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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/predictprotein">Debian Med / predictprotein</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/predictprotein/commit/91019d7122d96c2e07a157e6d8d7d441d35871f9">91019d71</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-17T11:09:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.08</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/predictprotein/commit/529c4335a98d7ab494e8277634d651fc5c262af5">529c4335</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-17T11:09:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.1.08'
Update to upstream version '1.1.08'
with Debian dir 7db7de298c8f4af98cca8e017817d63ba756b6e8</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/predictprotein/commit/5d47d3fbcdf7f297981233bd53941aba41d5228c">5d47d3fb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-17T11:09:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/predictprotein/commit/0970fee502bdb53d56446c8aa0726e95d0e504bf">0970fee5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-17T11:11:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/predictprotein/commit/de0fe705f9cf3a2fe4bd1212a0b2e6ab5aeba379">de0fe705</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-17T11:11:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/predictprotein/commit/d5d9ec0d619867ca811ebd3c013a2c5572f96ddc">d5d9ec0d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-17T11:12:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>17 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</a>
</li>
<li class="file-stats">
<a href="#c335a27a082cc8d17dd36dc0eda3086cb0c9baaa">
INSTALL
</a>
</li>
<li class="file-stats">
<a href="#d5b4de16d947214ec306bd57bed1bd23a939b5f9">
Makefile.am
</a>
</li>
<li class="file-stats">
<a href="#4faecea6d9857941b442698cdcbd38a141ff746e">
Makefile.in
</a>
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<li class="file-stats">
<a href="#9bc9301cb8cdcf1f65ff337fbab0148e38d77888">
MakefilePP.mk
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<li class="file-stats">
<a href="#09be8533ff0a6ee5d577f971145ed449399fcda4">
configure
</a>
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#ae17d03698490f5127a163b6e68208610e3e5794">
examples/Makefile.am
</a>
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<li class="file-stats">
<a href="#c910d1786bfa887e59099b62cd3b4d9c0053357e">
examples/Makefile.in
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<li class="file-stats">
<a href="#95f2f96fb3bb83f587b513e6d56dc1cdcef67f8c">
helper_apps/Makefile.am
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<li class="file-stats">
<a href="#354597e473b867859bdc1cb6f877d91e692f2c95">
helper_apps/Makefile.in
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<li class="file-stats">
<a href="#547fe0db6ad3e73c693d3deaddf315f4b467815d">
install-sh
</a>
</li>
<li class="file-stats">
<a href="#c83c42b087f59afa3a5039b8fb9ecb2a626984ab">
predictprotein
</a>
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<li class="file-stats">
<a href="#95cefd1fcefc3ce0caed2b32ac225e2093e87d11">
resources/Makefile.am
</a>
</li>
<li class="file-stats">
<a href="#05f45975c292f520f85cbae2437eaabd8a0a1d91">
resources/Makefile.in
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">predictprotein (1.1.08) unstable; urgency=low</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Added predbind(1) prediction file handling.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Timothy Karl <karl@rostlab.org> Mon, 29 Oct 2018 15:25:37 +0100 </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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1
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">predictprotein (1.1.07) unstable; urgency=low</span>
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2
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<td class="diff-line-num new_line" data-linenumber="8" 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">
8
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Added metastudent CCO (Cellular Component Ontology) prediction file handling.</span>
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<li id="c335a27a082cc8d17dd36dc0eda3086cb0c9baaa">
<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#c335a27a082cc8d17dd36dc0eda3086cb0c9baaa"><strong>INSTALL</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">Installation</span> <span class="n" style="color: #333;">Instructions</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"><span class="p">*************************</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="mosel"><span class="n" style="color: #333;">Copyright</span> <span class="p">(</span><span class="n" style="color: #333;">C</span><span class="p">)</span> <span class="m" style="color: #099;">1994</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">1995</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">1996</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">1999</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2000</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2001</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2002</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2004</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff right">2005</span></span><span class="p">,</span></span>
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5
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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC5" class="line" lang="mosel"><span class="m" style="color: #099;"><span class="idiff left">2006</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2007</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2008</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2009</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Free</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Software</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Foundation</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Inc</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"><span class="n" style="color: #333;">Copyright</span> <span class="p">(</span><span class="n" style="color: #333;">C</span><span class="p">)</span> <span class="m" style="color: #099;">1994</span><span class="p"><span class="idiff left">-</span></span><span class="m" style="color: #099;"><span class="idiff">1996</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">1999</span></span><span class="p"><span class="idiff">-</span></span><span class="m" style="color: #099;"><span class="idiff">2002</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2004</span></span><span class="p"><span class="idiff">-</span></span><span class="m" style="color: #099;"><span class="idiff">2013</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Free</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Software</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Foundation</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Inc</span><span class="p">.</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"> <span class="n" style="color: #333;">Copying</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">distribution</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="k" style="font-weight: 600;">with</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">modification</span><span class="p">,</span></span>
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8
