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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-biopython">Debian Med / python-biopython</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/9e6f8193e50cd3da5c17f72fc33303c224d4f949">9e6f8193</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2020-12-05T23:32:08+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add mkdssp4.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/0a733cc53312f57204c466873fe3a1fa36b93310">0a733cc5</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-05T23:32:33+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/a8ec62f60bb955af667663c5f6896557ee9c152e">a8ec62f6</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2020-12-05T23:48:51+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#7019d2fa8049211f9c910f5fd9b7db79bed13252">
<span class="new-file">
+
debian/patches/mkdssp4.path
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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/python-biopython/-/compare/7bb20d63e89b02a4a5ebb1e1c7a55b550e36ec4f...a8ec62f60bb955af667663c5f6896557ee9c152e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.78</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">4</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Add</span> <span class="n" style="color: #333;">mkdssp4</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">.</span> <span class="p">(</span><span class="n" style="color: #333;">Closes</span><span class="p">:</span> <span class="p">#</span><span class="m" style="color: #099;">976542</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="p">*</span> <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;">4.5.1</span> <span class="p">(</span><span class="n" style="color: #333;">routine</span><span class="p">-</span><span class="n" style="color: #333;">update</span><span class="p">)</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"></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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="p">--</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">É</span><span class="n" style="color: #333;">tienne</span> <span class="n" style="color: #333;">Mollier</span> <span class="p"><</span><span class="n" style="color: #333;">etienne</span><span class="p">.</span><span class="n" style="color: #333;">mollier</span><span class="p">@</span><span class="n" style="color: #333;">mailoo</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;">Sat</span><span class="p">,</span> <span class="m" style="color: #099;">05</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2020</span> <span class="m" style="color: #099;">23</span><span class="p">:</span><span class="m" style="color: #099;">32</span><span class="p">:</span><span class="m" style="color: #099;">40</span> <span class="p">+</span><span class="m" style="color: #099;">0100</span></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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"></span>
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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="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.78</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">3</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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2
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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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"></span>
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<td class="diff-line-num new_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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Bumped</span> <span class="n" style="color: #333;">ncbi</span><span class="p">-</span><span class="n" style="color: #333;">blast</span><span class="p">+</span> <span class="k" style="font-weight: 600;">version</span> <span class="n" style="color: #333;">requirement</span> <span class="k" style="font-weight: 600;">to</span> <span class="m" style="color: #099;">2.10.1</span><span class="p">-</span><span class="m" style="color: #099;">3</span></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/7bb20d63e89b02a4a5ebb1e1c7a55b550e36ec4f...a8ec62f60bb955af667663c5f6896557ee9c152e#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,7 +45,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> samtools <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> t-coffee <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> wise <!nocheck></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-biopython</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-biopython.git</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">Homepage: http://biopython.org</span>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/7bb20d63e89b02a4a5ebb1e1c7a55b550e36ec4f...a8ec62f60bb955af667663c5f6896557ee9c152e#7019d2fa8049211f9c910f5fd9b7db79bed13252"><strong>debian/patches/mkdssp4.path</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: port PDB DSSP module to use dssp version 4</span></span>
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<pre style="margin: 0;">+<span id="LC2" 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="LC3" class="line" lang="diff"><span class="p">Bug: https://github.com/biopython/biopython/issues/3433</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=976542</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2020-12-05</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC7" 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="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-biopython.orig/Bio/PDB/DSSP.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-biopython/Bio/PDB/DSSP.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -229,7 +229,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> # (Debian distribution of DSSP includes a symlink for 'dssp' argument)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> p = subprocess.Popen(</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [DSSP, in_file],</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [DSSP, "--output-format=dssp", in_file],</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> universal_newlines=True,</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> stdout=subprocess.PIPE,</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> stderr=subprocess.PIPE,</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -238,7 +238,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> if DSSP == "mkdssp":</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> raise</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> p = subprocess.Popen(</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ["mkdssp", in_file],</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ["mkdssp", "--output-format=dssp", in_file],</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> universal_newlines=True,</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> stdout=subprocess.PIPE,</span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> stderr=subprocess.PIPE,</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/7bb20d63e89b02a4a5ebb1e1c7a55b550e36ec4f...a8ec62f60bb955af667663c5f6896557ee9c152e#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,3 +6,4 @@ fix-use-of-unversioned-python.patch</td>
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<td class="diff-line-num old_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">stabilize-phyml-test.patch</span>
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<td class="diff-line-num old_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext">spelling-error-in-binaries.patch</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">reproduciblebuild.patch</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">mkdssp4.path</span></pre>
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