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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/infernal">Debian Med / infernal</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/d0c0d54ab7239a160d1974d789049b49871b9547">d0c0d54a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2016-06-21T09:19:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">SVN-Git conversion failed - just commit status of 1.0.2 (oldstable at the time of conversion)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/1166e414ed8912c84f2957322c20d9046a3b9389">1166e414</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2016-06-21T09:20:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/1.1.1'
Upstream version 1.1.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/280ba637a9d23c668b44c833bf86daa6d3ba55e0">280ba637</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2016-06-21T09:21:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Commit status of 1.1.1-2 (stable at the time when moving from svn to git)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/c9c9685be28707cfe833dd768c2da7111cb334c7">c9c9685b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2016-06-21T09:23:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Commit status as uploaded at time of svn-git conversion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/74a329603b400947209637426221678d4f51f274">74a32960</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2016-06-21T09:26:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move packaging from SVN to Git
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/dc788b20625f3ecc8648a7c8fe9107b15b8bc1d8">dc788b20</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2016-06-21T09:27:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cme fix dpkg-control
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/6adbb8985b1efc5e16724bc15ffac53d2ee15619">6adbb898</a></strong>
<div>
<span>by cbk-guest</span>
<i>at 2016-06-22T02:39:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtests added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/a61b4c9deffc0e2d68de89b55218fbff75028cd7">a61b4c9d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2016-06-22T06:13:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/0afabb231b9ea938aaa0e9465803a70335654734">0afabb23</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2016-06-22T06:29:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better hardening, upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/1fbf0cb07fd41cbd1e2e2fc2f8dd2984507ed54d">1fbf0cb0</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2016-08-06T00:01:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix watchfile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/e5b003eca3bf6507040cb27ffbbef2c1928b6867">e5b003ec</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2016-08-06T00:01:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/1.1.2'
Upstream version 1.1.2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/5c8e52f5cda08010b29d036eae8708974d95549c">5c8e52f5</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2016-08-06T01:06:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make build reproducible
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/25d0decfed25b51334a1b0454efbc351d3c82fee">25d0decf</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2016-08-11T21:44:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">SOURCE_DATE_EPOCH support accepted upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/c1bd01403f9300d84bcd4e1432a811de14a22589">c1bd0140</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2017-01-18T11:57:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix homepage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/15c9f9044b05dfb603ca92ab256ffe11088e661b">15c9f904</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2017-01-18T12:00:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TODO: remove code copy of hmmer ... after stretch release
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/2ea2d3e048a5a7cb82af8c01984e74aa8b0920f9">2ea2d3e0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2017-01-18T12:01:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 10
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/0c2826461f8ed603c5e6ddce43a209a1c0aeb534">0c282646</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2017-01-18T12:02:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/watch: version=4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/25e1072b646ef7cd3bf8447203c1c864654d9033">25e1072b</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2017-09-01T14:10:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added references to registries.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/0c050e21b6493d87f09917ae57defac3ba92f3a2">0c050e21</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-04-09T12:22:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove invalid fields from debian/upstream/metadata
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/4058f0e448366675a6a8ed9ad51755773f88d90a">4058f0e4</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2018-05-11T22:50:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RRID -> SciCrunch</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/9124281e13661f776d26d7f9aeadd07aa45cd455">9124281e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-15T18:57:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/0b271fb2a3a6c7d1cc0a7ee0e47aec0dbc45abc3">0b271fb2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-15T18:57:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/b49cdc0d54013d42843c77830c815647d89f0578">b49cdc0d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-15T18:57:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.5
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/666df1091f19eda3f462c9002566d831a1579398">666df109</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-15T19:03:41Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/cd5470b8b564d0293d6338c21f064376452b42a8">cd5470b8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-15T19:12:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Obtain source package name
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/a9a0482f6c228e664b9aa5a45fd2a95d8e3df029">a9a0482f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-16T06:34:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix configure.ac to enable autoreconf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/3fce8ef53b60465a9b9b2ee6e1266d2ba1fe548d">3fce8ef5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-16T09:59:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Thanks again to Yavor Doganov <yavor@gnu.org> for another very helpful hint
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/421b9827590ee0f2d4b4925c7822d87b39bfbf96">421b9827</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-16T10:20:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/3cc895af4edfab54d50750ba8f7cf8970f63e894">3cc895af</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-16T10:30:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/d757f80dec6bc0c9bd1d0a55954eb27a4e0a9640">d757f80d</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2019-09-21T12:24:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added ref to conda</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/729095a6b61c8f36ba270796e7be40e0b0341b15">729095a6</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-29T23:03:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/dfa5dd7ac26e87ee5c7a733aaaba0ed45f19c668">dfa5dd7a</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-29T23:04:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.1.3'
Update to upstream version '1.1.3'
with Debian dir 9aea7cbf3c9d273ac6f787d461b2957b09f60a03</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/610230368a20d6605e17155f4546324ced8afdc4">61023036</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-29T23:04:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/1f738b7d7d291c5e39a2983570438fa6004b25ee">1f738b7d</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-29T23:04:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/a5757fc86967a76080cd65abe86b6a8769186430">a5757fc8</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-29T23:21:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/f40a6f6df2017c0cb803f3010e87460f4999f960">f40a6f6d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-30T10:06:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add python3 build-dep for 'make check'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/7e3cc6e299a87e8e2b6fb659dac8366d34ece519">7e3cc6e2</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-30T10:06:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Secure URI in copyright format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/ab53cb9582ce945d195b908240678d2a2a4b90ea">ab53cb95</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-30T10:06:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/3e4182b37fbc1b2ee7ab38e87a7f7afdd37f0470">3e4182b3</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-30T10:06:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/21c20708447abd0b24921c624af953f4983e555a">21c20708</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-30T10:06:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Submit.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/c763413aa1604000be7331d53c272514e46812c0">c763413a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-30T11:45:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable a verbose build log
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/f80d3b0e82e7edd03275127bca0d01fe95065ec3">f80d3b0e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-30T11:47:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">infernal-doc: mark Multi-Arch: foreign
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/aca65ff937b1cd5d961ba8f56e787444525ad5b4">aca65ff9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-30T12:31:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CPPFLAGS for easel
</pre>
</li>
<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>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install example binaries into /usr/lib/
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/847ca32158c03000deec505d920b7c7dbf0b19b2">847ca321</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-01T15:35:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">upload to unstable
</pre>
</li>
</ul>
<h4>23 changed files:</h4>
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debian/patches/format_security.patch
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debian/patches/hardening
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debian/patches/series
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debian/patches/spelling.patch
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debian/rules
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debian/source/format
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debian/tests/control
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debian/tests/run-unit-test
