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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/quicktree">Debian Med / quicktree</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/quicktree/-/commit/3dd0bc8e5e69c386988ca87877c9c40a07f02802">3dd0bc8e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-12T20:47:56+02:00</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/quicktree/-/commit/385a6fdd157ad428e2f403526b2992e5cae1742d">385a6fdd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-12T20:48:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Fixes: lintian: upstream-metadata-file-is-missing
See-also: https://lintian.debian.org/tags/upstream-metadata-file-is-missing.html
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/quicktree/-/commit/2e6bf72ad754f5d5d3ab1dd9780082d4a1019a5e">2e6bf72a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-12T20:48:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<strong><a href="https://salsa.debian.org/med-team/quicktree/-/commit/fe426a6598742190616d848b8a06773b570106f1">fe426a65</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-16T14:17:27+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">To enable removing quicktree source code copy from libsonlib package a static library is created here
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#da14b1587ca83f48c2a684ec60bc9b458f132a84">
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+
debian/libquicktree-dev.install
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<li class="file-stats">
<a href="#5a63a8c9d42440f4ceb7f328b69e46f03ac4c133">
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+
debian/patches/create_lib.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="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
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+
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/quicktree/-/compare/0a925f990469319ea72d460c52c96e191e31b10f...fe426a6598742190616d848b8a06773b570106f1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">quicktree (2.5-3) UNRELEASED; 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"> * To enable removing quicktree source code copy from libsonlib package</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> a static library is created here</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 16 Jun 2020 09:35:08 +0200</span>
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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">quicktree (2.5-2) unstable; 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="LC10" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new new_line" 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"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 12 Jun 2020 20:48:04 +0200</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">quicktree (2.5-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * Initial release (Closes: #961375)</span>
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<a href="https://salsa.debian.org/med-team/quicktree/-/compare/0a925f990469319ea72d460c52c96e191e31b10f...fe426a6598742190616d848b8a06773b570106f1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -3,8 +3,9 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Uploaders: Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> help2man</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> help2man,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> dh-exec</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Homepage: https://github.com/khowe/quicktree/</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/quicktree</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">@@ -29,3 +30,26 @@ Description: Neighbor-Joining algorithm for phylogenies</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> The tress are written to stdout, in the Newick/New-Hampshire format</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> use by PHYLIP and many other programs</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Package: libquicktree-dev</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Section: libdevel</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Description: Neighbor-Joining algorithm for phylogenies (development)</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> QuickTree is an efficient implementation of the Neighbor-Joining</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> algorithm (PMID: 3447015), capable of reconstructing phylogenies from</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> huge alignments in time less than the age of the universe.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> QuickTree accepts both distance matrix and multiple-sequence-aligment</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> inputs. The former should be in PHYLIP format. The latter should be</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> in Stockholm format, which is the native alignment format for the Pfam</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> database. Alignments in various formats can be converted to Stockholm</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> format with the sreformat program, which is part of the HMMer package</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> (hmmer.org).</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> The tress are written to stdout, in the Newick/New-Hampshire format</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> use by PHYLIP and many other programs</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> This package contains some header files from quicktree that are used</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> by other packages.</span></pre>
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<a href="https://salsa.debian.org/med-team/quicktree/-/compare/0a925f990469319ea72d460c52c96e191e31b10f...fe426a6598742190616d848b8a06773b570106f1#da14b1587ca83f48c2a684ec60bc9b458f132a84"><strong>debian/libquicktree-dev.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/dh-exec</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">quicktree</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">lib</span><span class="o" style="font-weight: 600;">*.</span><span class="nx">a</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="nx">DEB_HOST_MULTIARCH</span><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/quicktree/-/compare/0a925f990469319ea72d460c52c96e191e31b10f...fe426a6598742190616d848b8a06773b570106f1#5a63a8c9d42440f4ceb7f328b69e46f03ac4c133"><strong>debian/patches/create_lib.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -10,6 +10,13 @@</span> COMMON = $(OBJ)/align.o \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> $(OBJ)/options.o \</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> $(OBJ)/util.o \</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> $(OBJ)/sequence.o</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;">+LIBOBJ = $(OBJ)/buildtree.o \</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(OBJ)/cluster.o \</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(OBJ)/distancemat.o \</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(OBJ)/options.o \</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(OBJ)/util.o \</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(OBJ)/sequence.o \</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(OBJ)/tree.o \</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> QUICKTREEOBJ = $(COMMON) $(OBJ)/quicktree.o $(OBJ)/buildtree.o $(OBJ)/tree.o</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -21,11 +28,14 @@</span> CFLAGS += -c -I$(INC)</span>
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18
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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"> LDFLAGS += -g </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-all: quicktree</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;">+all: quicktree libquicktree.a</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"> quicktree : $(QUICKTREEOBJ)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> $(CC) $(LDFLAGS) -o $@ $(QUICKTREEOBJ) -lm</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libquicktree.a: $(LIBOBJ)</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;">+ ar rc $@ $(LIBOBJ)</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;">+</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> $(OBJ)/quicktree.o : $(SRC)/quicktree.c $(INC)/version.h</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> $(CC) $(CFLAGS) -o $(OBJ)/quicktree.o $(SRC)/quicktree.c</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/quicktree/-/compare/0a925f990469319ea72d460c52c96e191e31b10f...fe426a6598742190616d848b8a06773b570106f1#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">fixMake.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">create_lib.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/quicktree/-/compare/0a925f990469319ea72d460c52c96e191e31b10f...fe426a6598742190616d848b8a06773b570106f1#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">---</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Database: https://github.com/khowe/quicktree/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/khowe/quicktree/issues/new</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Repository: https://github.com/khowe/quicktree.git</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Repository-Browse: https://github.com/khowe/quicktree</span></pre>
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