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<h3>

Andreas Tille pushed to branch master

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/5e9f9fd7558213ebef0e3764b409f80dcc59595a">5e9f9fd7</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T07:46:40Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make the build reproducible

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/infernal/commit/212ae0f0b833e018bef5def1a1cfe411bf7c48a0">212ae0f0</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T07:48:57Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable "nocheck" build profile

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/infernal/commit/d39cc98792e5622f5bce71aa7a26cb59f28ca09a">d39cc987</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T07:56:30Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove patches autoreconf.patch, format_security.patch that are missing from debian/patches/series.

Fixes lintian: patch-file-present-but-not-mentioned-in-series

See https://lintian.debian.org/tags/patch-file-present-but-not-mentioned-in-series.html for more details.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/infernal/commit/8954d68c47ee14e8a509d6effa7d69997117d209">8954d68c</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T07:56:31Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/copyright: use spaces rather than tabs to start continuation lines.

Fixes lintian: tab-in-licence-text

See https://lintian.debian.org/tags/tab-in-licence-text.html for more details.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/infernal/commit/aa9d392e068d2bd658d7f37f3b501c34a1cd7e8e">aa9d392e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T07:56:32Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Name (from ./configure).</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/infernal/commit/9f56bdd80c80a2b70ffff0a598e8221974fa9447">9f56bdd8</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:11:02Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>8 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

debian/copyright

</a>

</li>

<li class="file-stats">

<a href="#9ede01a1ccab9d49b232b5476e893d798fe6e1d0">

<span class="deleted-file">

−

debian/patches/autoreconf.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#fa0b5e351d301ecb3f65aee8aa71f53728726b99">

<span class="deleted-file">

−

debian/patches/format_security.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#a8acb8f92d9ad3c7a79974b1b126f9309361c653">

<span class="new-file">

+

debian/patches/reproducible_build.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

<li class="file-stats">

<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">

debian/upstream/metadata

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/infernal/compare/847ca32158c03000deec505d920b7c7dbf0b19b2...9f56bdd80c80a2b70ffff0a598e8221974fa9447#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">infernal (1.1.3-3) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  [ Chris Lamb ]</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="4" 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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * Make the build reproducible</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">    Closes: #946315</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Enable "nocheck" build profile</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">    Closes: #946314</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>

</pre>

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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="plaintext">  [ Andreas Tille ]</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">  * Remove patches autoreconf.patch, format_security.patch that are</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">    missing from debian/patches/series.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="12" 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">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">  * debian/copyright: use spaces rather than tabs to start continuation</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">    lines.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="14" 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">

14

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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="LC14" class="line" lang="plaintext">  * Set upstream metadata fields: Name (from ./configure).</span>

</pre>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Sat, 07 Dec 2019 08:56:34 +0100</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>

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1

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">infernal (1.1.3-2) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>

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3

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/infernal/compare/847ca32158c03000deec505d920b7c7dbf0b19b2...9f56bdd80c80a2b70ffff0a598e8221974fa9447#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>

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2

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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="LC3" class="line" lang="plaintext"><span class="idiff left right"> </span>                 Diana Kolbe <kolbed janelia.hhmi.org></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"><span class="idiff left right"> </span>                 Eric Nawrocki <nawrockie janelia.hhmi.org></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"><span class="idiff left right"> </span>                 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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<li id="9ede01a1ccab9d49b232b5476e893d798fe6e1d0">

<a href="https://salsa.debian.org/med-team/infernal/compare/847ca32158c03000deec505d920b7c7dbf0b19b2...9f56bdd80c80a2b70ffff0a598e8221974fa9447#9ede01a1ccab9d49b232b5476e893d798fe6e1d0"><strong>debian/patches/autoreconf.patch</strong>

deleted

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

41

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> </span>

</pre>

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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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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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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>

</pre>

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"> esac</span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff">  </span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"> AS_IF([test "x$check_threads" != xno],</span>

</pre>

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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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff">                     AC_SUBST(PTHREAD_CFLAGS)],</span>

</pre>

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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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"> if test "$enable_mpi" = "yes"; then</span>

</pre>

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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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff">             AC_SUBST([MPI_UTESTS], ["mpi_utest"])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff">             AC_SUBST([MPI_BENCHMARKS], ["mpi_benchmark"])],</span>

