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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/9669ed471d6804a732564c2de2b766a24d00c44e">9669ed47</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-02-27T01:45:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">automatic update
</pre>
</li>
</ul>
<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6d55d24085decec06151dd27f30199089d856ca">
debian-med-tests.txt
</a>
</li>
<li class="file-stats">
<a href="#2654e31016bcee9bbe05d462121706cc8ed368af">
outdated_med-packages.txt
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6d55d24085decec06151dd27f30199089d856ca">
<a href="https://salsa.debian.org/med-team/community/helper-scripts/-/commit/9669ed471d6804a732564c2de2b766a24d00c44e#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">Wed, 26 Feb 2020 13</span>:42:03 +0000</span>
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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 01</span>:42:03 +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>
</pre>
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<br>
</li>
<li id="2654e31016bcee9bbe05d462121706cc8ed368af">
<a href="https://salsa.debian.org/med-team/community/helper-scripts/-/commit/9669ed471d6804a732564c2de2b766a24d00c44e#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">Wed, 26 Feb 2020 13</span>:42:03 +0000</span>
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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 01</span>:42:03 +0000</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,6 @@ Last-Update: Wed, 26 Feb 2020 13:42:03 +0000</td>
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<pre style="margin: 0;"> <span id="LC16" 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="LC17" 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="LC19" class="line" lang="plaintext"> cwltool                       | 2.0.20200126090152              | 2.0.20200224214940              | Michael R. Crusoe                                                           | Michael R. Crusoe    | 2020-02-14 12:34:12+00</span>
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<pre style="margin: 0;"> <span id="LC19" 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="LC20" 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="LC21" 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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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"> sumatra                       | 1.0.31                          | 1.0.34                          | Andreas Tille,Tim Booth                                                     | Andreas Tille        | 2018-10-16 10:06:33+00</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> t-coffee                      | 12.00.7fb08c2                   | 13.41.0.28bdc39                 | Andreas Tille,Steffen Moeller                                               | Andreas Tille        | 2019-02-15 07:57:10+00</span>
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<pre style="margin: 0;"> <span id="LC80" 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="LC82" class="line" lang="plaintext"> vg                            | 1.21.0                          | 1.22.0                          | Michael R. Crusoe                                                           | Michael R. Crusoe    | 2020-02-25 19:09:28+00</span>
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<pre style="margin: 0;"> <span id="LC81" 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="LC82" 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="LC83" class="line" lang="plaintext">(<span class="idiff left right">78</span> rows)</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"> source                        |   id   | severity  |                                                                                                                                                                                                                           title                                                                                                                                                                                                                           </span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> biojava4-live                 | 843712 | normal    | biojava4-live: FTBFS (failing tests)</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> biojava-live                  | 659824 | minor     | biojava-live: New version available</span>
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<pre style="margin: 0;"> <span id="LC105" 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="LC106" class="line" lang="plaintext"> brig                          | 952624 | serious   | brig: FTBFS: build-dependency not installable: blast2</span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"> bwa                           | 942447 | normal    | Build bwa on ppc64el</span>
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<pre style="margin: 0;"> <span id="LC108" 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="LC109" class="line" lang="plaintext"> cfflib                        | 936285 | serious   | cfflib: Python2 removal in sid/bullseye</span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"> gdcm                          | 749783 | normal    | gdcm: Conflicting declarations of jpeg_memory_mgr may lead to invalid function calls</span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"> gdcm                          | 826048 | wishlist  | Faulty CMake file impairs compiling against GDCM</span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"> gdcm                          | 947990 | important | gdcm: Doesn't build on ports without java</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> gdcm                          | 952597 | serious   | gdcm build depends on the removed swig3.0</span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"> gemma                         | 952190 | serious   | gemma: FTBFS: dh_auto_test: error: make -j1 check returned exit code 2</span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"> gentle                        | 732691 | normal    | Pressing "alignment or Ctrl+G"   only results in a dialog with a  cancel button</span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext"> ghmm                          | 936609 | normal    | ghmm: Python2 removal in sid/bullseye</span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext"> gnumed-client                 | 936630 | serious   | gnumed-client: Python2 removal in sid/bullseye</span>