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">permitted</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">medium</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">royalty</span> <span class="n" style="color: #333;">provided</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">copyright</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" 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="12" 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">@@ -12,8 +12,8 @@ without warranty of any kind.</td>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="mosel"><span class="n" style="color: #333;">Basic</span> <span class="n" style="color: #333;">Installation</span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"><span class="p">==================</span></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="mosel"> <span class="n" style="color: #333;">Briefly</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">shell</span> <span class="n" style="color: #333;">command<span class="idiff left">s</span></span><span class="idiff"> </span><span class="p"><span class="idiff">`./</span></span><span class="n" style="color: #333;"><span class="idiff">configure</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">install</span></span><span class="s1" style="color: #d14;"><span class="idiff right">' should</span></span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="mosel"><span class="s1" style="color: #d14;">configure, build, and install this package. The following</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"> <span class="n" style="color: #333;">Briefly</span><span class="p">,</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">shell</span> <span class="nf" style="color: #900; font-weight: 600;">command</span><span class="idiff left"> </span><span class="p"><span class="idiff">`./</span></span><span class="n" style="color: #333;"><span class="idiff">configure</span></span><span class="idiff"> </span><span class="p"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make</span></span><span class="idiff"> </span><span class="p"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">install</span></span><span class="s1" style="color: #d14;"><span class="idiff right">'</span></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"><span class="s1" style="color: #d14;"><span class="idiff left right">should </span>configure, build, and install this package. The following</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"><span class="s1" style="color: #d14;">more-detailed instructions are generic; see the `README'</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">for</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"><span class="n" style="color: #333;">instructions</span> <span class="n" style="color: #333;">specific</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">package</span><span class="p">.</span> <span class="n" style="color: #333;">Some</span> <span class="n" style="color: #333;">packages</span> <span class="n" style="color: #333;">provide</span> <span class="n" style="color: #333;">this</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="mosel"><span class="p">`</span><span class="n" style="color: #333;">INSTALL</span><span class="s1" style="color: #d14;">' file but do not implement all of the features documented</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="226" 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="226" 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">@@ -226,6 +226,11 @@ order to use an ANSI C compiler:</td>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="mosel"></span>
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="mosel"><span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">doesn</span><span class="s1" style="color: #d14;">'t work, install pre-built binaries of GCC for HP-UX.</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="mosel"><span class="s1" style="color: #d14;"> HP-UX `make'</span> <span class="n" style="color: #333;">updates</span> <span class="n" style="color: #333;">targets</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">same</span> <span class="n" style="color: #333;">time</span> <span class="n" style="color: #333;">stamps</span> <span class="k" style="font-weight: 600;">as</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="mosel"><span class="n" style="color: #333;">their</span> <span class="n" style="color: #333;">prerequisites</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">makes</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">generally</span> <span class="n" style="color: #333;">unusable</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">shipped</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="mosel"><span class="n" style="color: #333;">generated</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">such</span> <span class="k" style="font-weight: 600;">as</span> <span class="p">`</span><span class="n" style="color: #333;">configure</span><span class="s1" style="color: #d14;">' are involved. Use GNU `make'</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="mosel"><span class="n" style="color: #333;">instead</span><span class="p">.</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="mosel"></span>
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229
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="mosel"> <span class="n" style="color: #333;">On</span> <span class="n" style="color: #333;">OSF</span><span class="p">/</span><span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">k</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">.</span> <span class="n" style="color: #333;">Tru64</span><span class="p">,</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">versions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">default</span> <span class="n" style="color: #333;">C</span> <span class="n" style="color: #333;">compiler</span> <span class="n" style="color: #333;">cannot</span></span>
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230
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="mosel"><span class="n" style="color: #333;">parse</span> <span class="n" style="color: #333;">its</span> <span class="p">`<</span><span class="n" style="color: #333;">wchar</span><span class="p">.</span><span class="n" style="color: #333;">h</span><span class="p">></span><span class="s1" style="color: #d14;">' header file. The option `-nodtk'</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">as</span></span>
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231
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="mosel"><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">workaround</span><span class="p">.</span> <span class="k" style="font-weight: 600;">If</span> <span class="n" style="color: #333;">GNU</span> <span class="n" style="color: #333;">CC</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">installed</span><span class="p">,</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">therefore</span> <span class="n" style="color: #333;">recommended</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -304,9 +309,10 @@ causes the specified `gcc' to be used as the C compiler (unless it is</td>
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304
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="mosel"><span class="n" style="color: #333;">overridden</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">site</span> <span class="n" style="color: #333;">shell</span> <span class="n" style="color: #333;">script</span><span class="p">).</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="mosel"><span class="n" style="color: #333;">Unfortunately</span><span class="p">,</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">technique</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">work</span> <span class="n" style="color: #333;">for</span> <span class="p">`</span><span class="n" style="color: #333;">CONFIG_SHELL</span><span class="s1" style="color: #d14;">' due to</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="mosel"><span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">Autoconf</span> <span class="n" style="color: #333;">bug</span><span class="p">.</span> <span class="k" style="font-weight: 600;">Until</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">fixed</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">workaround</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="mosel"><span class="s1" style="color: #d14;">an Autoconf limitation. Until the limitation is lifted, you can use</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="mosel"><span class="s1" style="color: #d14;">this workaround:</span></span>
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308
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="mosel"></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="mosel"> <span class="n" style="color: #333;">CONFIG_SHELL</span><span class="p">=/</span><span class="n" style="color: #333;">bin</span><span class="p">/</span><span class="n" style="color: #333;">bash</span> <span class="p"><span class="idiff left">/</span></span><span class="n" style="color: #333;"><span class="idiff">bin</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">bash</span></span><span class="idiff right"> </span><span class="p">./</span><span class="n" style="color: #333;">configure</span> <span class="n" style="color: #333;">CONFIG_SHELL</span><span class="p">=/</span><span class="n" style="color: #333;">bin</span><span class="p">/</span><span class="n" style="color: #333;">bash</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="mosel"><span class="s1" style="color: #d14;"> CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash</span></span>
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="mosel"></span>
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311
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="mosel"><span class="s1" style="color: #d14;">`configure'</span> <span class="n" style="color: #333;">Invocation</span></span>