</pre>

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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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"> # Select our optimization level in CFLAGS.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"> if test "$enable_debugging" != "no"; then</span>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff">       CFLAGS="-g -Wall"</span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff">    fi</span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff">                                        __m128i b;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff">                                        b = _mm_castps_si128(a);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff">                                        a = _mm_castsi128_ps(b);]])],</span>

</pre>

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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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff">                      ssecast=yes])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff">   AC_MSG_RESULT([$ssecast])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff">   CFLAGS="$sre_save_cflags"</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff">                                  ]])],</span>

</pre>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff">         [ AC_MSG_RESULT([yes])</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff">         [ AC_MSG_RESULT([no])]</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">   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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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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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<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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<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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<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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<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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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff">       AC_SUBST([HMMERIMPLLIB], ["impl_sse/libhmmerimpl.a"])</span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff">       ;;</span>

</pre>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff">       AC_SUBST([HMMERIMPLLIB], ["impl_vmx/libhmmerimpl.a"])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff">       IMPL_CHOICE="vmx"</span>

</pre>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff">       INFERNAL_IMPLDIR=""</span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"> if test "${HAVE_GZIP}" = "no"; then</span>

</pre>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff">   AC_MSG_WARN([gzip not found])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"> else</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"> fi</span>

</pre>

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"> # 5. Checks for libraries</span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"> AC_CONFIG_FILES([easel/Makefile])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"> AC_CONFIG_FILES([easel/documentation/Makefile])</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"> </span>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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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<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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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ */</span></span>

</pre>

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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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<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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<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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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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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>

</pre>

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>

</pre>

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff"> ################################################################</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff"> # 13. AC_OUTPUT</span>

</pre>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"> ################################################################</span></pre>

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<br>

</li>

<li id="fa0b5e351d301ecb3f65aee8aa71f53728726b99">

<a href="https://salsa.debian.org/med-team/infernal/compare/847ca32158c03000deec505d920b7c7dbf0b19b2...9f56bdd80c80a2b70ffff0a598e8221974fa9447#fa0b5e351d301ecb3f65aee8aa71f53728726b99"><strong>debian/patches/format_security.patch</strong>

deleted

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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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<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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="p">@@ -3614,7 +3614,8 @@</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff">   ESL_MSA     *msa         = NULL;</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff">   fclose(fp); </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff">   fp = NULL;</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="p">@@ -149,7 +149,8 @@</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff">   ESL_TREE *T           = NULL;</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff">   if (esl_tmpfile(tmpfile, &fp)         != eslOK) goto ERROR;</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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42

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff">   rewind(fp);</span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff">   fclose(fp);</span></pre>

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<br>

</li>

<li id="a8acb8f92d9ad3c7a79974b1b126f9309361c653">

<a href="https://salsa.debian.org/med-team/infernal/compare/847ca32158c03000deec505d920b7c7dbf0b19b2...9f56bdd80c80a2b70ffff0a598e8221974fa9447#a8acb8f92d9ad3c7a79974b1b126f9309361c653"><strong>debian/patches/reproducible_build.patch</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Make the build reproducible</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Chris Lamb <lamby@debian.org></span></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/946315</span></span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2019-12-05</span></span>

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5

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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">--- infernal-1.1.3.orig/hmmer/src/p7_tophits.c</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal-1.1.3/hmmer/src/p7_tophits.c</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -2001,8 +2001,10 @@</span> p7_tophits_TabularTail(FILE *ofp, const</span>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">   if (fprintf(ofp, "# Query file:      %s\n",      (qfile    == NULL) ? "[none]" : qfile) < 0)    ESL_XEXCEPTION_SYS(eslEWRITE, "tabular output tail, write failed");</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">   if (fprintf(ofp, "# Target file:     %s\n",      (tfile    == NULL) ? "[none]" : tfile) < 0)    ESL_XEXCEPTION_SYS(eslEWRITE, "tabular output tail, write failed");</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">   if (fprintf(ofp, "# Option settings: %s\n",      spoof_cmd) < 0)                                ESL_XEXCEPTION_SYS(eslEWRITE, "tabular output tail, write failed");</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;">-  if (fprintf(ofp, "# Current dir:     %s\n",      (cwd      == NULL) ? "[unknown]" : cwd) < 0)   ESL_XEXCEPTION_SYS(eslEWRITE, "tabular output tail, write failed");</span></span>