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debian/upstream/metadata
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debian/watch
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</ul>
<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
<hr>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">infernal for Debian</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">-------------------</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">The documentation for easel contains many PDFs that are not buildable</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">from source - although Debian most likely provide the tools at least to</span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">prepare some of the figures, e.g., a sequence alignment. Other figures</span>
</pre>
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7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">would be more difficult to prepare. As an interim solution it was decided</span>
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8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">to leave that documentation out and users are requested to address the</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">web pages of the upstream developers in this matter.</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Infernal offers to be compiled for LAM-MPI. Please contact us if there is</span>
</pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">respective demand. Also, the Large File Support (LFS) was not activated,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">which may be of concern for large screening projects on files larger</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">than 2GB.</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="LC16" class="line" lang="plaintext">Infernal optionally uses the CFSQP library which is non-free. This is</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">not supported by this Debian package. Please address the Userguide for</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">instructions of a manual self-compilation and -installation.</span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">The packaging has become part of the Debian Med Blend</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">and everyone interested is invited to join in for maintaining it.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Mon, 10 Sep 2007 23:15:37 +0200</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">infernal - Changes to upstream source distribution</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"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Upstream provides a readily readable userguide</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">for Infernal, which is also available online at</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">ftp://selab.janelia.org/pub/software/infernal/Userguide.pdf</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">and should better not be distributed with the source to </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">save disk space.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">The PDFs that are coming with the sources from which</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">the userguide is built are indeed upstream's original</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">sources. They are edited with a PDF editor. Upstream,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Dr Eddy, was consulted in this issue.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Some figures like the sequence alignments could be prepared</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">with the infrastructure that Debian provides and thus would</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">not be ultimately required to be shipped as PDFs. This is however</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">tolerated.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">-- Steffen Moeller Sun, 20 Jan 2008 23:05:22 +0100</span></pre>
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<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Remove code copy of hmmer</span></pre>
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<li id="178ab9c50f81171011484f44a0c219029fcd51fd">
<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#178ab9c50f81171011484f44a0c219029fcd51fd"><strong>debian/bin/cmalign</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">BINNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> <span class="s1" style="color: #d14;">'^flags[[:space:]]*:.* sse2 '</span> /proc/cpuinfo <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"> /usr/lib/infernal/<span class="nv" style="color: #008080;">$BINNAME</span> <span class="nv" style="color: #008080;">$@</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="sh" style="color: #d14;">To run </span><span class="nv" style="color: #008080;">$BINNAME</span><span class="sh" style="color: #d14;"> from infernal package your proccessor needs SSE2 which is not</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="sh" style="color: #d14;">available on this machine.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="sh" style="color: #d14;"> ... Exiting</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...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) unstable; 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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Secure URI in copyright format</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Submit.</span>
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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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<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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<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="LC16" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Sun, 01 Dec 2019 16:35:34 +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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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> - Upstream accepted patch for reproducible builds</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> - autoreconf now works without respective non-applicable patch</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> * Still debian/TODO: remove code copy of hmmer</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Sat, 30 Nov 2019 00:03:03 +0100</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">infernal (1.1.2-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> * Fix homepage</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> * Add debian/TODO: remove code copy of hmmer</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> * debhelper 10</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> * d/watch: version=4</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> * Added references to RRID and OMICtools registries (Steffen Moeller)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> * debhelper 11</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> * Standards-Version: 4.1.5</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> * Fix configure.ac to enable autoreconf</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> * Fix spelling</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 16 Jul 2018 12:20:32 +0200</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">infernal (1.1.2-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> * New upstream release.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> * Fix watchfile.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> * Make build reproducible.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> -- Sascha Steinbiss <satta@debian.org> Sat, 06 Aug 2016 00:00:56 +0000</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">infernal (1.1.1-5) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> [Canberk Koç]</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> * Added Autopkgtest suite</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> * debian/rules file changed</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> * debian/tests directory added</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> * Move packaging from SVN to Git</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> * cme fix dpkg-control</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> * Better hardening</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> -- Canberk Koç <canberkkoc@gmail.com> Wed, 22 Jun 2016 05:35:41 +0300</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">infernal (1.1.1-4) unstable; urgency=medium</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> * Architecture: any-amd64 any-i386</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> Closes: #815310</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> * cme fix dpkg-control</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> * Secure Vcs-Browser</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 20 Feb 2016 23:07:53 +0100</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">infernal (1.1.1-3) unstable; urgency=medium</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> * cme fix dpkg-control</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> * drop dpg package at all since it is auto-generated by dpkg now</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> Closes: #766309</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 21 Dec 2015 09:35:57 +0100</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">infernal (1.1.1-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> * Re-enable i386 by checking availability of sse2</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> * d/copyright: Deleted unneeded paragraphs</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> * d/rules: drop redundant targets</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> * d/README*: drop pararaphs about squid which is not part of the</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> source any more</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 18 Sep 2014 10:00:12 +0200</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">infernal (1.1.1-1) unstable; urgency=medium</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> * Team upload.</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> * New upstream release.</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> -- Charles Plessy <plessy@debian.org> Fri, 08 Aug 2014 21:45:26 +0900</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">infernal (1.1-1) unstable; urgency=low</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> * New upstream release.</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> * Removed i386 architecture as some processors do not provide SSE2.</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> * Conforms with Policy 3.9.5.</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> -- Charles Plessy <plessy@debian.org> Sun, 01 Dec 2013 10:30:00 +0900</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">infernal (1.1~rc4-2) unstable; urgency=low</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> * Build-depends on libperl4-corelibs-perl (Closes: #724119).