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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/lambda-align2">Debian Med / lambda-align2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lambda-align2/commit/5ff8ca5e1a792769a42f6777ba13134d4b2f4edf">5ff8ca5e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-20T09:15:53Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix 32bit compatibility
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lambda-align2/commit/f51d1e08750897ad96d6c502753437aafae2d6ba">f51d1e08</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-20T09:15:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">return correct result of autopkgtests
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#b2ab4c8a863eeb0e4658dd5759a2f7906da8f42b">
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+
debian/patches/32bit
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#aab2726ed6daf419caf178b1480b6d7da8a85af6">
debian/tests/run-tests
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<h4>Changes:</h4>
<li id="b2ab4c8a863eeb0e4658dd5759a2f7906da8f42b">
<a href="https://salsa.debian.org/med-team/lambda-align2/compare/d3f174cc3d09fc5c5fc00da3c69dea1b8a6f4728...f51d1e08750897ad96d6c502753437aafae2d6ba#b2ab4c8a863eeb0e4658dd5759a2f7906da8f42b"><strong>debian/patches/32bit</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Subject: fix 32bit compatibility</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Forwarded: https://github.com/seqan/lambda/pull/123</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;">--- lambda-align2.orig/src/search_algo.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lambda-align2/src/search_algo.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1058,7 +1058,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> desiredOccs = (length(lH.matches) - oldTotalMatches) >= lH.options.maxMatches</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ? minResults</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> : (lH.options.maxMatches - (length(lH.matches) - oldTotalMatches)) * seedHeurFactor /</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std::max((needlesSum - needlesPos - seedBegin) / lH.options.seedOffset, 1ul);</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;">+ std::max((needlesSum - needlesPos - seedBegin) / lH.options.seedOffset, static_cast<size_t>(1));</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> if (desiredOccs == 0)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> desiredOccs = minResults;</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1127,7 +1127,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> desiredOccs = (length(lH.matches) - oldTotalMatches) >= lH.options.maxMatches</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> ? minResults</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> : (lH.options.maxMatches - (length(lH.matches) - oldTotalMatches)) * seedHeurFactor /</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std::max((needlesSum - needlesPos - seedBegin) / lH.options.seedOffset, 1ul);</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::max((needlesSum - needlesPos - seedBegin) / lH.options.seedOffset, static_cast<size_t>(1));</span></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"> if (desiredOccs == 0)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> desiredOccs = minResults;</span></pre>
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<a href="https://salsa.debian.org/med-team/lambda-align2/compare/d3f174cc3d09fc5c5fc00da3c69dea1b8a6f4728...f51d1e08750897ad96d6c502753437aafae2d6ba#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">enable_tests</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">32bit</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">set-seqan-cmake-dir.patch</span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">force-link-rt-pthread.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/lambda-align2/compare/d3f174cc3d09fc5c5fc00da3c69dea1b8a6f4728...f51d1e08750897ad96d6c502753437aafae2d6ba#aab2726ed6daf419caf178b1480b6d7da8a85af6"><strong>debian/tests/run-tests</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" 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="11" 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">@@ -11,7 +11,7 @@ cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON \</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>binary <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">$(</span>dpkg <span class="nt" style="color: navy;">-L</span> lambda-align2 | <span class="nb" style="color: #0086b3;">grep </span>bin/<span class="k" style="font-weight: 600;">)</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do </span><span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: navy;">-s</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">binary</span><span class="k" style="font-weight: 600;">}</span> bin/<span class="p">;</span> <span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>tests</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> +e</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell">ctest <span class="nt" style="color: navy;">--parallel</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">nproc</span><span class="k" style="font-weight: 600;">)</span> <span class="nt" style="color: navy;">-I</span> 1,10 <span class="o" style="font-weight: 600;"><span class="idiff left right">&&</span></span> <span class="nv" style="color: teal;">RESULT</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$?</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">ctest <span class="nt" style="color: navy;">--parallel</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">nproc</span><span class="k" style="font-weight: 600;">)</span> <span class="nt" style="color: navy;">-I</span> 1,10 <span class="p"><span class="idiff left right">;</span></span> <span class="nv" style="color: teal;">RESULT</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$?</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">ls </span>tests/<span class="k" style="font-weight: 600;">*</span>~ 1> /dev/null 2>&1<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>backup <span class="k" style="font-weight: 600;">in </span>tests/<span class="k" style="font-weight: 600;">*</span>~<span class="p">;</span> <span class="k" style="font-weight: 600;">do </span><span class="nb" style="color: #0086b3;">mv</span> <span class="nv" style="color: teal;">$$</span><span class="o" style="font-weight: 600;">{</span>backup<span class="o" style="font-weight: 600;">}</span> <span class="nv" style="color: teal;">$$</span><span class="o" style="font-weight: 600;">{</span>backup%<span class="se" style="color: #d14;">\~</span><span class="o" style="font-weight: 600;">}</span><span class="p">;</span> <span class="k" style="font-weight: 600;">done</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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