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312
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="mosel"><span class="p">======================</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -362,4 +368,3 @@ operates.</td>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="mosel"><span class="s1" style="color: #d14;">`configure'</span> <span class="n" style="color: #333;">also</span> <span class="n" style="color: #333;">accepts</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">widely</span> <span class="n" style="color: #333;">useful</span><span class="p">,</span> <span class="k" style="font-weight: 600;">options</span><span class="p">.</span> <span class="nf" style="color: #900; font-weight: 600;">Run</span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="mosel"><span class="p">`</span><span class="n" style="color: #333;">configure</span> <span class="p">--</span><span class="n" style="color: #333;">help</span><span class="s1" style="color: #d14;">' for more details.</span></span></pre>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="mosel"></span></pre>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#d5b4de16d947214ec306bd57bed1bd23a939b5f9"><strong>Makefile.am</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,7 +30,7 @@ install-data-local:</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"> pod2man <span class="nt" style="color: navy;">-c</span> <span class="s1" style="color: #d14;">'User Commands'</span> <span class="nt" style="color: navy;">-r</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$(VERSION)</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-name</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">tr</span> <span class="s1" style="color: #d14;">'[:lower:]'</span> <span class="s1" style="color: #d14;">'[:upper:]'</span> <span class="o" style="font-weight: 600;"><<<</span> <span class="s2" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="s2" style="color: #d14;">(basename </span><span class="nv" style="color: teal;">$@)</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">)</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"><span class="nl">dist-hook</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">svn</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">git</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="nl">install-data-hook</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s|__docdir__|</span><span class="nv" style="color: teal;">$(docdir)</span><span class="s1" style="color: #d14;">|g;s|__pkgdatadir__|</span><span class="nv" style="color: teal;">$(pkgdatadir)</span><span class="s1" style="color: #d14;">|g;s|__sysconfdir__|</span><span class="nv" style="color: teal;">$(sysconfdir)</span><span class="s1" style="color: #d14;">|g;s|__bindir__|</span><span class="nv" style="color: teal;">$(bindir)</span><span class="s1" style="color: #d14;">|g;'</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$(DESTDIR)$(pkgdatadir)</span><span class="s2" style="color: #d14;">/predictproteinrc.default"</span></span>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#4faecea6d9857941b442698cdcbd38a141ff746e"><strong>Makefile.in</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -901,7 +901,7 @@ install-data-local:</td>
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="make"> pod2man <span class="nt" style="color: navy;">-c</span> <span class="s1" style="color: #d14;">'User Commands'</span> <span class="nt" style="color: navy;">-r</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$(VERSION)</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-name</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">tr</span> <span class="s1" style="color: #d14;">'[:lower:]'</span> <span class="s1" style="color: #d14;">'[:upper:]'</span> <span class="o" style="font-weight: 600;"><<<</span> <span class="s2" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="s2" style="color: #d14;">(basename </span><span class="nv" style="color: teal;">$@)</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">)</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="make"><span class="nl">dist-hook</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC904" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">svn</span><span class="sb" style="color: #d14;">`</span></span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">git</span><span class="sb" style="color: #d14;">`</span></span>
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905
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<pre style="margin: 0;"> <span id="LC905" class="line" lang="make"></span>
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906
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<pre style="margin: 0;"> <span id="LC906" class="line" lang="make"><span class="nl">install-data-hook</span><span class="o" style="font-weight: 600;">:</span></span>
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907
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s|__docdir__|</span><span class="nv" style="color: teal;">$(docdir)</span><span class="s1" style="color: #d14;">|g;s|__pkgdatadir__|</span><span class="nv" style="color: teal;">$(pkgdatadir)</span><span class="s1" style="color: #d14;">|g;s|__sysconfdir__|</span><span class="nv" style="color: teal;">$(sysconfdir)</span><span class="s1" style="color: #d14;">|g;s|__bindir__|</span><span class="nv" style="color: teal;">$(bindir)</span><span class="s1" style="color: #d14;">|g;'</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$(DESTDIR)$(pkgdatadir)</span><span class="s2" style="color: #d14;">/predictproteinrc.default"</span></span>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#9bc9301cb8cdcf1f65ff337fbab0148e38d77888"><strong>MakefilePP.mk</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,6 +59,7 @@ PHDFILE:=$(INFILE:%.in=%.phdPred)</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">PHDRDBFILE:=$(INFILE:%.in=%.phdRdb)</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"># lkajan: never make PHDNOTHTMFILE a target - its creation depends on whether phd found an HTM region or not: it isn't always created</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">PHDNOTHTMFILE:=$(INFILE:%.in=%.phdNotHtm)</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">PREDBINDFILE:=$(INFILE:%.in=%.predbind)</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">PROFFILE:=$(INFILE:%.in=%.profRdb)</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"># prof output generated explicitely from one sequence - NO alignment - Chris Schaefer initiated this - B approved</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">PROF1FILE:=$(INFILE:%.in=%.prof1Rdb)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -187,7 +188,7 @@ subcell-loc:</td>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="plaintext">#</span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="plaintext"># Optional targets should never appear in other aggregate targets (such as 'interaction').</span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="plaintext">.PHONY: optional</span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="plaintext">optional: loctree3 metadisorder psic tmhmm tmseg somena consurf</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">optional: loctree3 metadisorder p<span class="idiff left right">redbind p</span>sic tmhmm tmseg somena consurf</span>
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191
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="plaintext"></span>
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192
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="plaintext">.PHONY: coiledcoils</span>
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193
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="plaintext">coiledcoils: $(COILSFILE)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -394,6 +395,13 @@ $(PROFTEXTFILE): $(PROFFILE)</td>
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394
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="plaintext"> # conv_prof creates query.profAscii.tmp in case query.profAscii already exists - make sure it does not</span>
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395
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="plaintext"> rm -f $(PROFTEXTFILE); $(PROFROOT)scr/conv_prof.pl $< fileOut=$@ ascii nohtml nodet nograph</span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext">.PHONY: predbind</span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext">predbind: $(PREDBINDFILE)</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext"></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext"># Predbind needs .fasta .blastPsiMat .profbval .mdisorder .profRdb to run</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext">$(PREDBINDFILE): $(FASTAFILE) $(BLASTMATFILE) $(PROFBVALFILE) $(METADISORDERFILE) $(PROFFILE)</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext"> predbind -p $(dir $(FASTAFILE)) -d $(BIG80BLASTDB) $(if $(DEBUG), -v True, ) -o $@</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext"></span>
