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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/canu">Debian Med / canu</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/canu/-/commit/7b542b7f9bdd75a92412a007a1668224916fae3c">7b542b7f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-29T01:56:44+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch to fix FTBFS with new glibc (Closes: #997215)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/canu/-/commit/7b465482ef6c6a20018a4e1de7b6361a730a6c2d">7b465482</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-29T01:57:30+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run cme
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/canu/-/commit/cb18223c245fc94bfa933e8fe09a85d98b991219">cb18223c</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-29T02:05:11+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
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</li>
<li class="file-stats">
<a href="#82921ae50906f4210c16d160eeeda1c479413873">
debian/patches/canu_version.patch
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<li class="file-stats">
<a href="#79a8177277c30a0ed50f36cd1f587d94ab368fe5">
<span class="new-file">
+
debian/patches/remove-deprecated-sysctl.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/canu/-/compare/5d1934b4bf09daddd794f2c466d8a86631a92801...cb18223c245fc94bfa933e8fe09a85d98b991219#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">canu (2.0+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<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"> * Team Upload.</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add patch to fix FTBFS with new glibc (Closes: #997215)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Run cme</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="LC7" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Fri, 29 Oct 2021 01:57:43 +0530</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">canu (2.0+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/canu/-/compare/5d1934b4bf09daddd794f2c466d8a86631a92801...cb18223c245fc94bfa933e8fe09a85d98b991219#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">@@ -2,13 +2,13 @@ Source: canu</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">Section: science</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC5" 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="LC5" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> libboost-dev,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> libmeryl-dev,</span>
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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># For File::Path</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libfilesys-df-perl,</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> mhap<span class="idiff left right"> (>= 2.1.3)</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5</span>.0</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> mhap</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6</span>.0</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/canu</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/canu.git</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: http://canu.readthedocs.org/en/latest/</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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="19" 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">@@ -19,7 +19,7 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> ${perl:Depends},</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> libfilesys-df-perl,</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> mhap<span class="idiff left right"> (>= 2.1.3)</span>,</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> mhap,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> gnuplot</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Suggests: pbgenomicconsensus,</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> nanopolish</span>
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<a href="https://salsa.debian.org/med-team/canu/-/compare/5d1934b4bf09daddd794f2c466d8a86631a92801...cb18223c245fc94bfa933e8fe09a85d98b991219#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">*-*/bin usr/lib/canu/</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">*-*/lib usr/lib/canu/</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">debian/bin/canu <span class="idiff left right">/</span>usr/bin/</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/bin/canu usr/bin/</span></pre>
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<a href="https://salsa.debian.org/med-team/canu/-/compare/5d1934b4bf09daddd794f2c466d8a86631a92801...cb18223c245fc94bfa933e8fe09a85d98b991219#82921ae50906f4210c16d160eeeda1c479413873"><strong>debian/patches/canu_version.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Canu_version</span></span>
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1
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: canu/src/canu_version_update.pl</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- canu.orig/src/canu_version_update.pl</span></span>
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<a href="https://salsa.debian.org/med-team/canu/-/compare/5d1934b4bf09daddd794f2c466d8a86631a92801...cb18223c245fc94bfa933e8fe09a85d98b991219#79a8177277c30a0ed50f36cd1f587d94ab368fe5"><strong>debian/patches/remove-deprecated-sysctl.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: sysctl.h has been removed with latest glibc, do not include it</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/997215</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-10-29</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/utility/system.C</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/utility/system.C</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -42,11 +42,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #include "jemalloc/jemalloc.h"</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #endif</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;">-#if !defined(__CYGWIN__) && !defined(_WIN32)</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;">-#include <sys/sysctl.h></span></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;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></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;">-</span></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"> double</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> getTime(void) {</span></pre>
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<a href="https://salsa.debian.org/med-team/canu/-/compare/5d1934b4bf09daddd794f2c466d8a86631a92801...cb18223c245fc94bfa933e8fe09a85d98b991219#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use-debian-mhap-at-runtime.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">external-mhap.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">canu_version.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">remove-deprecated-sysctl.patch</span></pre>
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