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<pre style="margin: 0;">+<span id="LC157" 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="LC158" 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="LC159" 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="LC160" 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="LC161" class="line" lang="plaintext"> htsjdk                        | 877590 | normal    | FTBFS: error: package org.testng does not exist</span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext"> htsjdk                        | 920588 | normal    | htsjdk: Autopkgtest for htsjdk</span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext"> htslib                        | 922860 | normal    | Packages do not contain the upstream README file</span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext"> insighttoolkit4               | 853752 | wishlist  | src:insighttoolkit4: Add documentation package</span>
</pre>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext"> insighttoolkit4               | 943677 | normal    | please package insighttoolkit5 (5.0 and 5.1 beta 1 are out)</span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="plaintext"> insighttoolkit4               | 944179 | important | insighttoolkit4: non-standard gcc/g++ used for build (gcc-8)</span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> insighttoolkit4               | 952599 | serious   | insighttoolkit4 build depends on the removed swig3.0</span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="plaintext"> ismrmrd                       | 863168 | important | ismrmrd FTBFS on armhf: 1 failure is detected in the test module "ISMRMRD Unit Tests"</span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="plaintext"> jellyfish1                    | 875328 | wishlist  | jellyfish1: FTBFS: __sync_val_compare_and_swap_8 undefined</span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="plaintext"> khmer                         | 851830 | minor     | arm64 has flaky tests</span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="plaintext"> python-pbcore                 | 919052 | normal    | python-pbcore: some docs for pbcore are not found</span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="plaintext"> python-pysam                  | 938092 | normal    | python-pysam: Python2 removal in sid/bullseye</span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="plaintext"> python-ruffus                 | 841073 | wishlist  | python-ruffus: Needs 18 GB of RAM to build</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"> python-tinyalign              | 952603 | normal    | python-tinyalign: license of buildwheels.sh is CC0</span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="plaintext"> q2-demux                      | 950933 | normal    | q2-demux: FTBFS with pandas 1.0: test failures</span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext"> q2templates                   | 950931 | normal    | q2templates: FTBFS with pandas 1.0: test failures</span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext"> q2-types                      | 950932 | normal    | q2-types: FTBFS with pandas 1.0: test failures</span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="plaintext"> seqan2                        | 892222 | normal    | seqan2: FTBFS on hppa: app_test_seqan_tcoffee fails on 2trx.mlcs.fasta</span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="plaintext"> seqan2                        | 917851 | important | seqan2 2.4.0+dfsg-9: FTBFS, alignment problem</span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="plaintext"> simpleitk                     | 949355 | serious   | simpleitk FTBFS: test failures</span>
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<pre style="margin: 0;">+<span id="LC266" 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>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="plaintext"> smalr                         | 938500 | serious   | smalr: Python2 removal in sid/bullseye</span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="plaintext"> smrtanalysis                  | 945737 | serious   | smrtanalysis: Python2 removal in sid/bullseye</span>
</pre>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="plaintext"> snakemake                     | 943956 | wishlist  | snakemake: please make the build reproducible</span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="plaintext"> sofa-framework                | 735099 | normal    | sofa-framework: FTBFS on sparc, powerpc (and ia64)</span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="plaintext"> sofa-framework                | 875184 | serious   | [sofa-framework] Future Qt4 removal from Buster</span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="plaintext"> spades                        | 853113 | normal    | spades: Fails to build with unhelpful error message in a "low" memory machine</span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"> spdlog                        | 952625 | serious   | libspdlog-dev: .pc Requires: fmt which doesn't have a .pc file, breaking pkg-config on spdlog.pc</span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="plaintext"> sprai                         | 943280 | normal    | sprai: Python2 removal in sid/bullseye</span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="plaintext"> sra-sdk                       | 943231 | normal    | sra-sdk: Python2 removal in sid/bullseye</span>
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<td class="diff-line-num new new_line" data-linenumber="280" 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="LC280" class="line" lang="plaintext"> sra-sdk                       | 952623 | serious   | sra-sdk: FTBFS: ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_entropy_init'</span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="plaintext"> sumaclust                     | 952093 | serious   | sumaclust: FTBFS: mtcompare_sumaclust.c:18:10: fatal error: libfasta/sequence.h: No such file or directory</span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="plaintext"> tree-puzzle                   | 806214 | normal    | tree-puzzle: Package fails test suite</span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="plaintext"> tree-puzzle                   | 890790 | minor     | tree-puzzle: Please provide autopkgtest</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="282" 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="289" 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">@@ -282,5 +289,5 @@ Last-Update: Wed, 26 Feb 2020 13:42:03 +0000</td>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="plaintext"> xmedcon                       | 671828 | normal    | xmedcon: Cannot open file with YBR photometric interpretation</span>
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<pre style="margin: 0;"> <span id="LC290" 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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<pre style="margin: 0;"> <span id="LC291" class="line" lang="plaintext"> xmedcon                       | 924017 | normal    | desktop entry</span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="plaintext">(<span class="idiff left right">195</span> rows)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">(<span class="idiff left right">204</span> rows)</span>
</pre>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="plaintext"></span></pre>
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