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397
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="plaintext">.PHONY: metastudent</span>
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398
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="plaintext">metastudent: $(METASTUDENTBPO) $(METASTUDENTCCO) $(METASTUDENTMPO)</span>
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399
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -497,6 +505,7 @@ install:</td>
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497
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="plaintext"> $(NORSFILE) $(NORSSUMFILE) \</span>
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498
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="plaintext"> $(NORSNETFILE) \</span>
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499
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="plaintext"> $(PHDFILE) $(PHDNOTHTMFILE) $(PHDRDBFILE) \</span>
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="plaintext"> $(PREDBINDFILE) \</span>
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500
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="plaintext"> $(PROFTEXTFILE) $(PROFFILE) $(PROF1FILE) \</span>
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501
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510
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="plaintext"> $(PROFBVALFILE) $(PROFB4SNAPFILE) \</span>
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<td class="diff-line-num old_line" data-linenumber="502" 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">
502
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511
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC511" class="line" lang="plaintext"> $(PROFTMBFILE) $(PROFTMBDATFILE) \</span>
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<li id="09be8533ff0a6ee5d577f971145ed449399fcda4">
<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#09be8533ff0a6ee5d577f971145ed449399fcda4"><strong>configure</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/sh</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Guess values for system-dependent variables and create Makefiles.</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Generated by GNU Autoconf 2.69 for predictprotein 1.1.0<span class="idiff left right">7</span>.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Generated by GNU Autoconf 2.69 for predictprotein 1.1.0<span class="idiff left right">8</span>.</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Report bugs to <https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein>.</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -580,8 +580,8 @@ MAKEFLAGS=</td>
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580
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Identity of this package.</span></span>
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_NAME</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'predictprotein'</span></span>
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582
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_TARNAME</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'predictprotein'</span></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'1.1.0<span class="idiff left right">7</span>'</span></span>
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584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_STRING</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'predictprotein 1.1.0<span class="idiff left right">7</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'1.1.0<span class="idiff left right">8</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_STRING</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'predictprotein 1.1.0<span class="idiff left right">8</span>'</span></span>
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585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_BUGREPORT</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein'</span></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="shell"><span class="nv" style="color: teal;">PACKAGE_URL</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">''</span></span>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="shell"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1202,7 +1202,7 @@ if test "$ac_init_help" = "long"; then</td>
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Omit some internal or obsolete options to make the list less imposing.</span></span>
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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># This message is too long to be a string in the A/UX 3.1 sh.</span></span>
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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">_ACEOF</span></span>
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<pre style="margin: 0;">-<span id="LC1205" class="line" lang="shell"><span class="sh" style="color: #d14;">\`configure' configures predictprotein 1.1.0<span class="idiff left right">7</span> to adapt to many kinds of systems.</span></span>
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="shell"><span class="sh" style="color: #d14;">\`configure' configures predictprotein 1.1.0<span class="idiff left right">8</span> to adapt to many kinds of systems.</span></span>
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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="shell"><span class="sh" style="color: #d14;">Usage: </span><span class="nv" style="color: teal;">$0</span><span class="sh" style="color: #d14;"> [OPTION]... [VAR=VALUE]...</span></span>
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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="shell"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1268,7 +1268,7 @@ fi</td>
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ac_init_help</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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1270
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1270
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<pre style="margin: 0;"> <span id="LC1270" class="line" lang="shell"><span class="k" style="font-weight: 600;"> case</span> <span class="nv" style="color: teal;">$ac_init_help</span> <span class="k" style="font-weight: 600;">in</span></span>
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1271
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<pre style="margin: 0;">-<span id="LC1271" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>short <span class="p">|</span> recursive <span class="p">)</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Configuration of predictprotein 1.1.0<span class="idiff left right">7</span>:"</span><span class="p">;;</span></span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>short <span class="p">|</span> recursive <span class="p">)</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Configuration of predictprotein 1.1.0<span class="idiff left right">8</span>:"</span><span class="p">;;</span></span>
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1272
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1272
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<pre style="margin: 0;"> <span id="LC1272" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span></span>
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<td class="diff-line-num old_line" data-linenumber="1273" 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">
1273
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1273
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<pre style="margin: 0;"> <span id="LC1273" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="sh" style="color: #d14;">\</span><span class="no" style="color: teal;">_ACEOF</span></span>
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1274
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1274
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<pre style="margin: 0;"> <span id="LC1274" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1342" 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="1342" 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">@@ -1342,7 +1342,7 @@ fi</td>
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1342
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1342