</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> * debian/control: removed myself from Uploaders.</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> -- Charles Plessy <plessy@debian.org> Mon, 23 Sep 2013 10:57:17 +0900</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">infernal (1.1~rc4-1) unstable; urgency=low</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> * New upstream source</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> * debian/source/format: 3.0 (quilt)</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> * debian/control:</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> - cme fix dpkg-control</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> - debhelper 9</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> - do not Build-Depend: quilt since source format implies this</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> - The package builds only on architectures with SSE instructions.</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> Quoting from build log on armel:</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> configure: WARNING: Infernal 1.1 requires VMX or SSE capability for</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> parallel instructions.</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> configure: error: It appears your platform has neither and will not</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> support Infernal.</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> So all non i386/amd64 architectures were excluded</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> Closes: #718742</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> - use anonscm in Vcs fields</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> * debian/rules:</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> - remove redundant setting for flags which is handled by debhelper 9</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> automatically</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> - use xz compression</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> * debian/copyright: DEP5</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 05 Aug 2013 12:06:12 +0200</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">infernal (1.1~rc2-1) unstable; urgency=low</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> * New upstream version - aiming to support RNAWorld BOINC project,</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> with many thanks and regards to Yoyo!</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> - cmscore no longer available</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> * Bumped policy to 3.9.4 (no changes needed)</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> - introduced hardening, with it build dep on</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> dpkg-dev (>= 1.16.1~)</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Wed, 01 May 2013 20:24:17 +0200</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">infernal (1.0.2-3) UNRELEASED; urgency=low</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> * Extra fixed for lintian cleanliness (Steffen)</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> * debian/upstream:</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> - do not specify DOI twice</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> - Moved PMID to references</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> * debian/control:</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> - Fixed Vcs-Svn field</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> - Standards-Version: 3.9.3 (no changes needed)</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 08 Mar 2012 11:44:54 +0100</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">infernal (1.0.2-2) unstable; urgency=low</span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> * Series of mall fixes (Closes: #643407).</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> * source/format 3.0</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> * Policy to 3.9.2</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> * added infernal-dbg</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> * corrected upstream's email address</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Tue, 27 Sep 2011 15:48:27 +0200</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">infernal (1.0.2-1) unstable; urgency=low</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> * New upstream version</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 03 Nov 2009 11:15:34 +0100</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">infernal (1.0-2) unstable; urgency=low</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> * Switch to CDBS to benefit from automagical config.{sub,guess}</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> update (debian/rules). Closes: #550253.</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"> * debian/control:</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> - Depend on cdbs, downgraded requirement on debhelper from 7.1 to 7.</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"> - Transferred bibliographic information from the package description</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"> to debian/upstream-metadata.yaml.</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> - Clarified the short description of the documentation package.</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"> * Removed debian/infernal.dirs, not needed.</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"> * Edited README.source, removing mention that infernal is in contrib.</span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"> * debian/copyright points at the version 3 of the GPL.</span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"> -- Charles Plessy <plessy@debian.org> Sat, 10 Oct 2009 11:22:35 +0900</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">infernal (1.0-1) unstable; urgency=low</span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"> [ Charles Plessy ]</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"> * Updated my email address.</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"> * New upstream version</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext"> * debian/control:</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"> - Standards-Version: 3.8.3 (no changes needed)</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"> - Added myself to uploaders</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"> - s/Debian-Med/Debian Med/</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"> - Build-Depends: debhelper (>= 7.1) autotools-dev</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"> - Package: infernal-doc</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"> * debian/rules rewritten to make use of short dh</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext"> * debian/copyright:</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"> - added myself to Copyright holders of debian/*</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"> - squid is not part of the upstream tarball anymore so this</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> - files/Userguide.pdf: Copied comment about PDF = source from</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"> README.Debian</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> * debian/infernal-doc.doc-base</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> * debian/infernal.install: install src/{trcyk,truncyk_check} to</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"> /usr/bin</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> * TODO: Convince upstream to release libeazel which is also used in</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> hmmer as a separate library instead of copying the code into</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"> different projects</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 25 Sep 2009 15:17:22 +0200</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">infernal (0.81-1) experimental; urgency=low</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> * Initial release (Closes: #441840)</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Mon, 10 Sep 2007 23:15:37 +0200</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: infernal</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Steffen Moeller <moeller@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> libperl4-corelibs-perl,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python3</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.4.1</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/infernal</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/infernal.git</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Homepage: http://eddylab.org/infernal/</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Package: infernal</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Architecture: any-amd64 any-i386</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Description: inference of RNA secondary structural alignments</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Infernal ("INFERence of RNA ALignment") searches DNA sequence</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> databases for RNA structure and sequence similarities. It provides an</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> implementation of a special variant of profile stochastic context-free</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> grammars called covariance models (CMs). A CM is like a sequence</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> profile, but it scores a combination of sequence consensus and RNA</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> secondary structure consensus, so in many cases, it is more capable of</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> identifying RNA homologs that conserve their secondary structure more</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> than their primary sequence.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> The tool is an integral component of the Rfam database.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Package: infernal-doc</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Section: doc</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Description: inference of RNA secondary structural alignments – documentation</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> Infernal ("INFERence of RNA ALignment") searches DNA sequence</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> databases for RNA structure and sequence similarities. It provides an</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> implementation of a special case of profile stochastic context-free</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> grammars called covariance models (CMs). A CM is like a sequence</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> profile, but it scores a combination of sequence consensus and RNA</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> secondary structure consensus, so in many cases, it is more capable of</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> identifying RNA homologs that conserve their secondary structure more</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> than their primary sequence.