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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/salmon">Debian Med / salmon</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/fd2cee9e7e359ef5a363e3b04644879bf7d0113f">fd2cee9e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-11T09:36:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use sphinx theme that is packaged for Debian
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/557b0c2005eda2982e03c6af8116b92625e992a1">557b0c20</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-11T09:37:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">I do not see any reason to remove license.rst from doc/source
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/e6d1717a91d9a32451ee946e9fb5608da9ef7244">e6d1717a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-11T09:38:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/bf67a606acd3cf2440116d1959a85805f5160060">bf67a606</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-11T09:47:15+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#bae08dca7af50ae6494331a147cd30150ecb5714">
debian/patches/disable-version-check.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#0325e4f25102e77f8a7e2b29dd07d7e574a1b96e">
<span class="new-file">
+
debian/patches/sphinx.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/d009c20a5b2d33d680ba03c60c4262228311b5e1...bf67a606acd3cf2440116d1959a85805f5160060#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">salmon (1.5.2+ds1-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">salmon (1.5.2+ds1-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<td class="new_line diff-line-num" data-linenumber="2" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="plaintext"> [ Steffen Moeller ]</span>
</pre>
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<td class="new_line diff-line-num" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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<td class="old_line diff-line-num new" 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">
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github (routine-update)</span>
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<td class="old_line diff-line-num" 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">
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<td class="new_line diff-line-num" data-linenumber="6" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * New upstream version</span>
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<td class="old_line diff-line-num" data-linenumber="5" 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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<td class="new_line diff-line-num" data-linenumber="7" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * d/u/metadata: Added ref to SciCrunch (SCR_017036)</span>
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> * source: Added deleted-during-build doc/source/license.rst</span>
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> to files-excluded</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> * TODO</span>
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> - missing indep-buildep https://github.com/pradyunsg/furo</span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> ./doc/requirements.txt:furo</span>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> ./doc/source/conf.py:html_theme = 'furo'</span>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> Theme error:</span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> no theme named 'furo' found (missing theme.conf?)</span>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Fri, 03 Sep 2021 15:35:41 +0200</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">salmon (1.4.0+ds1-1.1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> <span class="idiff left right">* Non-maintainer upload.</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> * <span class="idiff left right">Fix watchfile to detect new versions on github (routine-update)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right">[ Andreas Tille ]</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * <span class="idiff left right">Build-Depends: python3-docs-theme and use this instead of furo</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> -- <span class="idiff left">Steffen Moe</span>lle<span class="idiff">r</span> <<span class="idiff">moe</span>lle<span class="idiff">r</span>@debian.org> <span class="idiff right">Fri, 03 Sep 2021 15:34:51</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- <span class="idiff left">Andreas Ti</span>lle <<span class="idiff">ti</span>lle@debian.org> <span class="idiff right">Mon, 11 Oct 2021 09:38:42</span> +0200</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">salmon (1.4.0+ds1-1) unstable; urgency=medium</span>
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26
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/salmon/-/compare/d009c20a5b2d33d680ba03c60c4262228311b5e1...bf67a606acd3cf2440116d1959a85805f5160060#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" 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="29" 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">@@ -29,6 +29,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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29
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> sphinx-doc,</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> python3-sphinx,</span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> python3-sphinx-rtd-theme,</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> python3-docs-theme,</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> zlib1g-dev,</span>
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33
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> libeigen3-dev,</span>
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34
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> libbz2-dev,</span>
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<a href="https://salsa.debian.org/med-team/salmon/-/compare/d009c20a5b2d33d680ba03c60c4262228311b5e1...bf67a606acd3cf2440116d1959a85805f5160060#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -6,7 +6,6 @@ Files-Excluded: include/eigen3</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> src/posix.cc</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cmake/Modules/FindTBB.cmake</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> scripts/cpld.bash</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> doc/source/license.rst</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Copyright: © 2015 The Salmon Authors</span>
