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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/t-coffee">Debian Med / t-coffee</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/t-coffee/-/commit/77b14fb539660719f11074d10ca7d9e3924be7b6">77b14fb5</a></strong>
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<span>by Etienne Mollier</span>
<i>at 2020-06-17T20:10:30+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added patch to increase MAX_N_PID to 4194304
</pre>
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<strong><a href="https://salsa.debian.org/med-team/t-coffee/-/commit/899e3cb4779e81f0bfe673b4dfb581d3bf9cc742">899e3cb4</a></strong>
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<span>by Etienne Mollier</span>
<i>at 2020-06-17T20:13:26+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated homepage
The former homepage points to a deprecated redirection leading to
the newer one; an update of the URL was welcome perhaps.
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<h4>4 changed files:</h4>
<ul>
<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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<li class="file-stats">
<a href="#180518057ab5292461a3a1546d28405dcadcc1df">
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+
debian/patches/increase_max_pid.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/t-coffee/-/compare/39db5055efdce635a4ddbf74e34b4376306c0a71...899e3cb4779e81f0bfe673b4dfb581d3bf9cc742#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">t-coffee (13.41.0.28bdc39+dfsg-4) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Increase MAX_N_PID to 4194304. (Closes: #962974)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Updated the homepage, following permanent redirection.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Etienne Mollier <etienne.mollier@mailoo.org> Wed, 17 Jun 2020 19:22:31 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext">t-coffee (13.41.0.28bdc39+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> [ Aaron M. Ucko ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/t-coffee/-/compare/39db5055efdce635a4ddbf74e34b4376306c0a71...899e3cb4779e81f0bfe673b4dfb581d3bf9cc742#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 12)</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.5.0</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Browser</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">t</span><span class="p">-</span><span class="n" style="color: #333;">coffee</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Git</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">t</span><span class="p">-</span><span class="n" style="color: #333;">coffee</span><span class="p">.</span><span class="n" style="color: #333;">git</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="mosel"><span class="n" style="color: #333;">Homepage</span><span class="p">:</span> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">tcoffee</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">Projects<span class="idiff left">_home_page</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff right">t_coffee_home_page</span></span><span class="p">.</span><span class="n" style="color: #333;">html</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"><span class="n" style="color: #333;">Homepage</span><span class="p">:</span> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">tcoffee</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">Projects</span><span class="p"><span class="idiff left">/</span></span><span class="n" style="color: #333;"><span class="idiff">tcoffee</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff right">index</span></span><span class="p">.</span><span class="n" style="color: #333;">html</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="mosel"><span class="n" style="color: #333;">Rules</span><span class="p">-</span><span class="n" style="color: #333;">Requires</span><span class="p">-</span><span class="n" style="color: #333;">Root</span><span class="p">:</span> <span class="n" style="color: #333;">no</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Package</span><span class="p">:</span> <span class="n" style="color: #333;">t</span><span class="p">-</span><span class="n" style="color: #333;">coffee</span></span>
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<a href="https://salsa.debian.org/med-team/t-coffee/-/compare/39db5055efdce635a4ddbf74e34b4376306c0a71...899e3cb4779e81f0bfe673b4dfb581d3bf9cc742#180518057ab5292461a3a1546d28405dcadcc1df"><strong>debian/patches/increase_max_pid.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: increase MAX_N_PID to Linux 64 bits theoretical maximum</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Since Debian Bullseye, the system now has a default pid_max of 4194304 instead</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> of the historical 32768. This renders t-coffee much more likely to crash on</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> compute nodes always powered on in computer centers. This patch addresses</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> that issue with a value set to the theoretical upper limit of Linux on 64 bits</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> systems.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962974</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">Last-Update: 2020-06-17</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</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;">--- t-coffee.orig/t_coffee_source/coffee_defines.h</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ t-coffee/t_coffee_source/coffee_defines.h</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -40,7 +40,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> #define TMP_MAX_KEEP 10</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> #define CACHE_MAX_SIZE 2000</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #define CACHE_MAX_KEEP 180</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#define MAX_N_PID 260000</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define MAX_N_PID 4194304</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> //Importnat Values Affecting the Program Behavior</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> #define O2A_BYTE 50</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> #define SCORE_K 10</span></pre>
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<a href="https://salsa.debian.org/med-team/t-coffee/-/compare/39db5055efdce635a4ddbf74e34b4376306c0a71...899e3cb4779e81f0bfe673b4dfb581d3bf9cc742#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -8,3 +8,4 @@ mayhem.patch</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">stable-linking-inputs.patch</span>
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<td class="diff-line-num old_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext">clustalw2.patch</span>
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<td class="diff-line-num old_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext">verbose_build</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">increase_max_pid.patch</span></pre>
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