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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/jellyfish">Debian Med / jellyfish</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/-/commit/863be65ea6c77a23f06eca55a2b0f6c4ef02cb0e">863be65e</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T15:18:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/watch: repair broken link to github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/-/commit/02ca089066f65cb5252bc29ce98e06a1ee721766">02ca0890</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T19:56:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add fix-autoreconf.patch; address ftbfs
This patch provides protection to a couple of macros in configure.ac
to avoid breakage of the script configure which is produced by the
autoconf 2.70.
Closes: #978843
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/-/commit/2831b80958b320c1139ae4804be3099fbdc0e5fc">2831b809</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T20:46:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/-/commit/0f6e0163183d3c8b785a794e05f77086f2a49400">0f6e0163</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T20:46:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/-/commit/31d0371ae440eba10fbd694fa7cd936a3e3e5aad">31d0371a</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T20:46:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Apply multi-arch hints.
+ libjellyfish-2.0-dev: Drop Multi-Arch: same.
+ jellyfish-examples: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/-/commit/c67201e5ef165d1394a1e293b3986dcac4ea5bab">c67201e5</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T20:59:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: add myself to uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/-/commit/aeb41686415b03bc2dd5d40759b06a4af6d58d8b">aeb41686</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T21:00:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/-/commit/4623cfc195c54e268081f43a3cf70996471ea9e1">4623cfc1</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T21:10:28+02:00</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/jellyfish/-/commit/ecd0fc033d5ff80d117177b8d098835ea7fe3cd4">ecd0fc03</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T21:19:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix-autoreconf.patch forwarded
</pre>
</li>
</ul>
<h4>5 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="#6f5b5ed58ad74732edccdbcc5b531572e13cbc91">
<span class="new-file">
+
debian/patches/fix-autoreconf.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/jellyfish/-/compare/9098ae203ec441f4e3ea27558dec2e4a52d53b1f...ecd0fc033d5ff80d117177b8d098835ea7fe3cd4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">jellyfish (2.3.0-11) <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">jellyfish (2.3.0-11) <span class="idiff left right">unstable</span>; 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"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Fix Homepage</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Closes: #983273</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 15 Mar 2021 19:28:29 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Étienne Mollier ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * d/watch: repair broken link to github</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * add fix-autoreconf.patch; fix ftbfs with autoreconf 2.70 (Closes: #978843)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Apply multi-arch hints.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> + libjellyfish-2.0-dev: Drop Multi-Arch: same.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> + jellyfish-examples: Add Multi-Arch: foreign.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * d/control: add myself to uploaders</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> Sat, 28 Aug 2021 21:01:20 +0200</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">jellyfish (2.3.0-10) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/jellyfish/-/compare/9098ae203ec441f4e3ea27558dec2e4a52d53b1f...ecd0fc033d5ff80d117177b8d098835ea7fe3cd4#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">@@ -2,7 +2,8 @@ Source: jellyfish</td>
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<pre style="margin: 0;"> <span id="LC2" 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="LC3" class="line" lang="plaintext">Uploaders: Shaun Jackman <sjackman@debian.org>,</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Michael R. Crusoe <crusoe@debian.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Michael R. Crusoe <crusoe@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Étienne Mollier <emollier@debian.org></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Section: science</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 (= 13),</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">@@ -20,7 +21,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> libhts-dev,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dos2unix,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> samtools</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/jellyfish</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Homepage: https://github.com/gmarcais/Jellyfish</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" 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">@@ -74,7 +75,6 @@ Description: count k-mers in DNA sequences (dynamic library of jellyfish)</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">Package: libjellyfish-2.0-dev</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">Multi-Arch: same</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">Section: libdevel</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"> libjellyfish-2.0-2 (= ${binary:Version})</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" 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">@@ -148,6 +148,7 @@ Architecture: all</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext">Recommends: jellyfish</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext">Description: count k-mers in DNA sequences (examples for testing)</span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"> JELLYFISH is a tool for fast, memory-efficient counting of k-mers in</span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"> DNA. A k-mer is a substring of length k, and counting the occurrences</span>
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<li id="6f5b5ed58ad74732edccdbcc5b531572e13cbc91">
<a href="https://salsa.debian.org/med-team/jellyfish/-/compare/9098ae203ec441f4e3ea27558dec2e4a52d53b1f...ecd0fc033d5ff80d117177b8d098835ea7fe3cd4#6f5b5ed58ad74732edccdbcc5b531572e13cbc91"><strong>debian/patches/fix-autoreconf.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix ftbfs with autoconf 2.70</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> This patch provides protection to a couple of macros in configure.ac</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> to avoid breakage of the script configure which is produced by the</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> autoconf 2.70.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=978843</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: https://github.com/gmarcais/Jellyfish/pull/178</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Last-Update: 2021-08-28</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></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;">--- jellyfish.orig/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ jellyfish/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -41,9 +41,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> # Check for md5 or md5sum</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> AC_ARG_VAR([MD5], [Path to md5 hashing program])</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;">-AS_IF([test "x$MD5" = "x"], AC_CHECK_PROG([MD5], [md5sum], [md5sum]), [])</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AS_IF([test "x$MD5" = "x"], AC_CHECK_PROG([MD5], [md5], [md5 -r]), [])</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AS_IF([test "x$MD5" = "x"], AC_MSG_ERROR([Could not find md5 hashing program in your path]), [])</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AS_IF([test "x$MD5" = "x"], [AC_CHECK_PROG([MD5], [md5sum], [md5sum])], [])</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AS_IF([test "x$MD5" = "x"], [AC_CHECK_PROG([MD5], [md5], [md5 -r])], [])</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;">+AS_IF([test "x$MD5" = "x"], [AC_MSG_ERROR([Could not find md5 hashing program in your path])], [])</span></span>
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23
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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"> # Check for yaggo</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> AC_ARG_VAR([YAGGO], [Yaggo switch parser generator])</span></pre>
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<a href="https://salsa.debian.org/med-team/jellyfish/-/compare/9098ae203ec441f4e3ea27558dec2e4a52d53b1f...ecd0fc033d5ff80d117177b8d098835ea7fe3cd4#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">@@ -7,3 +7,4 @@ fix_replacement_of_-L_option.patch</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">test_needs_bash</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">python3</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">fix-32-bit.patch</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">fix-autoreconf.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/jellyfish/-/compare/9098ae203ec441f4e3ea27558dec2e4a52d53b1f...ecd0fc033d5ff80d117177b8d098835ea7fe3cd4#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">https://github.com/gmarcais/Jellyfish/releases .*/[jelyfishv]*\.*(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">https://github.com/gmarcais/Jellyfish/tags \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> archive/refs/tags/[vV]?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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