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> This package provides the documentation which is shipped with the</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> code of infernal.</span></pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Contact: Infernal developer team at HHMI Janelia Farm:</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Diana Kolbe <kolbed janelia.hhmi.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Eric Nawrocki <nawrockie janelia.hhmi.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Sean Eddy <eddys janelia.hhmi.org>.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Source: ftp://infernal.janelia.org/pub/software/infernal/infernal-1.1.1.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Copyright: © 2001-2014 HHMI Janelia Farm</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> © 1991-2013 Sean R. Eddy</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> © 2005-2013 Eric P. Nawrocki</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> © 2005-2011 Diana L. Kolbe</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> © 2004 Zasha Weinberg</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> © 1990 Don G. Gilbert</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> © 1995-2006 Washington University in St. Louis</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> © 1992-1995 Medical Research Council, UK</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> © 2004 University of Washington, Seattle</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> © 1986,1993,1995 University of Toronto</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> © 1989-2001 Free Software Foundation</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> © 1991 Massachusetts Institute of Technology</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">License: GPL-3</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Files: debian/*</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Copyright: © 2007-2008 Steffen Moeller <moeller@debian.org></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> © 2009-2014 Andreas Tille <tille@debian.org></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">License: GPL-3</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Files: easel/*</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Copyright: © 2004-2014 Sean R. Eddy</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> © 2006-2008 Howard Hughes Medical Institute</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">License: BSD-Easel</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Files: easel/esl_sse.c easel/esl_vmx.c</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Copyright: © 2007 Julien Pommier</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> © 1992 Stephen Moshier</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">License: BSD-Easel</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Files: easel/easel.c</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Copyright: © 1999-2001 David A. Wheeler</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">License: BSD-Easel</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Comment: This only concerns esl_tmpfile()</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Files: easel/esl_regexp.c</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Copyright: © 1986, 1993, 1995 by University of Toronto</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">License: BSD-Easel</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">License: BSD-Easel</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> @EASEL_COPYRIGHT@</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> .</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> The Easel library is freely modifiable and redistributable under the</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> Janelia Farm Software License, a BSD license:</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> .</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> Redistribution and use in source and binary forms, with or without</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> modification, are permitted provided that the following conditions are</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> met:</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> .</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> 1. Redistributions of source code must retain the above copyright</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer.</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> .</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> 2. Redistributions in binary form must reproduce the above copyright</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer in</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> the documentation and/or other materials provided with the</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> distribution.</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> .</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> 3. Neither the name of the Howard Hughes Medical Institute nor the</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> names of its contributors may be used to endorse or promote</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> products derived from this software without specific prior written</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> permission.</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> .</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY,</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> REASONABLE ROYALTIES; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> DAMAGE.</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">Files: Userguide.pdf</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">Copyright: Sean R. Eddy</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">License: GPL-3</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">Comment: The PDFs that are coming with the sources from which the userguide is</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> built are indeed upstream's original sources. They are edited with a PDF</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> editor. Upstream, Dr Eddy, was consulted in this issue.</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">License: GPL-3</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> This suite of programs is free software. You can redistribute it</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> and/or modify it under the terms of the GNU General Public License as</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> published by the Free Software Foundation; either version 2 of the</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> License, or (at your option) any later version.</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> .</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> In other words, you may modify, copy, or redistribute this source code</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> and its documentation, but if you do, you must preserve all these</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> copyrights and distribute all derivative versions as free software</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> under the GNU General Public License.</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> .</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> This software is distributed in the hope that it will be useful, but</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> General Public License for more details.</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> .</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> You should have received a copy of the GNU General Public License</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> along with this software, in the file LICENSE; if not, write to the</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> MA 02110-1301, USA or see http://www.gnu.org/</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">Comment: On Debian systems, the complete text of the GNU General Public</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> License version 3 can be found in `/usr/share/common-licenses/GPL-3'.</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#e28c7ef74334204b1282d72fdefcf1f176234363"><strong>debian/infernal-doc.doc-base</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Document: infernal-doc</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Title: INFERNAL User’s Guide</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Author: Diana Kolbe, Eric Nawrocki, Sean Eddy</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Abstract: Sequence analysis using profiles of RNA secondary structure consensus</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Infernal ("INFERence of RNA ALignment") is for searching DNA sequence</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> databases for RNA structure and sequence similarities. It is an</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> implementation of a special case of profile stochastic context-free</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> grammars called covariance models (CMs). A CM is like a sequence</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> profile, but it scores a combination of sequence consensus and RNA</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> secondary structure consensus, so in many cases, it is more capable of</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> identifying RNA homologs that conserve their secondary structure more</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> than their primary sequence.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Section: Science/Biology</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Format: pdf</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Files: /usr/share/doc/infernal/Userguide.pdf</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#1a81aa218ceb4c11f7c78f284ad4df72c82baf09"><strong>debian/infernal-doc.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Userguide</span><span class="o" style="font-weight: 600;">.</span><span class="nx">pdf</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">infernal</span></span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#b9b805bfceb39273e3f6bf22d1ac59465bc6c87e"><strong>debian/infernal.docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">README</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">RELEASE-*.md</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#ecab0285d237a7bea24772404f5bdeb4c91cbbb6"><strong>debian/infernal.