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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/cufflinks">Debian Med / cufflinks</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cufflinks/-/commit/5f3ad42983ed9c2247eb0230f3a2bd15452a3871">5f3ad429</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-11-02T10:56:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix FTBFS with GCC 10
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cufflinks/-/commit/cd5534ee0b2f88981b48c5de4f52910b57c494ed">cd5534ee</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-11-02T10:56:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cufflinks/-/commit/47f9111662a92d4f07bb84e12783ca8def2c9d19">47f91116</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-11-02T10:56:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cufflinks/-/commit/d5754eb749a4bb9d2972ddc379f148893ff3305c">d5754eb7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-11-02T10:56:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cme fix dpkg-control
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cufflinks/-/commit/fdee7c120b369278e77dad65005eb01762510216">fdee7c12</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-11-02T10:56:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cufflinks/-/commit/463404e8d607c3c05df4998c01a91f07a811c9b1">463404e8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-11-02T10:56:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cufflinks/-/commit/e0f1b29a5b7fe08663a8b24e8737152760b6a7bb">e0f1b29a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-11-02T10:56:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
Changes-By: lintian-brush
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cufflinks/-/commit/88fffb27418151e2f3192b08c75b8cf70a488e9b">88fffb27</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-11-02T10:56:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cufflinks/-/commit/daa7a02557702a42b49de1b1768b6344e140f96e">daa7a025</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-11-02T12:10:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix autoconf issue
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#c380dd360f216fd789904f2794009be1ce992d4b">
<span class="new-file">
+
debian/patches/gcc-11.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#81a9a5b123fb5e9473f68e4733e9d389fa7872c9">
<span class="new-file">
+
debian/patches/gcc10.patch
</span>
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</li>
<li class="file-stats">
<a href="#d4f3127ca0c7660377d4511b5cbe618a872e47d0">
<span class="new-file">
+
debian/patches/no_svnversion.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/cufflinks/-/compare/20dd8e73d810a72c26da75106b2dfbc953810eaa...daa7a02557702a42b49de1b1768b6344e140f96e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">cufflinks (2.2.1+dfsg.1-9) UNRELEASED; urgency=medium</span>
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<td class="new_line diff-line-num new" data-linenumber="2" 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="LC2" class="line" lang="plaintext"></span>
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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"> * Fix autoconf issue</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #998241</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></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"> -- Andreas Tille <tille@debian.org> Tue, 02 Nov 2021 12:00:24 +0100</span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">cufflinks (2.2.1+dfsg.1-8) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> [ Reiner Herrmann ]</span>
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * fix FTBFS with GCC 10</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Closes: #966191</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<td class="new_line diff-line-num new" data-linenumber="16" 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="LC16" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<td class="new_line diff-line-num new" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> * Use secure URI in Homepage field.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> * Remove obsolete field Name from debian/upstream/metadata (already present in</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> machine-readable debian/copyright).</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sun, 02 Aug 2020 10:02:34 +0200</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">cufflinks (2.2.1+dfsg.1-7) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> * Team upload</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/cufflinks/-/compare/20dd8e73d810a72c26da75106b2dfbc953810eaa...daa7a02557702a42b49de1b1768b6344e140f96e#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<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 +6,7 @@ Uploaders: Alexandre Mestiashvili <mestia@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: non-free/science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">XS-Autobuild: yes</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> help2man,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libboost-dev,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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">@@ -18,16 +18,16 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libeigen3-dev</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Rules-requires-root: no</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/cufflinks</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/cufflinks.git</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">Homepage: http://cufflinks.cbcb.umd.edu</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Homepage: https://cufflinks.cbcb.umd.edu</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Package: cufflinks</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> ${python3:Depends}<span class="idiff left right">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> ${python3:Depends}</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Recommends: gffread</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Enhances: tophat</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Description: Transcript assembly, differential expression and regulation for RNA-Seq</span>
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<li id="c380dd360f216fd789904f2794009be1ce992d4b">
<a href="https://salsa.debian.org/med-team/cufflinks/-/compare/20dd8e73d810a72c26da75106b2dfbc953810eaa...daa7a02557702a42b49de1b1768b6344e140f96e#c380dd360f216fd789904f2794009be1ce992d4b"><strong>debian/patches/gcc-11.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Attempt to fix gcc-11 issues with `byte` - but failed</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Tue, 02 Nov 2021 12:00:24 +0100</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/src/gdna.h</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/src/gdna.h</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -9,7 +9,7 @@</span> char* reverseComplement(char* seq, int s</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"> bool gDnaInit();</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-byte gdna2bit(char* &nt, int n=4); //pack n bases into a byte (n can be 1..4)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-char g2bit2base(byte v2bit); //convert the 2-bit value into 'A', 'C', 'G' or 'T'</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;">+std::byte gdna2bit(char* &nt, int n=4); //pack n bases into a byte (n can be 1..4)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+char g2bit2base(std::byte v2bit); //convert the 2-bit value into 'A', 'C', 'G' or 'T'</span></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"> #endif</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;">--- a/src/gff.h</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;">+++ b/src/gff.h</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -16,11 +16,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </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"><span class="gd" style="color: #000; background-color: #fdd;">-const byte exMskMajSpliceL = 0x01;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const byte exMskMajSpliceR = 0x02;</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const byte exMskMinSpliceL = 0x04;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const byte exMskMinSpliceR = 0x08;</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const byte exMskTag = 0x80;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const std::byte exMskMajSpliceL = 0x01;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const std::byte exMskMajSpliceR = 