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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/mapsembler2">Debian Med / mapsembler2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapsembler2/-/commit/f59a42b405c4255bc8c1628dc5b4f72198b67ae9">f59a42b4</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-20T20:16:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dropped 32bits.patch
mapsembler2 has been removed out of the archive for 32 bits
architectures.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapsembler2/-/commit/a2611c4d78583eee55680aa14e6aec59e98275e6">a2611c4d</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-20T20:17:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">clarifier description of gcc10.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapsembler2/-/commit/73543abdefd35ea0ba8814db662fba2aec46d898">73543abd</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-20T20:18:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check_memory.patch: updated description
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapsembler2/-/commit/c454eeef5178f1058c97bf943d187862a300d9d8">c454eeef</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-20T20:23:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/changelog: updated to reflect archives removal
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapsembler2/-/commit/8d5ae6529a7104d1065890e4424b4e3a635b8e33">8d5ae652</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-20T21:59:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">no_std_hash_redefinition.patch: removed TODO
Verified autopkgtests were running on remaining architectures
still supported by Debian and declared for mapsembler2, e.g.:
- amd64
- arm64
- ppc64el
- s390x
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapsembler2/-/commit/91bb00377ada779b9135c1a2f92fd3e09cfd1da2">91bb0037</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-10-20T22:10:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
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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="#018aff3b6d61c8d71176ba043502300e2252d580">
<span class="deleted-file">
−
debian/patches/32bits.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#fb2c1bd22474ead69d2a100504742e9208b1a91a">
debian/patches/check_memory.patch
</a>
</li>
<li class="file-stats">
<a href="#81a9a5b123fb5e9473f68e4733e9d389fa7872c9">
debian/patches/gcc10.patch
</a>
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<li class="file-stats">
<a href="#20b82b6e3db84b535d4d280f2067c8d12c692cb9">
debian/patches/no_std_hash_redefinition.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/mapsembler2/-/compare/73d9dae0c0c876a415ba804e83602bb984a20ac0...91bb00377ada779b9135c1a2f92fd3e09cfd1da2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">mapsembler2 (2.2.4+dfsg1-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mapsembler2 (2.2.4+dfsg1-1) <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"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * added no_std_hash_redefinition.patch and gcc10.patch to address compilation</span>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> failures with Gcc 10. (Closes: #957519)</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> * <span class="idiff left right">added check_memory.patch and 32bits.patch to address autopkgtest failures</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right">on CPUs with 32bit architectures (work in progress)</span>.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * <span class="idiff left right">package removed from 32 bits architecture repostories due to test failure</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right">and end of maintenance upstream</span>.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * excluded cmake build directory in gatb-core examples, as they are unusable,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> and the CMakeCache.txt triggers a lintian error.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org> Tue, <span class="idiff left right">13 Oct 2020 22:58:46</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org> Tue, <span class="idiff left right">20 Oct 2020 22:08:22</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">mapsembler2 (2.2.4+dfsg-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<li id="018aff3b6d61c8d71176ba043502300e2252d580">
<a href="https://salsa.debian.org/med-team/mapsembler2/-/compare/73d9dae0c0c876a415ba804e83602bb984a20ac0...91bb00377ada779b9135c1a2f92fd3e09cfd1da2#018aff3b6d61c8d71176ba043502300e2252d580"><strong>debian/patches/32bits.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mapsembler2.orig/run_mapsembler2_pipeline.sh</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;">+++ mapsembler2/run_mapsembler2_pipeline.sh</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">@@ -11,7 +11,11 @@</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> k=31 # size of kmers</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> c=5 # minimal coverage</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> d=1 # estimated number of error per read</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-g=3000000000 # estimated genome size. Used only to control memory usage. e.g. 3 billion (3000000000) uses 4Gb of RAM.</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;">+# g is estimated genome size. Used only to control memory usage:</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+case "$(uname -m)" in</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+*64*) g=3000000000 ;; # 3 billion uses 4Gb of RAM.</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* ) g=600000000 ;; # reduce to 800M on 32bits archs</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;">+esac</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> t=0</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> f=1 #kind of process (search mode 1=Breadth and 2=Depth)</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> x=40 #node length limit</span></pre>
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<a href="https://salsa.debian.org/med-team/mapsembler2/-/compare/73d9dae0c0c876a415ba804e83602bb984a20ac0...91bb00377ada779b9135c1a2f92fd3e09cfd1da2#fb2c1bd22474ead69d2a100504742e9208b1a91a"><strong>debian/patches/check_memory.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: check memory of OAHash construction</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> This has been written to try debugging why autopkgtest failures occurred on</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> 32bit architectures, but this sort of control may remain useful to users of</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> 32bit architectures. While the package ended up being removed out of 32 bits</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> architectures repositories, this sort of control may remain useful to users of</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> mapsembler2 to diagnose issues; this is more useful message than "Segmentation</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> fault".</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">Author: Étienne Mollier</span></span>
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<a href="https://salsa.debian.org/med-team/mapsembler2/-/compare/73d9dae0c0c876a415ba804e83602bb984a20ac0...91bb00377ada779b9135c1a2f92fd3e09cfd1da2#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">Description: fix common gcc10 FTBFS issue</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> After fixing #957519 with no_std_hash_redefinition.patch, a few more issues</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> more generic than the ones described in this bug report turned out to crop up.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> This patch addresses them.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> common to Gcc 10 cropped up. This patch addresses them.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957519</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<li id="20b82b6e3db84b535d4d280f2067c8d12c692cb9">
<a href="https://salsa.debian.org/med-team/mapsembler2/-/compare/73d9dae0c0c876a415ba804e83602bb984a20ac0...91bb00377ada779b9135c1a2f92fd3e09cfd1da2#20b82b6e3db84b535d4d280f2067c8d12c692cb9"><strong>debian/patches/no_std_hash_redefinition.patch</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">@@ -2,8 +2,6 @@ Description: remove redefinition of ‘struct std::hash<__int128 unsigned>’</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> This definition is not needed anymore with recent compiler versions apparently</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> on _LP64 systems. I'm not sure yet of The proper approach to address it in a</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> more architecture independent way.</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"> TODO: check behavior on other archs supported by Debian.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.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=957519</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/mapsembler2/-/compare/73d9dae0c0c876a415ba804e83602bb984a20ac0...91bb00377ada779b9135c1a2f92fd3e09cfd1da2#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">@@ -8,4 +8,3 @@ spelling.patch</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">no_std_hash_redefinition.patch</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">gcc10.patch</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">check_memory.patch</span></pre>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">32bits.patch</span></pre>
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