</pre>

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13

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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 (fprintf(ofp, "# Date:            %s",        timestamp) < 0) /* timestamp ends in \n */     ESL_XEXCEPTION_SYS(eslEWRITE, "tabular output tail, write failed");</span></span>

</pre>

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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 (getenv("SOURCE_DATE_EPOCH") != NULL) {</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    if (fprintf(ofp, "# Current dir:     %s\n",    (cwd      == NULL) ? "[unknown]" : cwd) < 0)   ESL_XEXCEPTION_SYS(eslEWRITE, "tabular output tail, write failed");</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    if (fprintf(ofp, "# Date:            %s",      timestamp) < 0) /* timestamp ends in \n */     ESL_XEXCEPTION_SYS(eslEWRITE, "tabular output tail, write failed");</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  }</span></span>

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff">   if (fprintf(ofp, "# [ok]\n") < 0)                                                               ESL_XEXCEPTION_SYS(eslEWRITE, "tabular output tail, write failed");</span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>

</pre>

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff">   free(spoof_cmd);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal-1.1.3.orig/src/cm_tophits.c</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal-1.1.3/src/cm_tophits.c</span></span>

</pre>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -2780,8 +2780,10 @@</span> cm_tophits_TabularTail(FILE *ofp, const</span>

</pre>

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24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff">   fprintf(ofp, "# Query file:      %s\n",      (qfile    == NULL) ? "[none]" : qfile);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff">   fprintf(ofp, "# Target file:     %s\n",      (tfile    == NULL) ? "[none]" : tfile);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff">   fprintf(ofp, "# Option settings: %s\n",      spoof_cmd);</span>

</pre>

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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="gd" style="color: #000; background-color: #fdd;">-  fprintf(ofp, "# Current dir:     %s\n",      (cwd      == NULL) ? "[unknown]" : cwd);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="28" 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">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  fprintf(ofp, "# Date:            %s",        timestamp); /* timestamp ends in \n */</span></span>

</pre>

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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"><span class="gi" style="color: #000; background-color: #dfd;">+  if (getenv("SOURCE_DATE_EPOCH") != NULL) {</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="30" 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="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    fprintf(ofp, "# Current dir:     %s\n",      (cwd      == NULL) ? "[unknown]" : cwd);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    fprintf(ofp, "# Date:            %s",        timestamp); /* timestamp ends in \n */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff">   fprintf(ofp, "# [ok]\n");</span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>

</pre>

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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff">   free(spoof_cmd);</span></pre>

</td>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/infernal/compare/847ca32158c03000deec505d920b7c7dbf0b19b2...9f56bdd80c80a2b70ffff0a598e8221974fa9447#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,3 +2,4 @@</td>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">#autoreconf.patch</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">spelling.patch</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">hardening</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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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="LC5" class="line" lang="plaintext">reproducible_build.patch</span></pre>

</td>

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</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/infernal/compare/847ca32158c03000deec505d920b7c7dbf0b19b2...9f56bdd80c80a2b70ffff0a598e8221974fa9447#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,7 +41,9 @@ override_dh_installexamples:</td>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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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>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<pre style="margin: 0;"> <span id="LC45" 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>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<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="make"><span class="k" style="font-weight: 600;">endif</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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-reformat <span class="nv" style="color: #008080;">$(sampledir_lib)</span>/easel/miniapps/</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

48

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<pre style="margin: 0;"> <span id="LC48" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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<pre style="margin: 0;"> <span id="LC49" 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>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">

<a href="https://salsa.debian.org/med-team/infernal/compare/847ca32158c03000deec505d920b7c7dbf0b19b2...9f56bdd80c80a2b70ffff0a598e8221974fa9447#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,3 +20,4 @@ Registry:</td>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">- Name: bio.tools</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

</td>

<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">  Entry: NA   # infernal_cmscan does not fit</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

</td>

<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Bug-Submit: eric.nawrocki@nih.gov</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="23" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" 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">

23

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Name: Infernal</span></pre>

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