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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/6371465c5dec33bd5737863553e4bcded626e357">6371465c</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-22T16:36:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/changelog: prepare for unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/934d22fc52f65c09b744283086e92a10593cece3">934d22fc</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-22T16:53:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mark spelling.patch as not needing forward
It seems that the file being package might not exists in upcoming
Biopython versions anymore.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/ffbef548926712ac111716c1d6ea6bd015833401">ffbef548</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-22T18:04:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adjust-test_GraphicsBitmaps.patch: forwarded upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/1b3afa09eeef80a20b518d2467a8d7f4b59ba472">1b3afa09</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-22T18:06:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/93a94954103ec694ff26b57c75e8121155872943">93a94954</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-22T18:09:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: breaks ncbi-acc-download (<< 0.2.7-2~)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/cc95b59c605fd0185406c7fcb71c67636b5909d2">cc95b59c</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-22T18:10:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/676bb97a40d3752fa951980145c153fb989253db">676bb97a</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-22T18:39:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#75a5a96c230fa6ebdb811c926fdee83a4bee7e7b">
debian/patches/adjust-test_GraphicsBitmaps.patch
</a>
</li>
<li class="file-stats">
<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
debian/patches/spelling.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/955331683926a4b741af8ff819e972de46ab042c...676bb97a40d3752fa951980145c153fb989253db#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;">1.79</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">1</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>
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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;">Migrate</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Experimental</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Unstable</span><span class="p">.</span></span>
</pre>
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<td class="new_line diff-line-num new" 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;">Mark</span> <span class="n" style="color: #333;">spelling</span><span class="p">.</span><span class="n" style="color: #333;">patch</span> <span class="k" style="font-weight: 600;">as</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">needing</span> <span class="k" style="font-weight: 600;">forward</span><span class="p">.</span></span>
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<td class="new_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="n" style="color: #333;">It</span> <span class="n" style="color: #333;">seems</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">being</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">might</span> <span class="k" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">exists</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">upcoming</span></span>
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<td class="new_line diff-line-num new" 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="n" style="color: #333;">Biopython</span> <span class="n" style="color: #333;">versions</span> <span class="n" style="color: #333;">anymore</span><span class="p">.</span></span>
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<td class="new_line diff-line-num new" 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 class="p">*</span> <span class="n" style="color: #333;">adjust</span><span class="p">-</span><span class="n" style="color: #333;">test_GraphicsBitmaps</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">:</span> <span class="n" style="color: #333;">forwarded</span> <span class="n" style="color: #333;">upstream</span><span class="p">.</span></span>
</pre>
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<td class="new_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">d</span><span class="p">/</span><span class="n" style="color: #333;">control</span><span class="p">:</span> <span class="n" style="color: #333;">breaks</span> <span class="n" style="color: #333;">ncbi</span><span class="p">-</span><span class="n" style="color: #333;">acc</span><span class="p">-</span><span class="n" style="color: #333;">download</span> <span class="p">(<<</span> <span class="m" style="color: #099;">0.2.7</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">~)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC10" 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;">emollier</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;">Fri</span><span class="p">,</span> <span class="m" style="color: #099;">22</span> <span class="n" style="color: #333;">Oct</span> <span class="m" style="color: #099;">2021</span> <span class="m" style="color: #099;">18</span><span class="p">:</span><span class="m" style="color: #099;">10</span><span class="p">:</span><span class="m" style="color: #099;">48</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC12" 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;">1.79</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">1</span><span class="p">~</span><span class="m" style="color: #099;">0</span><span class="n" style="color: #333;">exp0</span><span class="p">)</span> <span class="n" style="color: #333;">experimental</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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<td class="new_line diff-line-num" data-linenumber="13" 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="LC13" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">New</span> <span class="n" style="color: #333;">upstream</span> <span class="k" style="font-weight: 600;">version</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">@@ -89,7 +89,8 @@ Suggests: python3-tk,</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> t-coffee,</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> wise,</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> w3-dtd-mathml</span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">Breaks: cnvkit (<< 0.9.7-1~)</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">Breaks: cnvkit (<< 0.9.7-1~),</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> ncbi-acc-download (<< 0.2.7-2~)</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">Description: Python3 library for bioinformatics</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> The Biopython Project is an international association</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"> of developers of freely available Python tools for</span>
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<li id="75a5a96c230fa6ebdb811c926fdee83a4bee7e7b">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/955331683926a4b741af8ff819e972de46ab042c...676bb97a40d3752fa951980145c153fb989253db#75a5a96c230fa6ebdb811c926fdee83a4bee7e7b"><strong>debian/patches/adjust-test_GraphicsBitmaps.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: adjust test skipping logic for new error message in renderpm</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">no</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">https://github.com/biopython/biopython/pull/3767</span></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-10-16</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC6" 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="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-biopython.orig/Tests/test_GraphicsBitmaps.py</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-biopython/Tests/test_GraphicsBitmaps.py</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -102,7 +102,<span class="idiff left right">7</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -102,7 +102,<span class="idiff left right">8</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> raise</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> except RenderPMError as err:</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;">- if str(err).startswith("Can't setFont("):</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;">+ if str(err).startswith("Can't setFont(") or str(err).startswith("Error in setFont("):</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;">+ if (str(err).startswith("Can't setFont(")</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;">+ or str(err).startswith("Error in setFont(")):</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> # TODO - can we raise the error BEFORE the unit test function</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> # is run? That way it can be skipped in run_tests.py</span>
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17
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> raise MissingExternalDependencyError(</span></pre>
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<li id="45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/955331683926a4b741af8ff819e972de46ab042c...676bb97a40d3752fa951980145c153fb989253db#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: fix spelling-error-in-binary</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no<span class="idiff left right">t-needed</span></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">Last-Update: 2021-10-16</span></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="diff"><span class="p">---</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" 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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