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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/clustalo">Debian Med / clustalo</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/clustalo/-/commit/9ac92b60bd4dbd4f26d77c163c2f4b9ac6fe8202">9ac92b60</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-01T07:28:54+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">No optimisation for valgrind - FIXME: This needs to be restricted to mipsel only
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/clustalo/-/commit/4362a44382ecca118e6658ec6593b55efe640c52">4362a443</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-01T07:50:15+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix syntax error that are exposed only in debug mode
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#9ffbea523f68ec2af6eb4481d50c985a8295dcf1">
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+
debian/patches/fix_syntax.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="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9ffbea523f68ec2af6eb4481d50c985a8295dcf1">
<a href="https://salsa.debian.org/med-team/clustalo/-/compare/9c43fd1341dfbe127be2a2d506d5d26a8de63f0e...4362a44382ecca118e6658ec6593b55efe640c52#9ffbea523f68ec2af6eb4481d50c985a8295dcf1"><strong>debian/patches/fix_syntax.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri, 17 Apr 2020 17:06:22 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix syntax error that are exposed only in debug mode</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/src/clustal/mbed.c</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/clustal/mbed.c</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -88,9 +88,9 @@</span> static const int RESTARTS_PER_SPLIT = 10</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #define USE_KMEANS_LLOYDS 0</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </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;">-//#ifndef HAVE_LOG2</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;">+/*#ifndef HAVE_LOG2*/</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> #ifndef CLUSTAL_OMEGA_HAVE_LOG2</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;">-//#define log2(x) (log(x) / 0.69314718055994530942)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/*#define log2(x) (log(x) / 0.69314718055994530942)*/</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="diff"> #define log2(x) ( x<=0 ? (float)(-100000) : 1.442695041*log(x) )</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #define NUMBER_OF_SEEDS(n) pow(log2(((double)n)), 2)</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;">--- a/src/hhalign/util-C.h</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;">+++ b/src/hhalign/util-C.h</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -53,10 +53,10 @@</span> inline double fmean(double x, double y,</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> // log base 2</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> //#ifndef CLUSTAL_OMEGA_HAVE_LOG2</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-//#ifndef HAVE_LOG2</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/*#ifndef HAVE_LOG2*/</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> inline float Log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));}</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> inline float Log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));}</span>
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<pre style="margin: 0;">+<span id="LC29" 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="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/*#endif*/</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> /////////////////////////////////////////////////////////////////////////////////////</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/hhalign/hhalignment-C.h</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/hhalign/hhalignment-C.h</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -655,7 +655,7 @@</span> Alignment::Compress(const char infile[])</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> if it is too big (L/2) then telomere logic has no effect,</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> don't think it should be changed (much) */</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> #define TELOMER_FRACTION 0.10</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- //#define HMM_MIN_LENGTH 0.923</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ /*//#define HMM_MIN_LENGTH 0.923*/</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> #define HMM_MIN_LENGTH 0.950</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> #define FORTRAN_OFFSET 1</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> double dDefaultMgaps;</span></pre>
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<a href="https://salsa.debian.org/med-team/clustalo/-/compare/9c43fd1341dfbe127be2a2d506d5d26a8de63f0e...4362a44382ecca118e6658ec6593b55efe640c52#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">clustalo-log-format-calls.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">array_out_of_bounds.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">memory_leak.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">fix_syntax.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/clustalo/-/compare/9c43fd1341dfbe127be2a2d506d5d26a8de63f0e...4362a44382ecca118e6658ec6593b55efe640c52#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -6,9 +6,17 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_BUILD_MAINT_OPTIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">hardening</span><span class="o" style="font-weight: 600;">=</span>+all</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># FIXME: this needs to be restricted to mipsel only</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">CXXFLAGS</span><span class="o" style="font-weight: 600;">:=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> dpkg-buildflags <span class="nt" style="color: #000080;">--get</span> CXXFLAGS | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/-O[1-9]//'</span><span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nt" style="color: #000080;">-O0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">CFLAGS</span><span class="o" style="font-weight: 600;">:=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> dpkg-buildflags <span class="nt" style="color: #000080;">--get</span> CFLAGS | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/-O[1-9]//'</span><span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nt" style="color: #000080;">-O0</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="nl">%</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"> dh <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># FIXME: this needs to be restricted to mipsel only</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"><span class="nl">override_dh_auto_configure</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"> dh_auto_configure <span class="nt" style="color: #000080;">--</span> <span class="nt" style="color: #000080;">--enable-debug</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="make"></span>
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12
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"><span class="nl">override_dh_auto_build-indep</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># nothing to do here</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"></span>
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