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="shell"><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ac_init_help</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="nv" style="color: teal;">$ac_status</span></span>
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<td class="diff-line-num old_line" data-linenumber="1343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1343
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1343
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">$ac_init_version</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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1344
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1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="sh" style="color: #d14;">\</span><span class="no" style="color: teal;">_ACEOF</span></span>
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1345
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<pre style="margin: 0;">-<span id="LC1345" class="line" lang="shell"><span class="sh" style="color: #d14;">predictprotein configure 1.1.0<span class="idiff left right">7</span></span></span>
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1345
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="shell"><span class="sh" style="color: #d14;">predictprotein configure 1.1.0<span class="idiff left right">8</span></span></span>
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1346
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1346
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<pre style="margin: 0;"> <span id="LC1346" class="line" lang="shell"><span class="sh" style="color: #d14;">generated by GNU Autoconf 2.69</span></span>
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1347
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1347
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="shell"></span>
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1348
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1348
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="shell"><span class="sh" style="color: #d14;">Copyright (C) 2012 Free Software Foundation, Inc.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1359" 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="1359" 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">@@ -1359,7 +1359,7 @@ cat >config.log <<_ACEOF</td>
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1359
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1359
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<pre style="margin: 0;"> <span id="LC1359" class="line" lang="shell"><span class="sh" style="color: #d14;">This file contains any messages produced by compilers while</span></span>
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<td class="diff-line-num old_line" data-linenumber="1360" 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">
1360
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1360
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<pre style="margin: 0;"> <span id="LC1360" class="line" lang="shell"><span class="sh" style="color: #d14;">running configure, to aid debugging if configure makes a mistake.</span></span>
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1361
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1361
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<pre style="margin: 0;"> <span id="LC1361" class="line" lang="shell"></span>
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1362
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<pre style="margin: 0;">-<span id="LC1362" class="line" lang="shell"><span class="sh" style="color: #d14;">It was created by predictprotein </span><span class="nv" style="color: teal;">$as_me</span><span class="sh" style="color: #d14;"> 1.1.0<span class="idiff left right">7</span>, which was</span></span>
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1362
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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="shell"><span class="sh" style="color: #d14;">It was created by predictprotein </span><span class="nv" style="color: teal;">$as_me</span><span class="sh" style="color: #d14;"> 1.1.0<span class="idiff left right">8</span>, which was</span></span>
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1363
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1363
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<pre style="margin: 0;"> <span id="LC1363" class="line" lang="shell"><span class="sh" style="color: #d14;">generated by GNU Autoconf 2.69. Invocation command line was</span></span>
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1364
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1364
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<pre style="margin: 0;"> <span id="LC1364" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC1365" class="line" lang="shell"><span class="sh" style="color: #d14;"> </span><span class="nv" style="color: teal;">$ $0</span><span class="sh" style="color: #d14;"> </span><span class="nv" style="color: teal;">$@</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2223,7 +2223,7 @@ fi</td>
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<pre style="margin: 0;"> <span id="LC2223" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC2224" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Define the identity of the package.</span></span>
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<pre style="margin: 0;"> <span id="LC2225" class="line" lang="shell"> <span class="nv" style="color: teal;">PACKAGE</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'predictprotein'</span></span>
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<pre style="margin: 0;">-<span id="LC2226" class="line" lang="shell"> <span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'1.1.0<span class="idiff left right">7</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC2226" class="line" lang="shell"> <span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'1.1.0<span class="idiff left right">8</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC2227" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC2228" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC2229" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;">>></span>confdefs.h <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">_ACEOF</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2876,7 +2876,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1</td>
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<pre style="margin: 0;"> <span id="LC2876" class="line" lang="shell"><span class="sh" style="color: #d14;"># report actual input values of CONFIG_FILES etc. instead of their</span></span>
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<pre style="margin: 0;"> <span id="LC2877" class="line" lang="shell"><span class="sh" style="color: #d14;"># values after options handling.</span></span>
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<pre style="margin: 0;"> <span id="LC2878" class="line" lang="shell"><span class="sh" style="color: #d14;">ac_log="</span></span>
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<pre style="margin: 0;">-<span id="LC2879" class="line" lang="shell"><span class="sh" style="color: #d14;">This file was extended by predictprotein </span><span class="nv" style="color: teal;">$as_me</span><span class="sh" style="color: #d14;"> 1.1.0<span class="idiff left right">7</span>, which was</span></span>
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<pre style="margin: 0;">+<span id="LC2879" class="line" lang="shell"><span class="sh" style="color: #d14;">This file was extended by predictprotein </span><span class="nv" style="color: teal;">$as_me</span><span class="sh" style="color: #d14;"> 1.1.0<span class="idiff left right">8</span>, which was</span></span>
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<pre style="margin: 0;"> <span id="LC2880" class="line" lang="shell"><span class="sh" style="color: #d14;">generated by GNU Autoconf 2.69. Invocation command line was</span></span>
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<pre style="margin: 0;"> <span id="LC2881" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC2882" class="line" lang="shell"><span class="sh" style="color: #d14;"> CONFIG_FILES = </span><span class="nv" style="color: teal;">$CONFIG_FILES</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2929,7 +2929,7 @@ _ACEOF</td>
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<pre style="margin: 0;"> <span id="LC2929" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;">>></span><span class="nv" style="color: teal;">$CONFIG_STATUS</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">_ACEOF</span><span class="sh" style="color: #d14;"> || ac_write_fail=1</span></span>
