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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/profisis">Debian Med / profisis</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/profisis/-/commit/8fb97b7419d64e13d397e4907d7791792c90978e">8fb97b74</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-18T21:07:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Stop using pp_popcon
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/profisis/-/commit/6c02279f4fd9082c9577a75cf792b6771ad3917f">6c02279f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-18T21:08:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream download vanished
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/profisis/-/commit/423b0357bacfbff10edb09abb4cc6a30d8fcba49">423b0357</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-18T21:08:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/profisis/-/commit/9009dd2e58c67fe45a5592b0ffaceebe95f344e4">9009dd2e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-18T21:08:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing build dependency on dh addon.
Changes-By: lintian-brush
Fixes: lintian: missing-build-dependency-for-dh_-command
See-also: https://lintian.debian.org/tags/missing-build-dependency-for-dh_-command.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/profisis/-/commit/76a60b7fc9711c2eac7d5a4d419eb0ac60b341bc">76a60b7f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-18T21:10:37+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/profisis/-/commit/f99fb6542cb25ce523e5b40dce162bbd0ea18f44">f99fb654</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-18T21:11:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
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−
debian/README.Debian
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#bfd92efca918a8208e7d50d7c50b0e804795c74a">
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+
debian/patches/no_pp-popcon.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/profisis/-/compare/1a87f43d743f90d1fc02e45c23e4dc206e511407...f99fb6542cb25ce523e5b40dce162bbd0ea18f44#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">profisis for Debian</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">===================</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">profisis nags the user that he/she has to install pp-popularity-contest (which already is a Recommends)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">-------------------------------------------------------------------------------------------------------</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">This is the explicit intention of upstream. The software being released free, this is upstream's way of keeping usage counts. That in turn is used to decide what to support upstream and what not.</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Q: How to silence the warning?</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> A1: Install the 'pp-popularity-contest' package.</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> A2: Create an executable (script) named 'pp_popcon_cnt' and put it somewhere on your $PATH. The program does not need to do anything, an 'exit' is enough.</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/profisis/-/compare/1a87f43d743f90d1fc02e45c23e4dc206e511407...f99fb6542cb25ce523e5b40dce162bbd0ea18f44#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">profisis (1.0.11-7) 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"> * Stop using pp_popcon</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Upstream download vanished</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Add missing build dependency on dh addon.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 18 Jan 2022 21:10:48 +0100</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">profisis (1.0.11-6) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * pp-popularity-contest only suggested</span>
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<a href="https://salsa.debian.org/med-team/profisis/-/compare/1a87f43d743f90d1fc02e45c23e4dc206e511407...f99fb6542cb25ce523e5b40dce162bbd0ea18f44#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -5,8 +5,8 @@ Uploaders: Cedric Staniewski <cedric@gmx.ca>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13)</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13)<span class="idiff left right">, debhelper</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/profisis</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/profisis.git</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: https://rostlab.org/owiki/index.php/PROFisis</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -19,7 +19,6 @@ Depends: ${misc:Depends},</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libconfig-inifiles-perl,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> profnet-isis</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Recommends: librg-utils-perl</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Suggests: pp-popularity-contest</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Description: prediction of protein-protein interaction sites from sequence</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> Profisis (ISIS) identifies interacting protein residues in protein-protein</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> interfaces from sequence alone.</span>
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<a href="https://salsa.debian.org/med-team/profisis/-/compare/1a87f43d743f90d1fc02e45c23e4dc206e511407...f99fb6542cb25ce523e5b40dce162bbd0ea18f44#bfd92efca918a8208e7d50d7c50b0e804795c74a"><strong>debian/patches/no_pp-popcon.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 18 Jan 2022 19:02:40 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Stop using pp_popcon</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/profisis</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/profisis</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -17,9 +17,6 @@</span> BEGIN {</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> $pkgdatadir = glob( $config->val('profisis', 'pkgdatadir') );</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# popularity contest</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if( system('pp_popcon_cnt', '-p', 'profisis') == -1 ){ warn("The Rost Lab recommends you install the pp-popularity-contest package that provides pp_popcon_cnt:\n\nsudo apt-get install pp-popularity-contest\n"); }</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> my $debug = 0;</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> #$Fil=""; # lkajan: this was empty string was used like this: $hssp="$out.hssp$Fil" or $hssp="hssp/$sfile.hssp$Fil"</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> # lkajan: $out however is not initialized and $struct is hard-coded to 'n'</span></pre>
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<a href="https://salsa.debian.org/med-team/profisis/-/compare/1a87f43d743f90d1fc02e45c23e4dc206e511407...f99fb6542cb25ce523e5b40dce162bbd0ea18f44#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">no_pp-popcon.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/profisis/-/compare/1a87f43d743f90d1fc02e45c23e4dc206e511407...f99fb6542cb25ce523e5b40dce162bbd0ea18f44#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">ftp://rostlab.org/free/profisis-([0-9.]+)\.tar\.gz debian uupdate</span></pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">opts=dversionmangle=s/.*/0.No-Site/ \</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">https://people.debian.org/~eriberto/ FakeWatchNoUpstreamSiteForThisPackage-(\d\S+)\.gz</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span></pre>
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