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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/trinityrnaseq">Debian Med / trinityrnaseq</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/c848a0473bb29b078484f782ac7fb59f6a7b2852">c848a047</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-10-09T10:46:51+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable more features and tests with r-cran-{argparse,dexseq} & tabix
</pre>
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<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/c450962e5f0a2c6200d46bfbb8e0bf1b8a796346">c450962e</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-10-09T15:17:31+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release 2.11.0+dfsg-1
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<h4>6 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="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#c09a689737a512e48ae26e435a69f8ff8fb69286">
debian/patches/skip_blat
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<li class="file-stats">
<a href="#94af5ac81c4aa36293c5d1cb777bba18e1c2a1ab">
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−
debian/patches/skip_r-bioc-dexseq
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<li class="file-stats">
<a href="#2bcf4d68c971c9bcc6743448d4d08161d7b393a9">
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−
debian/patches/skip_r-cran-argpase
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/6c20b127f9edc81ce924ae43bd7782fb4d8e9412...c450962e5f0a2c6200d46bfbb8e0bf1b8a796346#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">trinityrnaseq (2.11.0+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">trinityrnaseq (2.11.0+dfsg-1) <span class="idiff left right">unstable</span>; 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"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Fix gcc-10 build issue</span>
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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">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Closes: #966876</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<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">@@ -9,14 +8,14 @@ trinityrnaseq (2.11.0+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> *.jars</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Remove redundant debian/gbp.conf</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Remove __pycache__ from installed package</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> FIXME: seqtk-trinity is missing and thus autopkgtest fails</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Correct location of bamsifter installation</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * debian/patches/fix_system_paths: fix expected path for ParaFly</span>
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<td class="diff-line-num old_line" data-linenumber="17" 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"> * debian/patches/update-paths: fix paths to Butterfly.jar</span>
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<td class="diff-line-num new old_line" data-linenumber="18" 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="LC16" class="line" lang="plaintext"> * Enable more features and tests with r-cran-{argparse,dexseq} & tabix</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> -- <span class="idiff left right">Andreas Tille <tille@debian.org> Wed, 05 Aug 2020 12:44:59</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> -- <span class="idiff left right">Michael R. Crusoe <crusoe@debian.org> Fri, 09 Oct 2020 15:13:36</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">trinityrnaseq (2.10.0+dfsg-1) unstable; urgency=medium</span>
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<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/6c20b127f9edc81ce924ae43bd7782fb4d8e9412...c450962e5f0a2c6200d46bfbb8e0bf1b8a796346#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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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">@@ -37,10 +37,11 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> hisat2,</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> subread,</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> kallisto,</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> python3-hisat2</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"># r-cran-argparse,</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> python3-hisat2,</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> r-cran-argparse,</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> r-bioc-dexseq,</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> tabix</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"># r-cran-goplot,</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"># r-bioc-dexseq,</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"># r-bioc-glimma,</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"># r-bioc-tximportdata</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Standards-Version: 4.5.0</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">@@ -92,15 +93,16 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> hisat2,</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> subread,</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> kallisto,</span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext"> python3-hisat2</span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext"><span class="idiff left right">#</span> r-cran-argparse,</span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext"><span class="idiff left right"># r-cran-goplot,</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> python3-hisat2<span class="idiff left right">,</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> r-cran-argparse,</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"><span class="idiff left right"> r-cran-goplot</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"># r-bioc-dexseq,</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"># r-bioc-glimma</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">Recommends: ${java:Recommends},</span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> trinityrnaseq-examples,</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> r-cran-tidyverse,</span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext"> picard-tools</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> picard-tools,</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> tabix</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext">Suggests: collectl,</span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"> r-bioc-tximportdata</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext">Description: RNA-Seq De novo Assembly</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/6c20b127f9edc81ce924ae43bd7782fb4d8e9412...c450962e5f0a2c6200d46bfbb8e0bf1b8a796346#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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">@@ -15,8 +15,6 @@ seqtk-trinity-hardening</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">skip_gatk_test</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">skip_tximportData_tests</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">submake</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">skip_r-cran-argpase</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">skip_r-bioc-dexseq</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">skip_blat</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">fix-gcc-10.patch</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">bamsifter_build</span></pre>
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<li id="c09a689737a512e48ae26e435a69f8ff8fb69286">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/6c20b127f9edc81ce924ae43bd7782fb4d8e9412...c450962e5f0a2c6200d46bfbb8e0bf1b8a796346#c09a689737a512e48ae26e435a69f8ff8fb69286"><strong>debian/patches/skip_blat</strong></a>
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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">@@ -2,9 +2,9 @@ Author: Michael R. Crusoe <michael.crusoe></td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: skip tests with a dependency on blat</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -9,8 +9,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> test_PtR \</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -11,8 +11,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> test_SuperTranscript \</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> test_GOplot \</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> test_TPM_weighted_gene_length \</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-test_ExN50 \</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-test_Assembly_DiffReadFormattings</span></span>
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<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/6c20b127f9edc81ce924ae43bd7782fb4d8e9412...c450962e5f0a2c6200d46bfbb8e0bf1b8a796346#94af5ac81c4aa36293c5d1cb777bba18e1c2a1ab"><strong>debian/patches/skip_r-bioc-dexseq</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe></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">Description: skip tests with a dependency on r-bioc-dexseq</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -7,7 +7,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> test_GOSeq_trinotate_pipe \</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> test_profiling_report \</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> test_PtR \</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-test_DTU \</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> test_SuperTranscript \</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> test_TPM_weighted_gene_length \</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> test_ExN50 \</span></pre>
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<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/6c20b127f9edc81ce924ae43bd7782fb4d8e9412...c450962e5f0a2c6200d46bfbb8e0bf1b8a796346#2bcf4d68c971c9bcc6743448d4d08161d7b393a9"><strong>debian/patches/skip_r-cran-argpase</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: skip tests with a dependency on r-cran-argparse</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> </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;">-DIRS = Spombe_runGOseqOnly test_GOplot Spombe_analyzeDiffExprWithGOseq</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;">+DIRS = Spombe_runGOseqOnly Spombe_analyzeDiffExprWithGOseq</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> test:</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -9,7 +9,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> test_PtR \</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> test_DTU \</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> test_SuperTranscript \</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-test_GOplot \</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> test_TPM_weighted_gene_length \</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> test_ExN50 \</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> test_Assembly_DiffReadFormattings</span></pre>
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