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<pre style="margin: 0;"> <span id="LC2930" class="line" lang="shell"><span class="sh" style="color: #d14;">ac_cs_config="`</span><span class="nv" style="color: teal;">$as_echo</span><span class="sh" style="color: #d14;"> "</span><span class="nv" style="color: teal;">$ac_configure_args</span><span class="sh" style="color: #d14;">" | sed 's/^ //; s/[\\""\`\</span><span class="nv" style="color: teal;">$]</span><span class="sh" style="color: #d14;">/\\\\&/g'`"</span></span>
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<pre style="margin: 0;"> <span id="LC2931" class="line" lang="shell"><span class="sh" style="color: #d14;">ac_cs_version="\\</span></span>
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<pre style="margin: 0;">-<span id="LC2932" class="line" lang="shell"><span class="sh" style="color: #d14;">predictprotein config.status 1.1.0<span class="idiff left right">7</span></span></span>
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<pre style="margin: 0;">+<span id="LC2932" class="line" lang="shell"><span class="sh" style="color: #d14;">predictprotein config.status 1.1.0<span class="idiff left right">8</span></span></span>
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<pre style="margin: 0;"> <span id="LC2933" class="line" lang="shell"><span class="sh" style="color: #d14;">configured by </span><span class="nv" style="color: teal;">$0</span><span class="sh" style="color: #d14;">, generated by GNU Autoconf 2.69,</span></span>
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<pre style="margin: 0;"> <span id="LC2934" class="line" lang="shell"><span class="sh" style="color: #d14;"> with options \\"\</span><span class="nv" style="color: teal;">$ac_cs_config</span><span class="sh" style="color: #d14;">\\"</span></span>
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<pre style="margin: 0;"> <span id="LC2935" class="line" lang="shell"></span>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">AC_INIT([predictprotein], [1.1.0<span class="idiff left right">7</span>], [https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein])</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AC_INIT([predictprotein], [1.1.0<span class="idiff left right">8</span>], [https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein])</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">AC_CONFIG_SRCDIR([predictprotein])</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">AM_INIT_AUTOMAKE</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_CONFIG_FILES([Makefile] [perl/Build.PL] [examples/Makefile] [helper_apps/Makefile] [resources/Makefile])</span>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">predictprotein (1.1.08-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Remove trailing whitespace in debian/copyright</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 17 Dec 2018 12:11:04 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">predictprotein (1.1.07-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * pp-popularity-contest only suggested</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -159,7 +167,7 @@ predictprotein (1.0.77) unstable; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext"> Added reprof in alpha mode</span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext"> -- Guy Yachdav <gyachdav@rostlab.org> Mon, 4 Jun 2012 21:03:15 +0200</span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"></span>
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext">predictprotein (1.0.76) unstable; urgency=low</span>
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164
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="plaintext"></span>
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165
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="plaintext"> * Depends on profdisis</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="443" 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">@@ -435,7 +443,7 @@ predictprotein (1.0.36) stable; urgency=low</td>
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435
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443
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="plaintext"></span>
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436
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="plaintext">predictprotein (1.0.35) stable; urgency=low</span>
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437
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445
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="plaintext"></span>
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438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="plaintext"> * switched from included norsp scripts to independent package<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext"> * switched from included norsp scripts to independent package</span>
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439
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="plaintext"> -- Guy Yachdav <gyachdav@rostlab.org> Thu, 23 Dec 2010 15:35:21 +0100</span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -647,7 +655,7 @@ predictprotein (1.0.6)</td>
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="plaintext"> * Man page had an incorrect example</span>
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648
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656
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="plaintext"> -- Guy Yachdav <gyachdav@rostlab.org> Sun, 18 Jul 2010 12:56:19 +0200</span>
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650
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="plaintext"></span>
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659
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="plaintext">predictprotein (1.0.1)</span>
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652
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660
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="plaintext"> * Bug Fixes</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="664" 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">@@ -656,7 +664,7 @@ predictprotein (1.0.1)</td>
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664
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="plaintext"> * Creates files into output folder and not one concatenated file</span>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="plaintext"> -- Guy Yachdav <gyachdav@rostlab.org> Sat, 17 Jul 2010 14:37:05 +0200</span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="plaintext">predictprotein (1.0.0)</span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="plaintext"> * Initial packaged version</span>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,12 +23,12 @@ Comment:</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-July/016408.html</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> On 14/07/12 21:51, Kay Hofmann wrote:</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> > Dear Lazlo,</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> ><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> ></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> > Like all other software I have made available (so far), the script prosite_scan.pl that you refer to is in the public domain.</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> > Feel free to do with it whatever you like.</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> ><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> ></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> > Best Wishes,</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> ><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> ></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> > Kay</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> The modifications were put under GPL-3+.</span>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#ae17d03698490f5127a163b6e68208610e3e5794"><strong>examples/Makefile.am</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,4 +8,4 @@ dist_docexamples_DATA = \</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nl">dist-hook</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">svn</span><span class="sb" style="color: #d14;">`</span></span></pre>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">git</span><span class="sb" style="color: #d14;">`</span></span></pre>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#c910d1786bfa887e59099b62cd3b4d9c0053357e"><strong>examples/Makefile.in</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -432,7 +432,7 @@ uninstall-am: uninstall-dist_docexamplesDATA</td>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="make"><span class="nl">dist-hook</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">svn</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">git</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Tell versions [3.59,3.63) of GNU make to not export all variables.