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">infernal</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#468e3c702db300a91035d94993f467d809753ce0"><strong>debian/infernal.manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#documentation/manpages/*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#share/man/man1/*.1</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tmp/share/man/man1/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#9ede01a1ccab9d49b232b5476e893d798fe6e1d0"><strong>debian/patches/autoreconf.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: Mon, 16 Jul 2018 07:59:38 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Origin: https://lists.debian.org/debian-mentors/2018/07/msg00193.html</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Description: Fix configure.ac to enable autoreconf</span></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">--- a/configure.ac</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -121,24 +121,24 @@</span> AC_SUBST(EASEL_VERSION)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> AC_SUBST(EASEL_URL)</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"> # Preprocessor symbols (replace #undefs in hmmer/src/p7_config.h and src/config.h)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(INFERNAL_DATE, "$INFERNAL_DATE")</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(INFERNAL_COPYRIGHT, "$INFERNAL_COPYRIGHT")</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(INFERNAL_LICENSE, "$INFERNAL_LICENSE")</span></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;">-AC_DEFINE_UNQUOTED(INFERNAL_VERSION, "$INFERNAL_VERSION")</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(INFERNAL_URL, "$INFERNAL_URL")</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;">-</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(HMMER_DATE, "$HMMER_DATE")</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(HMMER_COPYRIGHT, "$HMMER_COPYRIGHT")</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(HMMER_LICENSE, "$HMMER_LICENSE")</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(HMMER_VERSION, "$HMMER_VERSION")</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(HMMER_URL, "$HMMER_URL")</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(EASEL_DATE, "$EASEL_DATE")</span></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;">-AC_DEFINE_UNQUOTED(EASEL_COPYRIGHT, "$EASEL_COPYRIGHT")</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(EASEL_LICENSE, "$EASEL_LICENSE")</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE_UNQUOTED(EASEL_VERSION, "$EASEL_VERSION")</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([INFERNAL_DATE], ["$INFERNAL_DATE"], [Timestamp of infernal code])</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([INFERNAL_COPYRIGHT], ["$INFERNAL_COPYRIGHT"], [Infernal copyright information])</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([INFERNAL_LICENSE], ["$INFERNAL_LICENSE"], [Infernal license])</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([INFERNAL_VERSION], ["$INFERNAL_VERSION"], [Invernal version])</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([INFERNAL_URL], ["$INFERNAL_URL"], [Link to infernal homepage])</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" 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="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([HMMER_DATE], ["$HMMER_DATE"], [Timestamp of hmmer code])</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([HMMER_COPYRIGHT], ["$HMMER_COPYRIGHT"], [Hmmer copyright information])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" 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="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([HMMER_LICENSE], ["$HMMER_LICENSE"], [Hmmer license])</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([HMMER_VERSION], ["$HMMER_VERSION"], [Hmmer version])</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([HMMER_URL], ["$HMMER_URL"], [Link to hmmer homepage])</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([EASEL_DATE], ["$EASEL_DATE"], [Timestamp of easel code])</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;">+AC_DEFINE_UNQUOTED([EASEL_COPYRIGHT], ["$EASEL_COPYRIGHT"], [Easel copyright information])</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([EASEL_LICENSE], ["$EASEL_LICENSE"], [Easel license])</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([EASEL_VERSION], ["$EASEL_VERSION"], [Easel version])</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_DEFINE(eslLIBRARY)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE(eslLIBRARY, [], [esl library])</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> #AC_DEFINE(hmmerLIBRARY)</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> # Figure out what host we're compiling on.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="p">@@ -182,11 +182,11 @@</span> AS_HELP_STRING([--enable-debugging=x],[a</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> enable_debugging=$enableval, enable_debugging=no)</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> case $enable_debugging in</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- yes) AC_DEFINE(eslDEBUGLEVEL, 0);;</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 1) AC_DEFINE(eslDEBUGLEVEL, 1);;</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 2) AC_DEFINE(eslDEBUGLEVEL, 2);;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 3) AC_DEFINE(eslDEBUGLEVEL, 3);;</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- no) AC_DEFINE(eslDEBUGLEVEL, 0);;</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ yes) AC_DEFINE(eslDEBUGLEVEL, 0, [no debugging]);;</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 1) AC_DEFINE(eslDEBUGLEVEL, 1, [debug level 1]);;</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 2) AC_DEFINE(eslDEBUGLEVEL, 2, [debug level 2]);;</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 3) AC_DEFINE(eslDEBUGLEVEL, 3, [debug level 3]);;</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ no) AC_DEFINE(eslDEBUGLEVEL, 0, [no debugging]);;</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> *) AC_MSG_ERROR([Unknown argument to --enable-debugging: $enable_debugging]);;</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -293,7 +293,7 @@</span> case $enable_threads in</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> AS_IF([test "x$check_threads" != xno],</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [ACX_PTHREAD([AC_DEFINE(HMMER_THREADS)</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [ACX_PTHREAD([AC_DEFINE(HMMER_THREADS, [], [Threads for hmmer])</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> AC_DEFINE(HAVE_PTHREAD)</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> AC_SUBST(PTHREAD_LIBS)</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> AC_SUBST(PTHREAD_CFLAGS)],</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="p">@@ -356,7 +356,7 @@</span> AC_PROG_CC</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> AC_PROG_INSTALL</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> # MPI : set @CC@ to mpicc, sets @MPILIBS@, defines HAVE_MPI. </span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> if test "$enable_mpi" = "yes"; then</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ACX_MPI([AC_DEFINE(HAVE_MPI)</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ACX_MPI([AC_DEFINE(HAVE_MPI, [], [MPI enabled])</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> AC_SUBST([MPI_UTESTS], ["mpi_utest"])</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> AC_SUBST([MPI_BENCHMARKS], ["mpi_benchmark"])],</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> AC_MSG_ERROR([MPI library not found for --enable-mpi]))</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="p">@@ -376,7 +376,7 @@</span> CHECK_GNU_MAKE</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> # Select our optimization level in CFLAGS.</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> if test "$enable_debugging" != "no"; then</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AC_DEFINE(p7_DEBUGGING, 1)</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AC_DEFINE(p7_DEBUGGING, 1, [p7 debugging level 1])</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> if test "$GCC" = "yes" && test "$sre_cflags_env_set" = "no"; then</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> CFLAGS="-g -Wall"</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="p">@@ -454,7 +454,7 @@</span> if test "$impl_choice" = "sse"; then</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> __m128i b;</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> b = _mm_castps_si128(a);</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> a = _mm_castsi128_ps(b);]])],</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [AC_DEFINE([HAVE_SSE2_CAST])</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [AC_DEFINE([HAVE_SSE2_CAST], [], [compiler support for sse2 cast functions])</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> ssecast=yes])</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> AC_MSG_RESULT([$ssecast])</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> CFLAGS="$sre_save_cflags"</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -531,7 +531,7 @@</span> if test "$impl_choice" = "sse"; then</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> [[_MM_SET_FLUSH_ZERO_MODE (_MM_FLUSH_ZERO_ON);</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> ]])],</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> [ AC_MSG_RESULT([yes])</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AC_DEFINE([HAVE_FLUSH_ZERO_MODE])],</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AC_DEFINE([HAVE_FLUSH_ZERO_MODE], [], [_MM_SET_FLUSH_ZERO_MODE is supported])],</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> [ AC_MSG_RESULT([no])]</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> )</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> CFLAGS="$sre_save_cflags"</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="p">@@ -540,16 +540,16 @@</span> fi</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> # Now, we can enable the appropriate optimized implementation.