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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/community/helper-scripts">Debian Med / community / helper-scripts</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/community/helper-scripts/-/commit/429b424764c0488a1900f304b2bbc11f54ee9a72">429b4247</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-02-28T01:45:45+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">automatic update
</pre>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6d55d24085decec06151dd27f30199089d856ca">
debian-med-tests.txt
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<li class="file-stats">
<a href="#2654e31016bcee9bbe05d462121706cc8ed368af">
outdated_med-packages.txt
</a>
</li>
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<h4>Changes:</h4>
<li id="f6d55d24085decec06151dd27f30199089d856ca">
<a href="https://salsa.debian.org/med-team/community/helper-scripts/-/commit/429b424764c0488a1900f304b2bbc11f54ee9a72#f6d55d24085decec06151dd27f30199089d856ca"><strong>debian-med-tests.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Last-Update: <span class="idiff left right">Thu, 27 Feb 2020 13:42:04</span> +0000</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Last-Update: <span class="idiff left right">Fri, 28 Feb 2020 01:42:03</span> +0000</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> Source | Vote | Tasks | Tags </span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">-------------------------------+--------+--------------------------------------------+----------------------------------------------------------------------</span>
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<li id="2654e31016bcee9bbe05d462121706cc8ed368af">
<a href="https://salsa.debian.org/med-team/community/helper-scripts/-/commit/429b424764c0488a1900f304b2bbc11f54ee9a72#2654e31016bcee9bbe05d462121706cc8ed368af"><strong>outdated_med-packages.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Last-Update: <span class="idiff left right">Thu, 27 Feb 2020 13</span>:42:04 +0000</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Last-Update: <span class="idiff left right">Fri, 28 Feb 2020 01</span>:42:04 +0000</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"> source | version | upstream_version | uploaders | Last uploader | Last uploaded </span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">-------------------------------+---------------------------------+---------------------------------+-----------------------------------------------------------------------------+----------------------+------------------------</span>
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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">@@ -6,7 +6,6 @@ Last-Update: Thu, 27 Feb 2020 13:42:04 +0000</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> artemis | 17.0.1 | 18.1.0 | Andreas Tille | Andreas Tille | 2019-02-08 11:19:24+00</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> atropos | 1.1.24 | 2.0.0-alpha.4 | Andreas Tille | Steffen Moeller | 2019-11-30 12:19:31+00</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> baitfisher | 1.2.7+git20180107.e92dbf2 | 1.2.7+git20190123.241d060 | Olivier Sallou | Andreas Tille | 2018-09-24 13:04:18+00</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> bbmap | 38.73 | 38.79 | Andreas Tille | Andreas Tille | 2019-11-22 21:04:16+00</span>
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10
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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"> beast2-mcmc | 2.6.0 | 2.6.1 | Andreas Tille,Olivier Sallou | Andreas Tille | 2019-07-31 13:08:02+00</span>
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11
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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="plaintext"> biobambam2 | 2.0.153 | 2.0.156+ds | Andreas Tille | Andreas Tille | 2020-02-05 13:20:41+00</span>
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12
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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"> biojava-live | 1.7.1 | 1.9.3 | Andreas Tille,Olivier Sallou,Steffen Moeller | Andreas Tille | 2018-11-12 15:49:23+00</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" 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">@@ -15,7 +14,6 @@ Last-Update: Thu, 27 Feb 2020 13:42:04 +0000</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> biomaj3-download | 3.1.0 | 3.1.2 | Olivier Sallou | Olivier Sallou | 2019-11-12 13:19:24+00</span>