</span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Otherwise a system limit (for SysV at least) may be exceeded.</span></span>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#95f2f96fb3bb83f587b513e6d56dc1cdcef67f8c"><strong>helper_apps/Makefile.am</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,4 +6,4 @@ dist_helperapps_SCRIPTS = \</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"> <span class="nv" style="color: teal;">$(srcdir)</span>/prosite_scan.pl</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="nl">dist-hook</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">svn</span><span class="sb" style="color: #d14;">`</span></span></pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">git</span><span class="sb" style="color: #d14;">`</span></span></pre>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#354597e473b867859bdc1cb6f877d91e692f2c95"><strong>helper_apps/Makefile.in</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -444,7 +444,7 @@ uninstall-am: uninstall-dist_helperappsSCRIPTS</td>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="make"><span class="nl">dist-hook</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">svn</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">git</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Tell versions [3.59,3.63) of GNU make to not export all variables.</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Otherwise a system limit (for SysV at least) may be exceeded.</span></span>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#547fe0db6ad3e73c693d3deaddf315f4b467815d"><strong>install-sh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -345,34 +345,41 @@ do</td>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># is incompatible with FreeBSD 'install' when (umask & 300) != 0.</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># $RANDOM is not portable (e.g. dash); use it when possible to</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># lower collision chance</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="shell"> <span class="nv" style="color: teal;">tmpdir</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">TMPDIR</span><span class="p">-/tmp</span><span class="k" style="font-weight: 600;">}</span>/ins<span class="nv" style="color: teal;">$RANDOM</span>-<span class="nv" style="color: teal;">$$</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s1" style="color: #d14;">'ret=$?; rmdir "$tmpdir/<span class="idiff left right">d</span>" "$tmpdir" 2>/dev/null; exit $ret'</span> 0</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s1" style="color: #d14;">'ret=$?; rmdir "$tmpdir/<span class="idiff left right">a/b" "$tmpdir/a</span>" "$tmpdir" 2>/dev/null; exit $ret'</span> 0</span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># As "mkdir -p" follows symlinks and we work in /tmp possibly; so</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># create the $tmpdir first (and fail if unsuccessful) to make sure</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># that nobody tries to guess the $tmpdir name.</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">umask</span> <span class="nv" style="color: teal;">$mkdir_umask</span> <span class="o" style="font-weight: 600;">&&</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exec</span> <span class="nv" style="color: teal;">$mkdirprog</span> <span class="nv" style="color: teal;">$mkdir_mode</span> <span class="nt" style="color: navy;">-p</span> <span class="nt" style="color: navy;">--</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$tmpdir</span><span class="s2" style="color: #d14;">/d"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="shell"> <span class="nv" style="color: teal;">$mkdirprog</span> <span class="nv" style="color: teal;">$mkdir_mode</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$tmpdir</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&&</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exec</span> <span class="nv" style="color: teal;">$mkdirprog</span> <span class="nv" style="color: teal;">$mkdir_mode</span> <span class="nt" style="color: navy;">-p</span> <span class="nt" style="color: navy;">--</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$tmpdir</span><span class="s2" style="color: #d14;">/a/b"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1</span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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354
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if </span><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: navy;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$dir_arg</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">{</span></span>
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355
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Check for POSIX incompatibilities with -m.</span></span>
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356
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or</span></span>
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357
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># other-writable bit of parent directory when it shouldn't.</span></span>
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358
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># FreeBSD 6.1 mkdir -m -p sets mode of existing directory.</span></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="shell"> <span class="nv" style="color: teal;">ls_ld_tmpdir</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: navy;">-ld</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$tmpdir</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="shell"> <span class="nv" style="color: teal;">test_tmpdir</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$tmpdir</span><span class="s2" style="color: #d14;">/a"</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="shell"> <span class="nv" style="color: teal;">ls_ld_tmpdir</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: navy;">-ld</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$test_tmpdir</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="shell"> <span class="k" style="font-weight: 600;">case</span> <span class="nv" style="color: teal;">$ls_ld_tmpdir</span> <span class="k" style="font-weight: 600;">in</span></span>
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361
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>d????-?r-<span class="k" style="font-weight: 600;">*</span><span class="p">)</span> <span class="nv" style="color: teal;">different_mode</span><span class="o" style="font-weight: 600;">=</span>700<span class="p">;;</span></span>
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362
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="shell"> d????-?--<span class="k" style="font-weight: 600;">*</span><span class="p">)</span> <span class="nv" style="color: teal;">different_mode</span><span class="o" style="font-weight: 600;">=</span>755<span class="p">;;</span></span>
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363
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;;</span></span>
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364
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span> <span class="o" style="font-weight: 600;">&&</span></span>
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365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="shell"> <span class="nv" style="color: teal;">$mkdirprog</span> <span class="nt" style="color: navy;">-m</span><span class="nv" style="color: teal;">$different_mode</span> <span class="nt" style="color: navy;">-p</span> <span class="nt" style="color: navy;">--</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$tmpdir</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">{</span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="shell"> <span class="nv" style="color: teal;">ls_ld_tmpdir_1</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: navy;">-ld</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$tmpdir</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="shell"> <span class="nv" style="color: teal;">$mkdirprog</span> <span class="nt" style="color: navy;">-m</span><span class="nv" style="color: teal;">$different_mode</span> <span class="nt" style="color: navy;">-p</span> <span class="nt" style="color: navy;">--</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$t<span class="idiff left right">est_t</span>mpdir</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">{</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="shell"> <span class="nv" style="color: teal;">ls_ld_tmpdir_1</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: navy;">-ld</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$t<span class="idiff left right">est_t</span>mpdir</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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367
