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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/400d3881e3bb3e4f62a8c476a77289a6287ac625">400d3881</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-30T10:01:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/386e6c6451ac6304337efec40962df33b9a86314">386e6c64</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-30T10:02:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/rules: build avx and sse3 version for amd64
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/bd2e5ebf6c8f69c23ca8ff64ff3a87abfa8960de">bd2e5ebf</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-30T10:03:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1a0453e516e167132f0f9392c87de0ea5fe79145">
<span class="new-file">
+
debian/bin/simd-dispatch
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#63c3307a25f0c1334b59e145f9fc809c05bbfa70">
debian/patches/rm_arch_specific_flags.patch
</a>
</li>
<li class="file-stats">
<a href="#d185b62d54557160e7ddc743405a9cec66dcaa96">
debian/patches/use_debian_sqlite.patch
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="1a0453e516e167132f0f9392c87de0ea5fe79145">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/335d827edf4ee4f2ae700bd95bd855ac4d44e76c...bd2e5ebf6c8f69c23ca8ff64ff3a87abfa8960de#1a0453e516e167132f0f9392c87de0ea5fe79145"><strong>debian/bin/simd-dispatch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">DIR</span><span class="o" style="font-weight: 600;">=</span>/usr/lib/hyphy/bin</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">EXE</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">DIR</span><span class="k" style="font-weight: 600;">}</span>/<span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">CMDARGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell">test_and_run <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span>lscpu | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-x</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">EXE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Using </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">EXE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> 1>&2</span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">EXE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CMDARGS</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</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">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</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">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>SIMD <span class="k" style="font-weight: 600;">in </span>avx sse3 <span class="p">;</span> <span class="k" style="font-weight: 600;">do </span>test_and_run <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SIMD</span><span class="k" style="font-weight: 600;">}</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fallback to plain option</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Using </span><span class="nv" style="color: #008080;">$EXE</span><span class="s2" style="color: #d14;"> without SIMD support"</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">EXE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CMDARGS</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 1>&2</span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/335d827edf4ee4f2ae700bd95bd855ac4d44e76c...bd2e5ebf6c8f69c23ca8ff64ff3a87abfa8960de#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy (2.5.27+dfsg-2) unstable; urgency=medium</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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Refresh patches.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debian/rules: build avx and sse3 version for amd64</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> Sat, 30 Jan 2021 10:03:12 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">hyphy (2.5.27+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version</span>
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<li id="63c3307a25f0c1334b59e145f9fc809c05bbfa70">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/335d827edf4ee4f2ae700bd95bd855ac4d44e76c...bd2e5ebf6c8f69c23ca8ff64ff3a87abfa8960de#63c3307a25f0c1334b59e145f9fc809c05bbfa70"><strong>debian/patches/rm_arch_specific_flags.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ Last-Update: 2020-09-28</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hyphy.orig/CMakeLists.txt</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hyphy/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left right">54,9 +154</span>,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left right">81,9 +181</span>,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> #set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -fopt-info")</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> if(NOAVX)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,16 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> else(NOSSE3)</span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> PCL_CHECK_FOR_SSE3()</span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> if(${HAVE_SSE3_EXTENSIONS})</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="p">@@ -192,7 +191,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -194,7 +193,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> else(NOAVX)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> PCL_CHECK_FOR_AVX()</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> if(${HAVE_AVX_EXTENSIONS})</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=native -mtune=native -mavx")</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mavx")</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> add_definitions (-D_SLKP_USE_AVX_INTRINSICS)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> PCL_CHECK_FOR_FMA3()</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> if (${HAVE_FMA3})</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -219,7 +218,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 ")</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> if(NOAVX)</span>
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24
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> if(NOSSE3)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" 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="36" 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">@@ -27,3 +36,12 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> else(NOSSE3)</span>
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28
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> PCL_CHECK_FOR_SSE3()</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> if(${HAVE_SSE3_EXTENSIONS})</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -230,7 +229,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> else(NOAVX)</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> PCL_CHECK_FOR_AVX()</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> if(${HAVE_AVX_EXTENSIONS})</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=native -mtune=native -mavx")</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mavx")</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> add_definitions (-D_SLKP_USE_AVX_INTRINSICS)</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> PCL_CHECK_FOR_FMA3()</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> if (${HAVE_FMA3})</span></pre>
