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<h3>
Michael R. Crusoe 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/4abc9eac694e88b45dbd42fda474fed51d32c10e">4abc9eac</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-03-01T12:18:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/{rules,clean: specify the source directory, and simplify
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/-/commit/b6ca725010b3acae006c9118f28e5cda08b51c13">b6ca7250</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-03-01T12:18:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">document Nilesh's work
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/-/commit/70e0d4ddc42cc8a556bdfd2a962574f5d6a9b5e7">70e0d4dd</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-03-01T12:18:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">some patches don't need forwarding
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<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/-/commit/b411154c5226858e75760000714138824180ad7d">b411154c</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2021-03-01T12:33:23+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/patches/reproducible.patch: Reproducibly include the build time using SOURCE_DATE_EPOCH
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#f5f51601866c86e59a004bd93fa415f5675be8c5">
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+
debian/clean
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<li class="file-stats">
<a href="#e15fe6a3aa4284cb8b1685bd77b426cd5fbd7737">
debian/patches/donotuse_own_htslib.patch
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<li class="file-stats">
<a href="#76258ff6f1526200cf3fda90e9f37fd9ee4b4364">
debian/patches/reproducible.patch
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<li class="file-stats">
<a href="#5dc91bdd30262777c0556235b73413cd5865a144">
debian/patches/simde.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/rna-star/-/compare/4cc0e70f4a97bbc77e2d38992d949258cd530f8a...b411154c5226858e75760000714138824180ad7d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rna-star (2.7.8a+dfsg-2) UNRELEASED; urgency=high</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"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debian/{rules,clean: specify the source directory, and simplify</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"> [ Nilesh Patra ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * debian/{rules,control,patches/simde.patch}: use libsimde-dev to enable</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> building on non-x86 systems.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Removed "-march=native" architecture baseline violation. Closes: #983723</span>
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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"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * debian/patches/reproducible.patch: Reproducibly include the build</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> time using SOURCE_DATE_EPOCH</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> Mon, 01 Mar 2021 12:10:42 +0100</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">rna-star (2.7.8a+dfsg-1) unstable; urgency=medium</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"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/compare/4cc0e70f4a97bbc77e2d38992d949258cd530f8a...b411154c5226858e75760000714138824180ad7d#f5f51601866c86e59a004bd93fa415f5675be8c5"><strong>debian/clean</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">source/parametersDefault.xxd</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">opal/opal.o</span></pre>
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<a href="https://salsa.debian.org/med-team/rna-star/-/compare/4cc0e70f4a97bbc77e2d38992d949258cd530f8a...b411154c5226858e75760000714138824180ad7d#e15fe6a3aa4284cb8b1685bd77b426cd5fbd7737"><strong>debian/patches/donotuse_own_htslib.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller <moeller@debian.org>,</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Changed: Thu, 29 Jan 2015 14:18:44 +0100</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Use Debian packaged htslib</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">Index: rna-star/source/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rna-star.orig/source/Makefile</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/compare/4cc0e70f4a97bbc77e2d38992d949258cd530f8a...b411154c5226858e75760000714138824180ad7d#76258ff6f1526200cf3fda90e9f37fd9ee4b4364"><strong>debian/patches/reproducible.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: make build reproducible</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> Stops build hostname and directory from being recorded in the artifact.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <sascha@steinbiss.name></span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gh" style="color: #999;">Index: rna-star/source/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</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;">--- rna-star.orig/source/Makefile</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;">+++ rna-star/source/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -18,7 +18,<span class="idiff left">7</span> @@</span><span class="idiff right"> LDFLAGS_Mac :=-pthread -lz htslib/libhts</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -18,7 +18,<span class="idiff left right">14</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> LDFLAGS_gdb := $(LDFLAGS_shared)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="<not set in Debian>"'</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;">+DATE_FMT = --iso-8601=seconds</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;">+ifdef SOURCE_DATE_EPOCH</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ BUILD_DATE ?= $(shell date -u -d "@$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u -r "$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u "$(DATE_FMT)")</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ BUILD_DATE ?= $(shell date "$(DATE_FMT)")</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif</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;">+</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) <place not set in Debian package>"</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> # Defaults, can be overridden by make arguments or environment</span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> CXXFLAGS ?= -pipe -Wall -Wextra</span></pre>