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">test</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ls_ld_tmpdir</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ls_ld_tmpdir_1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="shell"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="shell"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then </span><span class="nv" style="color: teal;">posix_mkdir</span><span class="o" style="font-weight: 600;">=</span>:</span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">rmdir</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$tmpdir</span><span class="s2" style="color: #d14;">/<span class="idiff left right">d</span>"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$tmpdir</span><span class="s2" style="color: #d14;">"</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">rmdir</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$tmpdir</span><span class="s2" style="color: #d14;">/<span class="idiff left">a/b"</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: teal;"><span class="idiff">$tmpdir</span></span><span class="s2" style="color: #d14;"><span class="idiff right">/a</span>"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$tmpdir</span><span class="s2" style="color: #d14;">"</span></span>
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373
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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374
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Remove any dirs left behind by ancient mkdir implementations.</span></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rmdir</span> ./<span class="nv" style="color: teal;">$mkdir_mode</span> ./-p ./-- 2>/dev/null</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rmdir</span> ./<span class="nv" style="color: teal;">$mkdir_mode</span> ./-p ./-- <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: teal;"><span class="idiff">$tmpdir</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff right"> </span>2>/dev/null</span>
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376
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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377
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">trap</span> <span class="s1" style="color: #d14;">''</span> 0<span class="p">;;</span></span>
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378
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span><span class="p">;;</span></span>
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<li id="c83c42b087f59afa3a5039b8fb9ecb2a626984ab">
<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#c83c42b087f59afa3a5039b8fb9ecb2a626984ab"><strong>predictprotein</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,6 +75,7 @@ our %meth_ext_hash = (</td>
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75
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="perl"><span class="s" style="color: #d14;"> phdNotHtm => '</span><span class="nv" style="color: teal;">phd</span><span class="s" style="color: #d14;">',</span></span>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="perl"><span class="s" style="color: #d14;"> phdPred => '</span><span class="nv" style="color: teal;">phd</span><span class="s" style="color: #d14;">',</span></span>
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77
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="perl"><span class="s" style="color: #d14;"> phdRdb => '</span><span class="nv" style="color: teal;">phd</span><span class="s" style="color: #d14;">',</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="perl"><span class="s" style="color: #d14;"> predbind => '</span><span class="nv" style="color: teal;">predbind</span><span class="s" style="color: #d14;">',</span></span>
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78
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="perl"><span class="s" style="color: #d14;"> profAscii => '</span><span class="nv" style="color: teal;">prof</span><span class="s" style="color: #d14;">',</span></span>
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79
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="perl"><span class="s" style="color: #d14;"> reprof => '</span><span class="nv" style="color: teal;">reprof</span><span class="s" style="color: #d14;">',</span></span>
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80
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="perl"><span class="s" style="color: #d14;"> profbval => '</span><span class="nv" style="color: teal;">profbval</span><span class="s" style="color: #d14;">',</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="651" 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="652" 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">@@ -651,6 +652,10 @@ These methods are run by the target 'optional'.</td>
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651
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652
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="perl"><span class="cp" style="color: #999; font-weight: 600;"> protein-RNA, somena somena somena(1)</span></span>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="perl"><span class="cp" style="color: #999; font-weight: 600;"> protein-DNA</span></span>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="perl"><span class="cp" style="color: #999; font-weight: 600;"> interaction sites</span></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="perl"><span class="cp" style="color: #999; font-weight: 600;"> DNA- , RNA- and predbind predbind predbind(1)</span></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="perl"><span class="cp" style="color: #999; font-weight: 600;"> Protein-binding</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="perl"><span class="cp" style="color: #999; font-weight: 600;"> protein and binding</span></span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="perl"><span class="cp" style="color: #999; font-weight: 600;"> sites</span></span>
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="perl"><span class="cp" style="color: #999; font-weight: 600;"> position-specific psic* psic, clustalngz psic(1),</span></span>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="perl"><span class="cp" style="color: #999; font-weight: 600;"> independent counts runNewPSIC(1),</span></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="perl"><span class="cp" style="color: #999; font-weight: 600;"> and its base multi- clustalw(1)</span></span>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#95cefd1fcefc3ce0caed2b32ac225e2093e87d11"><strong>resources/Makefile.am</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,4 +2,4 @@ pkgdataexampledir = $(pkgdatadir)/resources</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nv" style="color: teal;">dist_pkgdataexample_DATA</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$(srcdir)</span>/HtmlQuote.html <span class="nv" style="color: teal;">$(srcdir)</span>/HtmlHr.html</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="nl">dist-hook</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">svn</span><span class="sb" style="color: #d14;">`</span></span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">git</span><span class="sb" style="color: #d14;">`</span></span></pre>
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<a href="https://salsa.debian.org/med-team/predictprotein/compare/3f8c76a6f38523d7bcefa9feb5fc1b2eb8bd72c3...d5d9ec0d619867ca811ebd3c013a2c5572f96ddc#05f45975c292f520f85cbae2437eaabd8a0a1d91"><strong>resources/Makefile.in</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -425,7 +425,7 @@ uninstall-am: uninstall-dist_pkgdataexampleDATA</td>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="make"><span class="nl">dist-hook</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">svn</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: teal;">$(distdir)</span> <span class="nt" style="color: navy;">-name</span> .<span class="idiff left right">git</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Tell versions [3.59,3.63) of GNU make to not export all variables.</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Otherwise a system limit (for SysV at least) may be exceeded.</span></span>
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