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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pftools">Debian Med / pftools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/cc312d1b1e88de6f6742951912454318d5c05840">cc312d1b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-03T15:15:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">There is no need to exclude anything any more
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/91e9e35a1a32e329f0c301c60fdc9939606edead">91e9e35a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-03T15:17:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.6</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/011649097f21220233797bbcbfe74f28cb49d3bf">01164909</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-03T15:20:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.2.6'
Update to upstream version '3.2.6'
with Debian dir 426d6f4cc4bc5f103d14013cc272ad8c643be07d</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#c335a27a082cc8d17dd36dc0eda3086cb0c9baaa">
<span class="new-file">
+
INSTALL
</span>
</a>
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
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<li class="file-stats">
<a href="#bcd74a0bd3eb1727e503919bce010ec5b463a401">
<span class="deleted-file">
−
debian/missing-sources/get
</span>
</a>
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<li class="file-stats">
<a href="#33a08aca934f37c2d0beb1888a2a6794fe9b0219">
debian/missing-sources/config.h.cmake
→
src/C/config.h.cmake
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="c335a27a082cc8d17dd36dc0eda3086cb0c9baaa">
<a href="https://salsa.debian.org/med-team/pftools/-/compare/faa7014383b252e2bf8cb20ce3020433e5d2acde...011649097f21220233797bbcbfe74f28cb49d3bf#c335a27a082cc8d17dd36dc0eda3086cb0c9baaa"><strong>INSTALL</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">REQUIREMENTS</span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">- 64bit processors</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- cmake >= 3.7</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">- gcc >= 4.6</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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">
7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">- gfortran (or g77 or f77) for release 2.3 source code</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">- perl >= 5.5.3 for ps_scan.pl</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Optional:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">- pcre*</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">- GD*</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">- libpng</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">- libjpeg</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">- zlib</span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext">- libharu* (hpdf)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">* copy of the source code is provided and could be used during build, if requested.</span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="20" 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="LC20" class="line" lang="plaintext">INSTALLATION</span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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="LC21" class="line" lang="plaintext">------------</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">In order to compile the programs, type:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">BUILD:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> git clone https://github.com/sib-swiss/pftools3.git</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> cd pftools3</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> mkdir build</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> cd build/</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> cmake ..</span>
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31
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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"> OPTIONS:</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> - Build static binaries:</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> cmake -DSTANDALONE=ON ..</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> - Build a version using 32bits integers to represent profile matrix values</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> instead of default 16bits (less problems with low/negative cutoff values,</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> might be slower & use more memory):</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> cmake -DUSE_32BIT_INTEGER=ON ..</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> - Change installation prefix:</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> cmake -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL PATH> ..</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> - Compile C only code (version 3 only):</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> cmake -DC_ONLY=ON ..</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> - Compile with graphical support for pfcalibrateV3 (highly optional):</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> cmake -DUSE_GRAPHICS=ON -DUSE_PDF=ON ..</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> - Compile without regular expression support:</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> cmake -DUSE_PCRE=OFF ..</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> ...</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> example:</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> cmake -DC_ONLY=ON -DUSE_32BIT_INTEGER=ON -DUSE_PCRE=OFF ..</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">COMPILE:</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> make</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">This will create the binaries. To install the</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">binaries and the corresponding manual pages type:</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">INSTALL (see above to change install path):</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> make install</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">CHECK/TEST:</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> make test</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/faa7014383b252e2bf8cb20ce3020433e5d2acde...011649097f21220233797bbcbfe74f28cb49d3bf#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">@@ -3,21 +3,6 @@ Upstream-Contact: pftools@isb-sib.ch</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> prosite@expasy.org (via request tracker)</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Alan.Bridge@sib.swiss, Christian.Sigrist@sib.swiss, Gregoire.Rossier@sib.swiss</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Source: https://github.com/sib-swiss/pftools3/releases</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Files-Excluded: */a.out</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> */pfdunp</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> *.deps</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> INSTALL</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> */Makefile</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> */Makefile.in</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> aclocal.m4</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> compile</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> config.*</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> configure</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> depcomp</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> install-sh</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> missing</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> */config.h*</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> */stamp-h1</span>
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21
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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22
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Files: *</span>
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23
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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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Copyright: 2002-2011 Alan Bridge, Christian Sigrist, Gregoire Rossier</span>
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<li id="bcd74a0bd3eb1727e503919bce010ec5b463a401">
<a href="https://salsa.debian.org/med-team/pftools/-/compare/faa7014383b252e2bf8cb20ce3020433e5d2acde...011649097f21220233797bbcbfe74f28cb49d3bf#bcd74a0bd3eb1727e503919bce010ec5b463a401"><strong>debian/missing-sources/get</strong>
deleted
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Upstream just forgot to include this file in the downloadable tarball</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;"># see https://github.com/sib-swiss/pftools3/issues/17</span></span>
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<td class="diff-line-num old old_line" 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">
4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell">wget https://raw.githubusercontent.com/sib-swiss/pftools3/master/src/C/config.h.cmake</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/faa7014383b252e2bf8cb20ce3020433e5d2acde...011649097f21220233797bbcbfe74f28cb49d3bf#33a08aca934f37c2d0beb1888a2a6794fe9b0219"><strong>debian/missing-sources/config.h.cmake</strong>
→
<strong>src/C/config.h.cmake</strong>
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