0x02;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const std::byte exMskMinSpliceL = 0x04;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const std::byte exMskMinSpliceR = 0x08;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const std::byte exMskTag = 0x80;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> //reserved Gffnames::feats entries -- basic feature types</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -43,7 +43,7 @@</span> extern const uint gfo_flag_DISCARDED; //</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> extern const uint gfo_flag_LST_KEEP; //GffObj from GffReader::gflst is to be kept (not deallocated)</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> //when GffReader is destroyed</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> extern const uint gfo_flag_LEVEL_MSK; //hierarchical level: 0 = no parent</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-extern const byte gfo_flagShift_LEVEL;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern const std::byte gfo_flagShift_LEVEL;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> extern bool gff_show_warnings;</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -502,18 +502,18 @@</span> public:</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> if (v) flags |= gfo_flag_CHILDREN_PROMOTED;</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> else flags &= ~gfo_flag_CHILDREN_PROMOTED;</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- void setLevel(byte v) {</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ void setLevel(std::byte v) {</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> if (v==0) flags &= ~gfo_flag_LEVEL_MSK;</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> else flags &= ~(((uint)v) << gfo_flagShift_LEVEL);</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- byte incLevel() {</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::byte incLevel() {</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> uint v=((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL);</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> v++;</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> flags &= ~(v << gfo_flagShift_LEVEL);</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> return v;</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- byte getLevel() {</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return ((byte)((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL));</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::byte getLevel() {</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return ((std::byte)((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL));</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> }</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> bool isValidTranscript() { </span></pre>
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<a href="https://salsa.debian.org/med-team/cufflinks/-/compare/20dd8e73d810a72c26da75106b2dfbc953810eaa...daa7a02557702a42b49de1b1768b6344e140f96e#81a9a5b123fb5e9473f68e4733e9d389fa7872c9"><strong>debian/patches/gcc10.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: Reiner Herrmann <reiner@reiner-h.de></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">Description: Fix FTBFS with GCC 10</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> curwin is declared in different source file. declare it as extern</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> to fix multiple definition linker error.</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/966191</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/src/locfit/startlf.c</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/locfit/startlf.c</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -233,7 +233,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> extern lfit lf;</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> extern design des;</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> extern plots pl[];</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int curwin;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern int curwin;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> vari *vb;</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> INT nofit()</span></pre>
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<a href="https://salsa.debian.org/med-team/cufflinks/-/compare/20dd8e73d810a72c26da75106b2dfbc953810eaa...daa7a02557702a42b49de1b1768b6344e140f96e#d4f3127ca0c7660377d4511b5cbe618a872e47d0"><strong>debian/patches/no_svnversion.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: Prevent that AM_INIT_AUTOMAKE is called twice</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/998241</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Tue, 02 Nov 2021 12:00:24 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/configure.ac</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -6,14 +6,14 @@</span> m4_include([ax_bam.m4])</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> m4_include([ax_check_zlib.m4])</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> m4_include([ax_check_eigen.m4])</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"><span class="gd" style="color: #000; background-color: #fdd;">-define([svnversion], esyscmd([sh -c "svnversion|tr -d '\n'"]))dnl</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;">+#define([svnversion], esyscmd([sh -c "svnversion|tr -d '\n'"]))dnl</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> AC_INIT([cufflinks], [2.2.1], [cole@cs.umd.edu])</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE(SVN_REVISION, "svnversion", [SVN Revision])</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;">+AC_DEFINE(SVN_REVISION, "Debian package", [Debian package])</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> AC_CONFIG_SRCDIR([config.h.in])</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> AC_CONFIG_HEADERS([config.h])</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> AC_CONFIG_AUX_DIR([build-aux])</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AM_INIT_AUTOMAKE</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# AM_INIT_AUTOMAKE</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> #AM_PATH_CPPUNIT(1.10.2)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/cufflinks/-/compare/20dd8e73d810a72c26da75106b2dfbc953810eaa...daa7a02557702a42b49de1b1768b6344e140f96e#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">@@ -8,3 +8,6 @@ fix_gcc-7_ftbfs.patch</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">format-security.patch</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">lib_eigen.patch</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">fix_gcc-6.1_issue_in_liblemon_code_copy.patch</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">gcc10.patch</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">no_svnversion.patch</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"># gcc-11.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/cufflinks/-/compare/20dd8e73d810a72c26da75106b2dfbc953810eaa...daa7a02557702a42b49de1b1768b6344e140f96e#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/cufflinks/-/compare/20dd8e73d810a72c26da75106b2dfbc953810eaa...daa7a02557702a42b49de1b1768b6344e140f96e#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Contact: Cole Trapnell <cole@cs.umd.edu></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Name: Cufflinks</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Database: https://github.com/cole-trapnell-lab/cufflinks/issues</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Bug-Submit: https://github.com/cole-trapnell-lab/cufflinks/issues/new</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> - Author: ></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Cole Trapnell and Brian A Williams and Geo Pertea and</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" 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="43" 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">@@ -42,3 +43,5 @@ Registry:</td>
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42
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> Entry: cufflinks</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> Entry: cufflinks</span>
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<td class="new_line diff-line-num new" data-linenumber="46" 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="LC46" class="line" lang="plaintext">Repository: https://github.com/cole-trapnell-lab/cufflinks.git</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Repository-Browse: https://github.com/cole-trapnell-lab/cufflinks</span></pre>
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