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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/salmon">Debian Med / salmon</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/511c139b3ea90600a526607de3f44a68898c9923">511c139b</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-07-28T14:49:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix the build by adding a missing include
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/4f68e1844b6e12c5e882460b4164b4e983f9a554">4f68e184</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-28T14:50:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release 1.3.0+ds1-2
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<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#40349202e4aa955a6a71882e02d308dd6cc8cedd">
debian/patches/0008-Remove-salmon_core-lib.patch
</a>
</li>
<li class="file-stats">
<a href="#64aced6e03dbb6e07f24819ae33fbe4458991d23">
debian/patches/add_MEM_F_SELF_OVLP.patch
</a>
</li>
<li class="file-stats">
<a href="#bae08dca7af50ae6494331a147cd30150ecb5714">
debian/patches/disable-version-check.patch
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<li class="file-stats">
<a href="#bc0e3b23fde090917b48569228290b5441386db6">
<span class="new-file">
+
debian/patches/include_fix
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<li class="file-stats">
<a href="#437309f583c719ba9e8c4ec03cab2167276859d7">
debian/patches/pufferfish
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
debian/patches/spelling
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<li class="file-stats">
<a href="#2c5169d8f75b7c6f4db2798448154c0c3c31d73a">
debian/patches/use-system-pkg-config-tbb.patch
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<li class="file-stats">
<a href="#ee54dc79014b3def963898e50c98877d46c6b27e">
debian/patches/use_debian_packaged_libs.patch
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">salmon (1.3.0+ds1-2) 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"> * Fix the build by adding a missing include.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> Tue, 28 Jul 2020 14:50:48 +0200</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">
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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">salmon (1.3.0+ds1-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Add a patch for portable pausing in spinlocks.</span>
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</li>
<li id="40349202e4aa955a6a71882e02d308dd6cc8cedd">
<a href="https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554#40349202e4aa955a6a71882e02d308dd6cc8cedd"><strong>debian/patches/0008-Remove-salmon_core-lib.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Kevin Murray <spam@kdmurray.id.au></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Date: Sat, 30 Jan 2016 18:06:52 +0200</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Subject: Remove salmon_core lib</span></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="p">Remark: This patch is deactivated</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> Upstream code has changed a lot and it is not documented why</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> salmon_core lib was removed. Before breaking anything the</span>
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<li id="64aced6e03dbb6e07f24819ae33fbe4458991d23">
<a href="https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554#64aced6e03dbb6e07f24819ae33fbe4458991d23"><strong>debian/patches/add_MEM_F_SELF_OVLP.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" 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="4" 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">@@ -4,6 +4,7 @@ Description: redefine MEM_F_SELF_OVLP</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> definition to fix an FTBFS.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Remark: This patch is deactivated since current source code</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> builds nicely without it.</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 class="p">Author: Sascha Steinbiss <sascha@steinbiss.name></span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/SalmonQuantify.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/SalmonQuantify.cpp</span></span>
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<a href="https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554#bae08dca7af50ae6494331a147cd30150ecb5714"><strong>debian/patches/disable-version-check.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">Author: Michael R. Crusoe <crusoe@<span class="idiff left right">ucdavis.edu</span>></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@<span class="idiff left right">debian.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: Disable the newer version check</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</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;">--- salmon.orig/src/Salmon.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;">+++ salmon/src/Salmon.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -214,13 +214,6 @@</span></span>
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<li id="bc0e3b23fde090917b48569228290b5441386db6">
<a href="https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554#bc0e3b23fde090917b48569228290b5441386db6"><strong>debian/patches/include_fix</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: add missing include</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/COMBINE-lab/salmon/pull/552</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;">--- salmon.orig/include/BAMUtils.hpp</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;">+++ salmon/include/BAMUtils.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -9,6 +9,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> }</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"> #include <unordered_map></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;">+#include <string></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> namespace salmon {</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> namespace bam_utils {</span></pre>
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<a href="https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554#437309f583c719ba9e8c4ec03cab2167276859d7"><strong>debian/patches/pufferfish</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: Use local copy of pufferfish source for now</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</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;">--- salmon.orig/CMakeLists.txt</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;">+++ salmon/CMakeLists.txt</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -297,11 +297,7 @@</span></span>
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<a href="https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554#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">@@ -6,3 +6,4 @@ disable-version-check.patch</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"># 0008-Remove-salmon_core-lib.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"># add_MEM_F_SELF_OVLP.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">spelling</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">include_fix</span></pre>
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<a href="https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: fix typos</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/COMBINE-lab/salmon/pull/548/</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;">--- salmon.orig/include/BAMQueue.tpp</span></span>
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<a href="https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554#2c5169d8f75b7c6f4db2798448154c0c3c31d73a"><strong>debian/patches/use-system-pkg-config-tbb.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">@@ -4,7 +4,8 @@ Remark: This patch is deactivated for the moment.</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> and there is no point to fiddle around now any more.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> However, may be this is more elegant and the patch is</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> left as documentation.</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@ucdavis.edu></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CMakeLists.txt</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="p">@@ -287,6 +287,9 @@</span> endif()</span>
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<li id="ee54dc79014b3def963898e50c98877d46c6b27e">
<a href="https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554#ee54dc79014b3def963898e50c98877d46c6b27e"><strong>debian/patches/use_debian_packaged_libs.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">Author: Andreas Tille <tille@debian.org></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">Last-Update: Tue, 11 Dec 2018 19:29:39 +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 libraries and make sure these are linked dynamically</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="gd" style="color: #000; background-color: #fdd;">--- salmon.orig/src/CMakeLists.txt</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;">+++ salmon/src/CMakeLists.txt</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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