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<a href="https://salsa.debian.org/med-team/salmon/-/compare/d009c20a5b2d33d680ba03c60c4262228311b5e1...bf67a606acd3cf2440116d1959a85805f5160060#bae08dca7af50ae6494331a147cd30150ecb5714"><strong>debian/patches/disable-version-check.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" 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="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;">--- <span class="idiff left right">salmon.orig</span>/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;">+++ <span class="idiff left right">salmon</span>/src/Salmon.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">@@ -21<span class="idiff left">4</span>,13 +21<span class="idiff right">4</span>,6 @@</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;">--- <span class="idiff left right">a</span>/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;">+++ <span class="idiff left right">b</span>/src/Salmon.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -21<span class="idiff left">5</span>,13 +21<span class="idiff">5</span>,6 @@</span><span class="idiff right"> int main(int argc, char* argv[]) {</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> std::transform(no_version_env.begin(), no_version_env.end(), no_version_env.begin(), </span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> [](unsigned char c){ return std::toupper(c); } // correct</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> );</span>
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<a href="https://salsa.debian.org/med-team/salmon/-/compare/d009c20a5b2d33d680ba03c60c4262228311b5e1...bf67a606acd3cf2440116d1959a85805f5160060#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">@@ -5,3 +5,4 @@ disable-version-check.patch</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"># use-system-pkg-config-tbb.patch</span>
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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">sphinx.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/salmon/-/compare/d009c20a5b2d33d680ba03c60c4262228311b5e1...bf67a606acd3cf2440116d1959a85805f5160060#0325e4f25102e77f8a7e2b29dd07d7e574a1b96e"><strong>debian/patches/sphinx.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 11 Oct 2021 09:34:54 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Use sphinx theme that is packaged for Debian</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="LC5" class="line" lang="diff">--- a/doc/source/conf.py</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;">+++ b/doc/source/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -32,6 +32,7 @@</span> extensions = [</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 'sphinx.ext.autodoc',</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> 'sphinx.ext.todo',</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> 'sphinx.ext.ifconfig',</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;">+ 'python_docs_theme'</span></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"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> # Add any paths that contain templates here, relative to this directory.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -107,7 +108,7 @@</span> pygments_style = 'sphinx'</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> #html_theme = "sphinx_rtd_theme"</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> #html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-html_theme = 'furo'</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+html_theme = 'python_docs_theme'</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> html_logo = '../logo.png'</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> #html_theme = 'classic'</span></pre>
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<li id="ee54dc79014b3def963898e50c98877d46c6b27e">
<a href="https://salsa.debian.org/med-team/salmon/-/compare/d009c20a5b2d33d680ba03c60c4262228311b5e1...bf67a606acd3cf2440116d1959a85805f5160060#ee54dc79014b3def963898e50c98877d46c6b27e"><strong>debian/patches/use_debian_packaged_libs.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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">@@ -2,8 +2,8 @@ Author: Andreas Tille <tille@debian.org></td>
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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 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;">--- <span class="idiff left right">salmon.orig</span>/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;">+++ <span class="idiff left right">salmon</span>/src/CMakeLists.txt</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;">--- <span class="idiff left right">a</span>/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;">+++ <span class="idiff left right">b</span>/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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> include_directories(</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> ${GAT_SOURCE_DIR}/include</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" 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">@@ -12,7 +12,7 @@ Forwarded: not-needed</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> ${GAT_SOURCE_DIR}/external</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> ${GAT_SOURCE_DIR}/external/cereal/include</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> ${GAT_SOURCE_DIR}/external/install/include</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left">09</span>,15 +2<span class="idiff right">09</span>,15 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left">12</span>,15 +2<span class="idiff">12</span>,15 @@</span><span class="idiff right"> target_link_libraries(salmon</span></span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> graphdump</span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> ntcard</span>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> gff</span>
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<td class="diff-line-num unfold js-unfold old_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>
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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">@@ -31,7 +31,7 @@ Forwarded: not-needed</td>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> ${BZIP2_LIBRARIES}</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> ${LIBSALMON_LINKER_FLAGS}</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> ${NON_APPLECLANG_LIBS}</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="p">@@ -22<span class="idiff left">5</span>,8 +22<span class="idiff right">5</span>,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -22<span class="idiff left">8</span>,8 +22<span class="idiff">8</span>,8 @@</span><span class="idiff right"> target_link_libraries(salmon</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> ## PUFF_INTEGRATION </span>
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> alevin_core</span>
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37
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> ${ASAN_LIB}</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">@@ -42,7 +42,7 @@ Forwarded: not-needed</td>
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42
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> ${LIBRT}</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> ${CMAKE_DL_LIBS}</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> #ubsan</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="p">@@ -24<span class="idiff left">0</span>,14 +24<span class="idiff right">0</span>,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -24<span class="idiff left">3</span>,14 +24<span class="idiff">3</span>,14 @@</span><span class="idiff right"> target_link_libraries(unitTests</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> salmon_core</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> gff</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> ${STADEN_LIBRARIES} </span>
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