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<td class="diff-line-num old_line" data-linenumber="16" 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="LC15" class="line" lang="plaintext"> biomaj3-process | 3.0.15 | 3.0.16 | Olivier Sallou | Olivier Sallou | 2019-11-12 11:20:38+00</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> charls | 2.0.0 | 2.1.0 | Andreas Tille | Andreas Tille | 2019-01-10 20:10:56+00</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> clonalframeml | 1.11 | 1.12 | Andreas Tille | Andreas Tille | 2019-05-23 07:03:34+00</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> dcm2niix | 1.0.20181125 | 1.0.20190902 | Ghislain Antony Vaillant | Andreas Tille | 2019-01-30 10:04:52+00</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> ea-utils | 1.1.2 | 1.04.807 | Andreas Tille,Tim Booth | Andreas Tille | 2018-04-26 21:48:01+00</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> elastix | 4.9.0 | 5.0.0 | Gert Wollny,Steve M. Robbins | Andreas Tille | 2019-01-15 11:50:11+00</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">@@ -24,7 +22,6 @@ Last-Update: Thu, 27 Feb 2020 13:42:04 +0000</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> fis-gtm | 6.3-007 | 6.3-010 | Amul Shah,Andreas Tille | Amul Shah | 2019-02-28 14:12:19+00</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> gatb-core | 1.4.1+git20191209.9398f28 | 1.4.1+git20200118.1dc23ff | Andreas Tille,Nadiya Sitdykova | Michael R. Crusoe | 2020-02-17 14:52:30+00</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> gdcm | 3.0.4 | 3.0.5 | Gert Wollny,Sébastien Jodogne,Steve M. Robbins | Gert Wollny | 2019-11-07 11:49:02+00</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> gnumed-server | 22.8 | 22.9 | Andreas Tille,Sebastian Hilbert | Andreas Tille | 2019-11-13 15:20:32+00</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> hdmf | 1.5.4 | 1.6.0 | Yaroslav Halchenko | Yaroslav Halchenko | 2020-02-03 03:01:25+00</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> htsjdk | 2.18.2 | 2.21.2 | Andreas Tille,Charles Plessy,Olivier Sallou,Vincent Danjean | Andreas Tille | 2019-03-01 22:19:40+00</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> hyphy | 2.5.1 | 2.5.4 | Andreas Tille | Andreas Tille | 2020-01-07 21:19:50+00</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">@@ -82,7 +79,7 @@ Last-Update: Thu, 27 Feb 2020 13:42:04 +0000</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> unanimity | 3.3.0 | 4.2.0 | Afif Elghraoui,Andreas Tille | Adrian Bunk | 2019-02-06 07:34:42+00</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"> vsearch | 2.14.1 | 2.14.2 | Andreas Tille,Tim Booth | Andreas Tille | 2019-12-17 10:07:09+00</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"> xmedcon | 0.16.1 | 0.16.2 | Andreas Tille,Roland Marcus Rutschmann | Andreas Tille | 2019-01-25 18:23:59+00</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext">(<span class="idiff left right">80</span> rows)</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">(<span class="idiff left right">77</span> rows)</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> source | id | severity | title </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">@@ -105,7 +102,6 @@ Last-Update: Thu, 27 Feb 2020 13:42:04 +0000</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> biojava4-live | 843712 | normal | biojava4-live: FTBFS (failing tests)</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> biojava-live | 659824 | minor | biojava-live: New version available</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> biomaj3 | 950914 | minor | python3-biomaj3: Depends on python-influxdb wich ftbs, patch to remove dependency</span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext"> brig | 952624 | serious | brig: FTBFS: build-dependency not installable: blast2</span>
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<td class="diff-line-num old_line" data-linenumber="109" 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="LC105" class="line" lang="plaintext"> bwa | 942447 | normal | Build bwa on ppc64el</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"> camp | 900181 | normal | camp: FTBFS on 32bit big endian: check metaclass->function("f4").call(object, camp::Args(1, 4, 15)).to<unsigned long>() == 20 has failed</span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"> cfflib | 936285 | serious | cfflib: Python2 removal in sid/bullseye</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" 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="153" 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">@@ -157,7 +153,6 @@ Last-Update: Thu, 27 Feb 2020 13:42:04 +0000</td>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"> ghmm | 936609 | normal | ghmm: Python2 removal in sid/bullseye</span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"> gnumed-client | 936630 | serious | gnumed-client: Python2 removal in sid/bullseye</span>
