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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/infernal">Debian Med / infernal</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/4bc3f382d4e3de279251a697ec7755028eea1e85">4bc3f382</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-01T12:25:37Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install example binaries into /usr/lib/
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<strong><a href="https://salsa.debian.org/med-team/infernal/commit/847ca32158c03000deec505d920b7c7dbf0b19b2">847ca321</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-12-01T15:35:55Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">upload to unstable
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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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="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/infernal/compare/aca65ff937b1cd5d961ba8f56e787444525ad5b4...847ca32158c03000deec505d920b7c7dbf0b19b2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">infernal (1.1.3-2) <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">infernal (1.1.3-2) <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"> * Add python3 build-dep for `make check`</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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="9" 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">@@ -9,8 +9,11 @@ infernal (1.1.3-2) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Enable a verbose build log</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * infernal-doc: mark Multi-Arch: foreign (thanks Multiarch hinter!)</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * debian/patches/hardening: added CPPFLAGS to easel, rmark, and hmmer/profmark</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Install example binaries into /usr/lib/ and symlink them into the</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> doc/infernal/examples directory (fixes a FHS violation)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Added missing autopkgtest dependency on python3</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> S<span class="idiff left right">at, 30 Nov 2019 11:00:30</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> S<span class="idiff left right">un, 01 Dec 2019 16:35:34</span> +0100</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">infernal (1.1.3-1) unstable; urgency=medium</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/infernal/compare/aca65ff937b1cd5d961ba8f56e787444525ad5b4...847ca32158c03000deec505d920b7c7dbf0b19b2#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,6 +6,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="k" style="font-weight: 600;">include</span><span class="sx" style="color: #d14;"> /usr/share/dpkg/default.mk</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">pkgdata</span><span class="o" style="font-weight: 600;">:=</span>infernal</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">sampledir</span><span class="o" style="font-weight: 600;">:=</span><span class="nv" style="color: #008080;">$(CURDIR)</span>/debian/<span class="nv" style="color: #008080;">$(DEB_SOURCE)</span>/usr/share/doc/<span class="nv" style="color: #008080;">$(DEB_SOURCE)</span>/examples</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">sampledir_lib</span><span class="o" style="font-weight: 600;">:=</span><span class="nv" style="color: #008080;">$(CURDIR)</span>/debian/<span class="nv" style="color: #008080;">$(DEB_SOURCE)</span>/usr/lib/<span class="nv" style="color: #008080;">$(DEB_TARGET_MULTIARCH)</span>/<span class="nv" style="color: #008080;">$(DEB_SOURCE)</span>/examples</span>
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9
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nl">%</span><span class="o" style="font-weight: 600;">:</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"> dh <span class="nv" style="color: #008080;">$@</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" 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>
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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">@@ -36,12 +37,15 @@ override_dh_install:</td>
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36
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"><span class="nl">override_dh_installexamples</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"> dh_installexamples</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$(sampledir)</span>/src/<span class="p">;</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$(sampledir)</span>/easel/miniapps/<span class="p">;</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="make"> find ./src <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*test"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">cp</span> <span class="se" style="color: #d14;">\{\}</span> <span class="nv" style="color: #008080;">$(sampledir)</span>/src/ <span class="se" style="color: #d14;">\;</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./src/itest_brute <span class="nv" style="color: #008080;">$(sampledir)</span>/src/<span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./easel/miniapps/esl-reformat <span class="nv" style="color: #008080;">$(sampledir)</span>/easel/miniapps/<span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./easel/miniapps/esl-shuffle <span class="nv" style="color: #008080;">$(sampledir)</span>/easel/miniapps/<span class="p">;</span></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./easel/miniapps/esl-sfetch <span class="nv" style="color: #008080;">$(sampledir)</span>/easel/miniapps/<span class="p">;</span></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-aR</span> testsuite <span class="nv" style="color: #008080;">$(sampledir)</span>/<span class="p">;</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./easel/devkit/sqc <span class="nv" style="color: #008080;">$(sampledir)</span>/<span class="p">;</span></span></pre>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$(sampledir)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/src/</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/easel/miniapps/</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="make"> find ./src <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*test"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">cp</span> <span class="se" style="color: #d14;">\{\}</span> <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/src/ <span class="se" style="color: #d14;">\;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./src/itest_brute <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/src/</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./easel/miniapps/esl-reformat <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/easel/miniapps/</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./easel/miniapps/esl-shuffle <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/easel/miniapps/</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./easel/miniapps/esl-sfetch <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/easel/miniapps/</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$(sampledir)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> ../../../../lib/<span class="nv" style="color: #008080;">$(DEB_TARGET_MULTIARCH)</span>/<span class="nv" style="color: #008080;">$(DEB_SOURCE)</span>/examples/easel ./easel <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="make"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> ../../../../lib/<span class="nv" style="color: #008080;">$(DEB_TARGET_MULTIARCH)</span>/<span class="nv" style="color: #008080;">$(DEB_SOURCE)</span>/examples/src ./src</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-aR</span> testsuite <span class="nv" style="color: #008080;">$(sampledir)</span>/</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./easel/devkit/sqc <span class="nv" style="color: #008080;">$(sampledir)</span>/</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/aca65ff937b1cd5d961ba8f56e787444525ad5b4...847ca32158c03000deec505d920b7c7dbf0b19b2#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @<span class="idiff left right">, python3</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions:</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/aca65ff937b1cd5d961ba8f56e787444525ad5b4...847ca32158c03000deec505d920b7c7dbf0b19b2#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">@@ -7,7 +7,7 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then</td>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-<span class="idiff left right">a</span></span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-<span class="idiff left right">Lr</span></span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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>
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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">@@ -16,5 +16,5 @@ find . -name "*.gz" -exec gunzip \{\} \;</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">chmod</span> <span class="nt" style="color: #000080;">-R</span> +x <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>infernal testsuite</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell">find /usr/bin <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"cm*"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> <span class="se" style="color: #d14;">\{\}</span> src <span class="se" style="color: #d14;">\;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">find /usr/bin <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"cm*"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> <span class="se" style="color: #d14;">\{\}</span> src<span class="idiff left right">/</span> <span class="se" style="color: #d14;">\;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell">./sqc 2 ./testsuite/testsuite.sqc <span class="nb" style="color: #0086b3;">.</span> ./testsuite/..</span></pre>
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