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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/mmseqs2">Debian Med / mmseqs2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/commit/fc0837b86eb08a60d4ca03050c3c8d618240a4b8">fc0837b8</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-20T15:28:12Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch to fix the matrix serialization test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/commit/b4ff22b5a7ae10f41c6b323ae956f2024fafd2f6">b4ff22b5</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-20T15:30:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of salsa.debian.org:med-team/mmseqs2
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
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+
debian/patches/fix_tests.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="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
<a href="https://salsa.debian.org/med-team/mmseqs2/compare/38968c9e4abd876d16cdf44cc84acac88f508bb0...b4ff22b5a7ae10f41c6b323ae956f2024fafd2f6#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70"><strong>debian/patches/fix_tests.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Fix some of the test src files to work in autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> as some of the tests do not work as the paths have either been hardcoded or SIGSEGV is thrown</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Author: Shayan Doust <hello@shayandoust.me></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Last-Update: 2019-07-20</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"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 16:21:13.549699250 +0100</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;">+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 16:21:13.545699216 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -18,10 +18,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> ScoreMatrix* unserialized = ScoreMatrix::unserialize(serialized, subMat.alphabetSize, 3);</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> Debug(Debug::INFO) << unserialized->elementSize << " " << unserialized->rowSize << " "</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;">- << unserialized->score[0] << " " << unserialized->index[0] << "\n";</span></span>
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<pre style="margin: 0;">+<span id="LC16" 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="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ScoreMatrix::cleanup(unserialized);</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ << unserialized->score[0] << "\n";</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> free(serialized);</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ScoreMatrix::cleanup(extMattwo);</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;">+ // Why not use an operator. Will free & destruct & will not SIGSEGV</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ delete(unserialized);</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> return EXIT_SUCCESS;</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/compare/38968c9e4abd876d16cdf44cc84acac88f508bb0...b4ff22b5a7ae10f41c6b323ae956f2024fafd2f6#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">fix_tests.patch</span>
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1
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_src_zstd_includes.patch</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">fix_util_installation.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">use_system_zstd.patch</span>
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<a href="https://salsa.debian.org/med-team/mmseqs2/compare/38968c9e4abd876d16cdf44cc84acac88f508bb0...b4ff22b5a7ae10f41c6b323ae956f2024fafd2f6#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -55,3 +55,5 @@ echo "Invoking test_translate"</td>
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55
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="shell">./test_translate</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Invoking test_util"</span></span>
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell">./test_util</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Invoking test_scorematrixserialization"</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell">./test_scorematrixserialization</span></pre>
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