</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> case "$impl_choice" in </span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> sse) AC_MSG_NOTICE([Activating Intel/AMD SSE optimized DP implementation])</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AC_DEFINE([HAVE_SSE2])</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AC_DEFINE([p7_IMPL_SSE])</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AC_DEFINE([HAVE_SSE2], [], [Activating Intel/AMD SSE optimized DP implementation])</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AC_DEFINE([p7_IMPL_SSE], [], [Activating Intel/AMD SSE optimized DP implementation])</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> AC_SUBST([HMMERIMPLLIB], ["impl_sse/libhmmerimpl.a"])</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> IMPL_CHOICE="sse"</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> INFERNAL_IMPLDIR="impl_sse"</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> </span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> vmx) AC_MSG_NOTICE([Activating Altivec/VMX optimized DP implementation])</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AC_DEFINE([HAVE_VMX])</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AC_DEFINE([p7_IMPL_VMX])</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AC_DEFINE([HAVE_VMX], [], [Activating Altivec/VMX optimized DP implementation])</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AC_DEFINE([p7_IMPL_VMX], [], [Activating Altivec/VMX optimized DP implementation])</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> AC_SUBST([HMMERIMPLLIB], ["impl_vmx/libhmmerimpl.a"])</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> IMPL_CHOICE="vmx"</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> INFERNAL_IMPLDIR=""</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="p">@@ -582,7 +582,7 @@</span> AC_PATH_PROG(HAVE_GZIP, "gzip", "no")</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> if test "${HAVE_GZIP}" = "no"; then</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> AC_MSG_WARN([gzip not found])</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> else</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AC_DEFINE(HAVE_GZIP)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AC_DEFINE(HAVE_GZIP, [], [Use systm gzip library])</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> fi</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> </span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> # 5. Checks for libraries</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="p">@@ -731,6 +731,29 @@</span> AC_CONFIG_FILES([easel/testsuite/Makefil</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> AC_CONFIG_FILES([easel/Makefile])</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> AC_CONFIG_FILES([easel/documentation/Makefile])</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> </span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AH_TOP([</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* RAMLIMIT (in MB) defines how much memory we're</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * allowed to expend on alignment algorithms without</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * switching to more efficient memory forms - e.g.</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * in smallcyk.c</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ */</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifndef RAMLIMIT</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define RAMLIMIT 0</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* SRE_CONLEVEL will prob move to squid somewhere.</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * Set to 1 to activate contract checking, during debugging.</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ */</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SRE_CONLEVEL 1</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if (SRE_CONLEVEL >= 1)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <assert.h></span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define CMSEQDBENV "BLASTDB"</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define CMDBENV "RFAMDB"</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+])</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> ################################################################</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> # 13. AC_OUTPUT</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> ################################################################</span></pre>
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<li id="fa0b5e351d301ecb3f65aee8aa71f53728726b99">
<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#fa0b5e351d301ecb3f65aee8aa71f53728726b99"><strong>debian/patches/format_security.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">Author: Andreas Tille</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2016-06-21 11:19:17 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix format security issues</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">Index: infernal-1.0.2/easel/esl_getopts.c</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></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;">--- infernal-1.0.2.orig/easel/esl_getopts.c 2009-10-30 18:30:58.000000000 +0100</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;">+++ infernal-1.0.2/easel/esl_getopts.c 2011-09-27 15:52:41.490289335 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1270,7 +1270,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> "Arg looks like option? Use %.24s%.24s if you really mean it.",</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> g->opt[opti].name, *ret_optarg);</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> } else </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ESL_FAIL(eslESYNTAX, "Option %.24s requires an argument", g->opt[opti].name);</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ESL_FAIL(eslESYNTAX, g->errbuf, "Option %.24s requires an argument", g->opt[opti].name);</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> g->optstring = NULL; /* An optchar that takes an arg must terminate an optstring. */</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gh" style="color: #999;">Index: infernal-1.0.2/easel/esl_msa.c</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal-1.0.2.orig/easel/esl_msa.c 2009-10-30 18:30:55.000000000 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal-1.0.2/easel/esl_msa.c 2011-09-27 15:57:44.961318373 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">@@ -3614,7 +3614,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> ESL_MSA *msa = NULL;</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> if (esl_tmpfile_named(tmpfile, &fp) != eslOK) goto ERROR;</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(fp, s);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //fprintf(fp, s); // provokes error: format not a string literal and no format arguments [-Werror=format-security]</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fputs(s,fp);</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> fclose(fp); </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> fp = NULL;</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> if (esl_msafile_Open(tmpfile, fmt, NULL, &mfp) != eslOK) goto ERROR;</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gh" style="color: #999;">Index: infernal-1.0.2/easel/esl_tree.c</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></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;">--- infernal-1.0.2.orig/easel/esl_tree.c 2009-10-30 18:30:58.000000000 +0100</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;">+++ infernal-1.0.2/easel/esl_tree.c 2011-09-27 15:59:14.101032221 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -149,7 +149,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> ESL_TREE *T = NULL;</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> if (esl_tmpfile(tmpfile, &fp) != eslOK) goto ERROR;</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;">- fprintf(fp, s);</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;">+ //fprintf(fp, s); // provokes error: format not a string literal and no format arguments [-Werror=format-security]</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fputs(s,fp);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> rewind(fp);</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> if (esl_tree_ReadNewick(fp, NULL, &T) != eslOK) goto ERROR;</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> fclose(fp);</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#d6c09299b1f914372840e8fd6fcc850f8a11b236"><strong>debian/patches/hardening</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">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: insert CPPFLAGS in easel</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/easel/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/easel/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -549,7 +549,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> @${RANLIB} libeasel.a</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ${ALL_OBJS}: %.o : %.c ${HDRS} esl_config.h</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_CC}${CC} -I. -I${srcdir} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<</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;">+ ${QUIET_CC}${CC} -I. -I${srcdir} ${CPPFLAGS} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> # Driver compilation:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -573,10 +573,10 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> else DFILE=${srcdir}/esl_$${BASENAME}.c ;\</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> fi;\</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if test ${V} ;\</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${UTEST_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> else echo ' ' GEN $@ ;\</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> fi ;\</span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> ${ALL_BENCHMARKS}: libeasel.a</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> @BASENAME=`echo $@ | sed -e 's/_benchmark//'| sed -e 's/^esl_//'` ;\</span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -587,10 +587,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> else DFILE=${srcdir}/esl_$${BASENAME}.c ;\</span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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="LC29" class="line" lang="diff"> fi;\</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> if test ${V} ;\</span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="33" 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">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> else echo ' ' GEN $@ ;\</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> fi ;\</span>
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<td class="diff-line-num new new_line" data-linenumber="35" 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">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" 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">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" 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">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> ${ALL_EXPERIMENTS}: libeasel.a</span>
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<td class="diff-line-num new new_line" data-linenumber="39" 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">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> @BASENAME=`echo $@ | sed -e 's/_experiment//'| sed -e 's/^esl_//'` ;\</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -601,10 +601,10 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> else DFILE=${srcdir}/esl_$${BASENAME}.c ;\</span>