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<li id="d185b62d54557160e7ddc743405a9cec66dcaa96">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/335d827edf4ee4f2ae700bd95bd855ac4d44e76c...bd2e5ebf6c8f69c23ca8ff64ff3a87abfa8960de#d185b62d54557160e7ddc743405a9cec66dcaa96"><strong>debian/patches/use_debian_sqlite.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,10 +4,11 @@ Description: Use Debian packaged sqlite3</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> - in src/lib/setup.py</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Reviewed-by: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-09-24</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff">--- hyphy.orig/CMakeLists.txt</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hyphy/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left right">19,12 +119</span>,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left right">46,12 +146</span>,11 @@</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> file(GLOB SRC_CONTRIB src/contrib/*.cpp)</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> set(SRC_LINK src/lib/link/THyPhy.cpp)</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">@@ -21,7 +22,7 @@ Last-Update: 2020-09-24</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> set_source_files_properties(${SRC_CORE} ${SRC_NEW} {SRC_UTILS} PROPERTIES COMPILE_FLAGS "-Weffc++ -Wextra -Wall")</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> #-------------------------------------------------------------------------------</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">279,6 +278</span>,35 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">313,6 +312</span>,35 @@</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> add_definitions (-D__HYPHYCURL__)</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> endif(${CURL_FOUND} AND NOT APPLE)</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </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">@@ -57,7 +58,7 @@ Last-Update: 2020-09-24</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> #-------------------------------------------------------------------------------</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">13,11 +341</span>,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">47,11 +375</span>,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> )</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> set_property(</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">@@ -69,7 +70,7 @@ Last-Update: 2020-09-24</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> SOURCE src/core/calcnode2.cpp</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> APPEND_STRING PROPERTY COMPILE_FLAGS " -fstrict-aliasing -funroll-loops"</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">37,7 +360</span>,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">71,7 +394</span>,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> src/core/include</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> src/contrib</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> src/lib/Link src/new/include</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/335d827edf4ee4f2ae700bd95bd855ac4d44e76c...bd2e5ebf6c8f69c23ca8ff64ff3a87abfa8960de#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,13 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> dh_auto_configure --builddirectory obj_avx -- -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> dh_auto_configure --builddirectory obj_sse3 -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> # convert a few ISO-8859-1 files to address national-encoding</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">@@ -27,9 +33,31 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> ; do iconv -f ISO-8859-1 -t UTF-8 < $${file} > "$${file}.new" \</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> ; mv "$${file}.new" "$${file}" \</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> ; done</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> # no idea about the purpose of the dynamic library - executables are not simply linked against it</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> dh_auto_build -- MP MPI</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> dh_auto_build --builddirectory obj_avx -- MP MPI</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> dh_auto_build --builddirectory obj_sse3 -- MP MPI</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> dh_auto_build -- MP MPI</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> # LIB</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> mkdir -p debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> mkdir -p debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> cp obj_avx/HYPHYMPI debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin/HYPHYMPI-avx</span>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> cp obj_sse3/HYPHYMPI debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin/HYPHYMPI-sse3</span>
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<td class="diff-line-num new new_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> cp obj_avx/hyphy debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin/hyphy-avx</span>
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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> cp obj_sse3/hyphy debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin/hyphy-sse3</span>
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<td class="diff-line-num new new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> dh_install -phyphy-common debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/bin</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> mv debian/hyphy-mpi/usr/bin/HYPHYMPI debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin/</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> mv debian/hyphy-pt/usr/bin/hyphy debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin/</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> cd $(CURDIR)/debian/hyphy-mpi/usr/bin && \</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/bin/simd-dispatch HYPHYMPI</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> cd $(CURDIR)/debian/hyphy-pt/usr/bin && \</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/bin/simd-dispatch hyphy</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">endif</span>
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33
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_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">
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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