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<li id="5dc91bdd30262777c0556235b73413cd5865a144">
<a href="https://salsa.debian.org/med-team/rna-star/-/compare/4cc0e70f4a97bbc77e2d38992d949258cd530f8a...b411154c5226858e75760000714138824180ad7d#5dc91bdd30262777c0556235b73413cd5865a144"><strong>debian/patches/simde.patch</strong></a>
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1
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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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2
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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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3
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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="LC4" class="line" lang="diff"><span class="p">Forwarded: https://github.com/alexdobin/STAR/issues/1160</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rna-star.orig/source/opal/opal.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rna-star/source/opal/opal.cpp</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -6,7 +6,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> #include <vector></span>
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<pre style="margin: 0;"> <span id="LC9" 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">@@ -13,14 +14,14 @@ Last-Update: 2021-02-26</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC16" 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;">--- <span class="idiff left right">a</span>/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;">+++ <span class="idiff left right">b</span>/source/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">84</span>,7 +<span class="idiff right">84</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">rna-star.orig</span>/source/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">rna-star</span>/source/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">91</span>,7 +<span class="idiff right">91</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> opal/opal.o : opal/opal.cpp opal/opal.h</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> cd opal && \</span>
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<pre style="margin: 0;"> <span id="LC23" 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 class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) -c <span class="idiff left right">-O3 </span>$(CPPFLAGS) $(CXXFLAGS) -std=c++11 opal.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> .PHONY: clean</span>
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<pre style="margin: 0;"> <span id="LC27" 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/4cc0e70f4a97bbc77e2d38992d949258cd530f8a...b411154c5226858e75760000714138824180ad7d#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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">@@ -14,15 +14,13 @@ export DEB_CFLAGS_MAINT_APPEND+=-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3</td>
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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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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"> dh <span class="nv" style="color: #008080;">$@</span><span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff">--sourcedirectory</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">source</span></span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"><span class="nl">override_dh_auto_build</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="make"> dh_auto_build <span class="nt" style="color: #000080;"><span class="idiff left">--sourcedirectory</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">source</span></span><span class="idiff right"> </span><span class="nt" style="color: #000080;">--</span> <span class="nv" style="color: #008080;">CCFLAGS_common_add</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-flto </span><span class="nv" style="color: #008080;">$(CCFLAGS)</span><span class="s2" style="color: #d14;">"</span> <span class="nv" style="color: #008080;">CCFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(CCFLAGS)</span><span class="s2" style="color: #d14;">"</span> <span class="nv" style="color: #008080;">LDFLAGS_add</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(LDFLAGS)</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"> dh_auto_build <span class="nt" style="color: #000080;">--</span> <span class="nv" style="color: #008080;">CCFLAGS_common_add</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-flto </span><span class="nv" style="color: #008080;">$(CCFLAGS)</span><span class="s2" style="color: #d14;">"</span> <span class="nv" style="color: #008080;">CCFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(CCFLAGS)</span><span class="s2" style="color: #d14;">"</span> <span class="nv" style="color: #008080;">LDFLAGS_add</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(LDFLAGS)</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="nl">override_dh_auto_clean</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd source</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> clean</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> <span class="nb" style="color: #0086b3;">source</span>/parametersDefault.xxd</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> opal/opal.o</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd source</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">${MAKE}</span> clean</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="nl">override_dh_compress</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"> dh_compress <span class="nt" style="color: #000080;">--exclude</span><span class="o" style="font-weight: 600;">=</span>.pdf</span>
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