp_erand48</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">mptp_nrand48</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rstate</span><span class="p">);</span> </span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="c"></span>
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296
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* functions in mptp.c */</span></span>
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297
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="c"></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">@@ -366,6 +397,7 @@ void lca_destroy(void);</td>
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366
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="c"></span>
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367
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">arch_get_memused</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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368
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">arch_get_memtotal</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">arch_get_cores</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c"></span>
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370
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* functions in dp.c */</span></span>
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371
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="c"></span>
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<li id="c071ca59b5fdd284648c9b06098ae9faa464f921">
<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#c071ca59b5fdd284648c9b06098ae9faa464f921"><strong>src/multirun.c</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">@@ -155,7 +155,7 @@ void multirun(rtree_t * root, long method)</td>
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* generate one seed for each run */</span></span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c"> <span class="n" style="color: #333;">seeds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">opt_mcmc_runs</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">));</span></span>
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157
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opt_mcmc_runs</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="c"> <span class="n" style="color: #333;">seeds</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nrand48</span><span class="p">(</span><span class="n" style="color: #333;">global_xsubi</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c"> <span class="n" style="color: #333;">seeds</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">mptp_</span>nrand48</span><span class="p">(</span><span class="n" style="color: #333;">global_xsubi</span><span class="p">);</span></span>
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159
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c"> </span>
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160
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_mcmc_runs</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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161
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">seeds</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt_seed</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="174" 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="174" 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">@@ -174,7 +174,7 @@ void multirun(rtree_t * root, long method)</td>
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174
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> across all MCMC runs */</span></span>
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">combined_val</span><span class="p">;</span></span>
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="n" style="color: #333;">combined_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">));</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">combined_val</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">));</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">combined_val</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="p"><span class="idiff right">)(</span></span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">));</span></span>
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178
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="c"></span>
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179
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">inner_node_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">**</span><span class="p">)</span><span class="n" style="color: #333;">xmalloc</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span></span>
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c"> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="291" 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="291" 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">@@ -291,7 +291,6 @@ void multirun(rtree_t * root, long method)</td>
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291
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mean</span><span class="p">,</span> <span class="n" style="color: #333;">var</span><span class="p">,</span> <span class="n" style="color: #333;">stdev</span><span class="p">,</span> <span class="n" style="color: #333;">avg_stdev</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">support_count</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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295
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stdev</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opt_mcmc_runs</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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297
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="c"> <span class="n" style="color: #333;">mean</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">support</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#b76ede0b033220303429258462504f67f8e221ea"><strong>src/random.c</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">@@ -51,7 +51,7 @@ static int cb_node_select(rtree_t * node)</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* otherwise, we just throw a coin and select one of the two cases */</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">erand48</span><span class="p">(</span><span class="n" style="color: #333;">g_rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">mptp_</span>erand48</span><span class="p">(</span><span class="n" style="color: #333;">g_rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* don't select */</span></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">@@ -86,7 +86,7 @@ double random_delimitation(rtree_t * root,</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"> <span class="n" style="color: #333;">max_species</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_species_count</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">g_rstate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rstate</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">rand_long</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nrand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">rand_long</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">mptp_</span>nrand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_species_count</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">species_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rand_long</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></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">@@ -115,7 +115,14 @@ double random_delimitation(rtree_t * root,</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">edgelen_sum</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">edgelen_sum</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">inner_node_list</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">species_count</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">species_count</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* TODO: This fixes issue #82, but we should implement a better, non-biased</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> way of generatng random starting delimitations */</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"> <span class="n" style="color: #333;">species_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">species_count</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">delimited_species</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">species_count</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#a84dd12c0a2a7a35be02ff3fb545cdba7ab7c61b"><strong>src/rtree.c</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">@@ -205,7 +205,7 @@ static void rtree_traverse_recursive(rtree_t * node,</td>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c"></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="c"> <span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">erand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c"> <span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">mptp_</span>erand48</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rand_double</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="c"> <span