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<td class="diff-line-num old_line" data-linenumber="159" 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="LC155" class="line" lang="plaintext"> gnumed-client | 952633 | wishlist | gnumed-client: hints for py3 packaging</span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="plaintext"> gnumed-server | 936631 | normal | gnumed-server: Python2 removal in sid/bullseye</span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext"> harvest-tools | 943055 | normal | harvest-tools: Python2 removal in sid/bullseye</span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext"> hinge | 952615 | serious | hinge: FTBFS: fmt.h:22:10: fatal error: spdlog/fmt/bundled/core.h: No such file or directory</span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext"> htsjdk | 877590 | normal | FTBFS: error: package org.testng does not exist</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="214" 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="209" 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">@@ -214,9 +209,7 @@ Last-Update: Thu, 27 Feb 2020 13:42:04 +0000</td>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext"> orthanc-webviewer | 828949 | minor | orthanc-webviewer: "better" suggestion for cache location</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="215" 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="LC210" class="line" lang="plaintext"> paleomix | 933750 | normal | paleomix: Port to Python3 needed</span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext"> paleomix | 937232 | normal | paleomix: Python2 removal in sid/bullseye</span>
</pre>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="plaintext"> pbalign | 937252 | serious | pbalign: Python2 removal in sid/bullseye</span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext"> pbbam | 829741 | important | pbbam: FTBFS (32-bit): pbmerge assertion failure</span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="plaintext"> pbbarcode | 937253 | serious | pbbarcode: Python2 removal in sid/bullseye</span>
</pre>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext"> pbgenomicconsensus | 937255 | serious | pbgenomicconsensus: Python2 removal in sid/bullseye</span>
</pre>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="plaintext"> pbh5tools | 937256 | serious | pbh5tools: Python2 removal in sid/bullseye</span>
</pre>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="plaintext"> pdb2pqr | 937262 | normal | pdb2pqr: Python2 removal in sid/bullseye</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="267" 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">@@ -267,7 +260,6 @@ Last-Update: Thu, 27 Feb 2020 13:42:04 +0000</td>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="plaintext"> simpleitk | 949355 | serious | simpleitk FTBFS: test failures</span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="plaintext"> skesa | 952627 | serious | skesa: FTBFS: ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_entropy_init'</span>
</pre>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="plaintext"> smalr | 938500 | serious | smalr: Python2 removal in sid/bullseye</span>
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<td class="diff-line-num old old_line" data-linenumber="270" 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">
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="plaintext"> smrtanalysis | 945737 | serious | smrtanalysis: Python2 removal in sid/bullseye</span>
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<td class="diff-line-num old_line" data-linenumber="271" 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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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="plaintext"> snakemake | 943956 | wishlist | snakemake: please make the build reproducible</span>
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="plaintext"> snap | 927011 | minor | snap: Package info contains a 404 url</span>
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<td class="diff-line-num old_line" data-linenumber="273" 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="LC265" class="line" lang="plaintext"> snap-aligner | 848589 | normal | snap-aligner: Build requires 188 GB of memory (fortunately not used, just allocated)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="291" 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">@@ -291,5 +283,5 @@ Last-Update: Thu, 27 Feb 2020 13:42:04 +0000</td>
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="plaintext"> xmedcon | 671828 | normal | xmedcon: Cannot open file with YBR photometric interpretation</span>
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<td class="diff-line-num old_line" data-linenumber="292" 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="LC284" class="line" lang="plaintext"> xmedcon | 779707 | normal | Errors when reading dicomdir file: "No images found" / "Loading: DICM Error reading file"</span>
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<td class="diff-line-num old_line" data-linenumber="293" 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="LC285" class="line" lang="plaintext"> xmedcon | 924017 | normal | desktop entry</span>
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<td class="diff-line-num old old_line" data-linenumber="294" 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">
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="plaintext">(<span class="idiff left right">204</span> rows)</span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">(<span class="idiff left right">199</span> rows)</span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="plaintext"></span></pre>
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