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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> fi;\</span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> if test ${V} ;\</span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> else echo ' ' GEN $@ ;\</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> fi ;\</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> ${ALL_EXAMPLES}: libeasel.a</span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> @BASENAME=`echo $@ | sed -e 's/_example[0-9]*//'| sed -e 's/^esl_//'` ;\</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="p">@@ -614,10 +614,10 @@</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> else DFILE=${srcdir}/esl_$${BASENAME}.c ;\</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> fi ;\</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> if test ${V}; \</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> else echo ' ' GEN $@ ;\</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> fi ;\</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/easel/miniapps/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/easel/miniapps/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -94,13 +94,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> check: ${PROGS} easel</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> easel: % : %.c ../libeasel.a ${SUBCMDOBJS}</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${SUBCMDOBJS} ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} ${CPPFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${SUBCMDOBJS} ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> ${PROGS}: % : %.c ../libeasel.a </span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} ${CPPFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> ${SUBCMDOBJS}: %.o : %.c ../libeasel.a</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_CC}${CC} -I. -I.. -I${srcdir} -I${srcdir}/.. ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_CC}${CC} ${CPPFLAGS} -I. -I.. -I${srcdir} -I${srcdir}/.. ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> install: ${PROGS} </span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> ${INSTALL} -m 0755 easel ${DESTDIR}${bindir}/</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/hmmer/profmark/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/hmmer/profmark/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -43,12 +43,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> dev: ${PROGS}</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> ${PROGS}: % : %.o ../${ESLDIR}/libeasel.a ../src/libhmmer.a </span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_GEN}${CC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_GEN}${CC} ${CPPFLAGS} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> ${PROGOBJS}: ../src/hmmer.h ../src/p7_config.h</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> .c.o: </span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} -o $@ -c $< </span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_CC}${CC} ${CPPFLAGS} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} -o $@ -c $< </span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> -rm -f *.o *~ ${PROGS} </span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/rmark/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/rmark/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="p">@@ -43,12 +43,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> dev: ${PROGS}</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> ${PROGS}: % : %.o ../${HMMERDIR}/src/libhmmer.a ../${ESLDIR}/libeasel.a </span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_GEN}${CC} ${CFLAGS} ${DEFS} ${LDFLAGS} -L../${HMMERDIR}/src -L../${ESLDIR} -L${SRCDIR} -o $@ $@.o ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_GEN}${CC} ${CPPFLAGS} ${CFLAGS} ${DEFS} ${LDFLAGS} -L../${HMMERDIR}/src -L../${ESLDIR} -L${SRCDIR} -o $@ $@.o ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> ${PROGOBJS}: ../${HMMERDIR}/src/hmmer.h ../${HMMERDIR}/src/p7_config.h ../src/infernal.h ../src/config.h</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> .c.o: </span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${DEFS} -o $@ -c $< </span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_CC}${CC} ${CPPFLAGS} ${ESLINC} ${SRCINC} ${CFLAGS} ${DEFS} -o $@ -c $< </span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> distclean: clean</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> -rm -f Makefile</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#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">#format_security.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#autoreconf.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">spelling.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">hardening</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.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">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 16 Jul 2018 07:59:38 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix spelling</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">Index: infernal/src/cm_modelmaker.c</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></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;">--- infernal.orig/src/cm_modelmaker.c</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;">+++ infernal/src/cm_modelmaker.c</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1361,7 +1361,7 @@</span> ConsensusModelmaker(const ESL_ALPHABET *</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"> esl_wuss_nopseudo(ss_cons, ss_cons); /* remove pknots in place */</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> ESL_ALLOC(ct, (clen+1) * sizeof(int));</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ((status = esl_wuss2ct(ss_cons, clen, ct)) != eslOK) ESL_FAIL(status, errbuf, "Consensus string is inconsisent in ConsensusModelMaker().");</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ((status = esl_wuss2ct(ss_cons, clen, ct)) != eslOK) ESL_FAIL(status, errbuf, "Consensus string is inconsistent in ConsensusModelMaker().");</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> /* 2. Construct a guide tree. </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> * This codes is borrowed from HandModelmaker(), where it</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gh" style="color: #999;">Index: infernal/documentation/manpages/cmalign.man</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/documentation/manpages/cmalign.man</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/documentation/manpages/cmalign.man</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">@@ -309,7 +309,7 @@</span> only cells within the bands need be allo</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> Importantly, HMM banding sacrifices the guarantee of determining the</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> optimally accurarte or optimal alignment, which will be missed if it</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-lies outside the bands. The tau paramater is the amount of probability</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lies outside the bands. The tau parameter is the amount of probability</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> mass considered negligible during HMM band calculation; lower values</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> of tau yield greater speedups but also a greater chance of missing the</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> optimal alignment. The default tau is 1E-7, determined empirically as</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -500,7 +500,7 @@</span> in previous versions of</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> .B --mapstr</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> Must be used in combination with </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> .BI --mapali " <f>".</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Propogate structural information for any pseudoknots that exist in</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Propagate structural information for any pseudoknots that exist in</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> .I <f> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> to the output alignment. A similar option to this one was called</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> .B --withstr </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gh" style="color: #999;">Index: infernal/documentation/manpages/cmcalibrate.man</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/documentation/manpages/cmcalibrate.man</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/documentation/manpages/cmcalibrate.man</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -51,7 +51,7 @@</span> Interface) can be also be used for paral</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> .B --mpi </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> option if Infernal was built with MPI enabled, but using more than 161</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> processors is not recommended because increasing past 161 won't</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-accelerate the calibration. See the Installation seciton of the user</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+accelerate the calibration. See the Installation section of the user</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> guide for more information.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> .PP</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gh" style="color: #999;">Index: infernal/hmmer/src/p7_builder.c</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/hmmer/src/p7_builder.c</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/hmmer/src/p7_builder.c</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="p">@@ -481,7 +481,7 @@</span> p7_Builder(P7_BUILDER *bld, ESL_MSA *msa</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> * </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> * Args: bld - build configuration</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> * sq - query sequence</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * bg - null model (needed to paramaterize insert emission probs)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * bg - null model (needed to parameterize insert emission probs)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> * opt_hmm - optRETURN: new HMM</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> * opt_gm - optRETURN: profile corresponding to <hmm></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> * opt_om - optRETURN: optimized profile corresponding to <gm></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gh" style="color: #999;">Index: infernal/documentation/manpages/cmscan.man</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/documentation/manpages/cmscan.man</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/documentation/manpages/cmscan.man</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="p">@@ -746,7 +746,7 @@</span> option.