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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/rna-star">Debian Med / rna-star</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/-/commit/0748e186ac6fb3cc2409d44f4f4d0f9d3cd0a22c">0748e186</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-02-26T18:00:27+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Attempt adding simde support to build across more arches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/-/commit/529c6bd52b215d41e776025c87ef59c5e4bde802">529c6bd5</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-02-26T18:00:54+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add Build-Dep on libsimde-dev, propagaret relevant flags
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/-/commit/ad8e47ae81df6e95ded6ac488bb863f945c6faef">ad8e47ae</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-02-26T18:02:26+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add a Built-Using field for simde
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/-/commit/4cc0e70f4a97bbc77e2d38992d949258cd530f8a">4cc0e70f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-02-26T18:03:02+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update email
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#5dc91bdd30262777c0556235b73413cd5865a144">
<span class="new-file">
+
debian/patches/simde.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/rna-star/-/compare/b81811f3ec802e7056a90c0376fcb6c54f12a1d7...4cc0e70f4a97bbc77e2d38992d949258cd530f8a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,14 +3,15 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Steffen Moeller <moeller@debian.org>,</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Sascha Steinbiss <satta@debian.org>,</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Nilesh Patra <n<span class="idiff left right">patra974@gmail.com</span>></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Nilesh Patra <n<span class="idiff left right">ilesh@debian.org</span>></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Priority: optional</span>
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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libhts-dev,</span>
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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> vim-common,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> xxd,</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> libsimde-dev</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/rna-star</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/rna-star.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="22" 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">@@ -21,6 +22,7 @@ Package: rna-star</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Architecture: amd64 arm64 ppc64el mips64el</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> ${shlibs:Depends}</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Built-Using: ${simde:Built-Using}</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Description: ultrafast universal RNA-seq aligner</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> Spliced Transcripts Alignment to a Reference (STAR) software based on a</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> previously undescribed RNA-seq alignment algorithm that uses sequential</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/rna-star/-/compare/b81811f3ec802e7056a90c0376fcb6c54f12a1d7...4cc0e70f4a97bbc77e2d38992d949258cd530f8a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,3 +2,4 @@ donotuse_own_htslib.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">mips_shm_noreserve.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">reproducible.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">mathRoutinesNotInScope.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">simde.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/rna-star/-/compare/b81811f3ec802e7056a90c0376fcb6c54f12a1d7...4cc0e70f4a97bbc77e2d38992d949258cd530f8a#5dc91bdd30262777c0556235b73413cd5865a144"><strong>debian/patches/simde.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use simde instead of intel intrinsics</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2021-02-26</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/opal/opal.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/opal/opal.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -6,7 +6,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> #include <vector></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"> extern "C" {</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <immintrin.h> // AVX2 and lower</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/avx2.h> // AVX2 and lower</span></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"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> #include "opal.h"</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -84,7 +84,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> opal/opal.o : opal/opal.cpp opal/opal.h</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> cd opal && \</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) -c -O3 -std=c++11 -march=native opal.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) -std=c++11 opal.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> .PHONY: clean</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> clean:</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/rna-star/-/compare/b81811f3ec802e7056a90c0376fcb6c54f12a1d7...4cc0e70f4a97bbc77e2d38992d949258cd530f8a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,8 @@</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">CCFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-flto</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span> <span class="nv" style="color: #008080;">$(CPPFLAGS)</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++0x</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># export LDFLAGS+=-flto -pthread -lhts -lz</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_BUILD_MAINT_OPTIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">hardening</span><span class="o" style="font-weight: 600;">=</span>+all</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_CFLAGS_MAINT_APPEND</span><span class="o" style="font-weight: 600;">+=</span><span class="nt" style="color: #000080;">-DSIMDE_ENABLE_OPENMP</span> <span class="nt" style="color: #000080;">-fopenmp-simd</span> <span class="nt" style="color: #000080;">-O3</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_CXXFLAGS_MAINT_APPEND</span><span class="o" style="font-weight: 600;">+=</span><span class="nt" style="color: #000080;">-DSIMDE_ENABLE_OPENMP</span> <span class="nt" style="color: #000080;">-fopenmp-simd</span> <span class="nt" style="color: #000080;">-O3</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"><span class="nl">%</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"> dh <span class="nv" style="color: #008080;">$@</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" 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">@@ -29,3 +31,6 @@ override_dh_auto_test:</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"> debian/tests/run_test.sh <span class="nv" style="color: #008080;">$(CURDIR)</span>/source/STAR</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="make"><span class="nl">override_dh_gencontrol</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make"> dh_gencontrol <span class="nt" style="color: #000080;">--</span> <span class="nt" style="color: #000080;">-Vsimde</span>:Built-Using<span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="s2" style="color: #d14;">dpkg-query -f '</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">${source:Package}</span><span class="s2" style="color: #d14;"> (= </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">${source:Version}</span><span class="nf" style="color: #900; font-weight: 600;">)</span><span class="s2" style="color: #d14;">, ' -W "</span>libsimde-dev<span class="s2" style="color: #d14;">"</span><span class="nf" style="color: #900; font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span></pre>
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