class="n" style="color: #333;">rtree_traverse_recursive</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">cbtrav</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">rstate</span><span class="p">,</span> <span class="n" style="color: #333;">outbuffer</span><span class="p">);</span></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">@@ -450,7 +450,7 @@ static rtree_t ** rtree_tipstring_nodes(rtree_t * root,</td>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="c"> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">rtree_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* create a hashtable of tip labels */</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="c"> <span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashtable_create</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">root</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">leaves</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="c"> <span class="n" style="color: #333;">hashtable_t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ht</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashtable_create</span><span class="p">(<span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="p"><span class="idiff">)(</span></span><span class="n" style="color: #333;"><span class="idiff">root</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">leaves</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">leaves</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="c"> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/mptp/commit/9c16f116efc88f5dd5b5a3c15bc042e737b47c8b#67c319180cbcafb0d1d073f70f07d14aff317006"><strong>src/util.c</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">@@ -21,6 +21,11 @@</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "mptp.h"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MPTP_RAND48_MULT_0 (0xe66d)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MPTP_RAND48_MULT_1 (0xdeec)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MPTP_RAND48_MULT_2 (0x0005)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MPTP_RAND48_ADD (0x000b)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">progress_prompt</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">progress_next</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">progress_size</span><span class="p">;</span></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">@@ -144,23 +149,6 @@ long getusec(void)</td>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tv</span><span class="p">.</span><span class="n" style="color: #333;">tv_sec</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1000000</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tv</span><span class="p">.</span><span class="n" style="color: #333;">tv_usec</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">show_rusage</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c"><span class="p">{</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">rusage</span> <span class="n" style="color: #333;">r_usage</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">getrusage</span><span class="p">(</span><span class="n" style="color: #333;">RUSAGE_SELF</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">r_usage</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Time: %.3fs (user)"</span><span class="p">,</span> <span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_utime</span><span class="p">.</span><span class="n" style="color: #333;">tv_sec</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_utime</span><span class="p">.</span><span class="n" style="color: #333;">tv_usec</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.0e-6</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" %.3fs (sys)"</span><span class="p">,</span> <span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_stime</span><span class="p">.</span><span class="n" style="color: #333;">tv_sec</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_stime</span><span class="p">.</span><span class="n" style="color: #333;">tv_usec</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.0e-6</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if defined __APPLE__</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Mac: ru_maxrss gives the size in bytes */</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" Memory: %.0fMB</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_maxrss</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.0e-6</span><span class="p">);</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Linux: ru_maxrss gives the size in kilobytes */</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" Memory: %.0fMB</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">r_usage</span><span class="p">.</span><span class="n" style="color: #333;">ru_maxrss</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.0e-3</span><span class="p">);</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">xopen</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">);</span></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">@@ -177,3 +165,42 @@ void random_init(unsigned short * rstate, long seedval)</td>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seedval</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xffffl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"> <span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seedval</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">16</span><span class="p">;</span></span>
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179
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">mptp_randomize</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rstate</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">accu</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="n" style="color: #333;">temp</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">accu</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MPTP_RAND48_MULT_0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">MPTP_RAND48_ADD</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c"> <span class="n" style="color: #333;">temp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span><span class="n" style="color: #333;">accu</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* lower 16 bits */</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">accu</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">accu</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">MPTP_RAND48_MULT_0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">MPTP_RAND48_MULT_1</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"> <span class="n" style="color: #333;">temp</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span><span class="n" style="color: #333;">accu</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* middle 16 bits */</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="c"> <span class="n" style="color: #333;">accu</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="c"> <span class="n" style="color: #333;">accu</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">MPTP_RAND48_MULT_0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="c"> <span class="n" style="color: #333;">MPTP_RAND48_MULT_1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="c"> <span class="n" style="color: #333;">MPTP_RAND48_MULT_2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="c"> <span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="c"> <span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="190" 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">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="c"> <span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span><span class="p">)</span><span class="n" style="color: #333;">accu</span><span class="p">;</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="c"><span class="p">}</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">mptp_erand48</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rstate</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="c"><span class="p">{</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">mptp_randomize</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ldexp</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">48</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="c"> <span class="n" style="color: #333;">ldexp</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="c"> <span class="n" style="color: #333;">ldexp</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="c"><span class="p">}</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">mptp_nrand48</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rstate</span><span class="p">)</span> </span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"><span class="p">{</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">mptp_randomize</span><span class="p">(</span><span class="n" style="color: #333;">rstate</span><span class="p">);</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rstate</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="c"><span class="p">}</span></span></pre>
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