</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> .TP</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> .B --oskip</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Omit any hit h from the tabular output file that satisifies the</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Omit any hit h from the tabular output file that satisfies the</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> following: another hit h2 overlaps with h and the E-value of h2 is</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> lower than that of h. Hit h will not appear in the tabular output</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> file, although it will still exist in the standard output. </span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gh" style="color: #999;">Index: infernal/documentation/manpages/cmstat.man</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/documentation/manpages/cmstat.man</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/documentation/manpages/cmstat.man</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -115,7 +115,7 @@</span> include Rfam GA, TC, and/or NC bit score</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> and/or</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> .B --cut_nc </span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> options can be used to display E-values that correspond to the bit</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-score thresholds. Seperate bit scores or E-values will be displayed</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+score thresholds. Separate bit scores or E-values will be displayed</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> for each of the four possible CM search algorithm and model</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> configuration pairs: local Inside, local CYK, glocal Inside and glocal</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> CYK.</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#!/usr/bin/make -f</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># -*- makefile -*-</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC4" 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="LC5" class="line" lang="make"></span>
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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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<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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<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;">$@</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"><span class="nl">override_dh_auto_clean</span><span class="o" style="font-weight: 600;">:</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-r</span> Makefile <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="nv" style="color: #008080;">$(MAKE)</span> distclean<span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"> <span class="p">-</span><span class="nb" style="color: #0086b3;">cd </span>documentation/userguide <span class="o" style="font-weight: 600;">&&</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-r</span> Makefile <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span>make distclean<span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"> <span class="p">-</span><span class="nb" style="color: #0086b3;">cd </span>easel/documentation <span class="o" style="font-weight: 600;">&&</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-r</span> Makefile <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span>make distclean<span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"> dh_clean <span class="k" style="font-weight: 600;">*</span>.1 <span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.log <span class="k" style="font-weight: 600;">*</span>.log <span class="k" style="font-weight: 600;">*</span>/Makefile Makefile documentation/manpages/<span class="k" style="font-weight: 600;">*</span>.1</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> testsuite/i49.tbl</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"><span class="nl">override_dh_compress </span><span class="o" style="font-weight: 600;">:</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"> dh_compress <span class="nt" style="color: #000080;">-X</span>.pdf</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"><span class="nl">override_dh_auto_build</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"> dh_auto_build <span class="nt" style="color: #000080;">--</span> <span class="nv" style="color: #008080;">V</span><span class="o" style="font-weight: 600;">=</span>1</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="make"><span class="nl">override_dh_auto_install</span><span class="o" style="font-weight: 600;">:</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="make"> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-j</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">nproc</span><span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nv" style="color: #008080;">AM_UPDATE_INFO_DIR</span><span class="o" style="font-weight: 600;">=</span>no <span class="nv" style="color: #008080;">V</span><span class="o" style="font-weight: 600;">=</span>1 <span class="nv" style="color: #008080;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CURDIR)</span>/debian/tmp</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="make"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="make"><span class="nl">override_dh_install</span><span class="o" style="font-weight: 600;">:</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="make"> dh_install</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="make"> <span class="k" style="font-weight: 600;">for </span>bin <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nv" style="color: #008080;">$(CURDIR)</span>/debian/infernal/usr/lib/infernal<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span> <span class="se" style="color: #d14;">\</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>bin <span class="o" style="font-weight: 600;">!=</span> cmalign <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="make"> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> cmalign <span class="nv" style="color: #008080;">$(CURDIR)</span>/debian/infernal/usr/bin/<span class="nv" style="color: #008080;">$$</span>bin <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make"> <span class="k" style="font-weight: 600;">done</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="make"></span>
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38
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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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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="make"> dh_installexamples</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;">$(sampledir)</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/src/</span>
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42
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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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44
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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;">$(sampledir_lib)</span>/src/</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./easel/miniapps/esl-reformat <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/easel/miniapps/</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> ./easel/miniapps/esl-shuffle <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/easel/miniapps/</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> ./easel/miniapps/esl-sfetch <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/easel/miniapps/</span>
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48
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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;">$(DEB_SOURCE)</span>/examples/easel ./easel <span class="se" style="color: #d14;">\</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="make"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> ../../../../lib/<span class="nv" style="color: #008080;">$(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/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0 (quilt)</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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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: @, python3</span>
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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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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"infernal"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-Lr</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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;">$AUTOPKGTEST_TMP</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gz"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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16
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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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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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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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19
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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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20
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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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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> author: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> title: "Infernal 1.0: inference of RNA alignments"</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> journal: Bioinformatics</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> volume: 25</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> number: 10</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> pages: 1335-1337</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> doi: 10.1093/bioinformatics/btp157</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> PMID: 19307242</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> year: 2009</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/10/1335</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/25/10/1335.pdf</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">- Name: OMICtools</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Entry: OMICS_00977</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">- Name: SciCrunch</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Entry: SCR_011809</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Entry: infernal</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">- Name: bio.tools</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Entry: NA # infernal_cmscan does not fit</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Bug-Submit: eric.nawrocki@nih.gov</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/infernal/compare/78d138bc5db10e5324d4b4a538bd1dfd3efa4250...847ca32158c03000deec505d920b7c7dbf0b19b2#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">opts="uversionmangle=s/(rc\d+)/~$1/" \</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">http://eddylab.org/infernal/ infernal-([^-]*)\.tar\.gz</span></pre>
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