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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcbio">Debian Med / bcbio</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/1e5c05c402d8e7a25c7a71834491c3d016b24154">1e5c05c4</a></strong>
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<span>by Steffen Möller</span>
<i>at 2019-09-11T21:50:04Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update TODO - cthreadpool accepted, viennarna progressed</pre>
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<h4>1 changed file:</h4>
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<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
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<h4>Changes:</h4>
<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/bcbio/commit/1e5c05c402d8e7a25c7a71834491c3d016b24154#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" 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">@@ -43,10 +43,6 @@ package libjs-scribl (in new queue) (in crash space)</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="mosel"><span class="s1" style="color: #d14;"> A surprisingly neat JavaScript library to show genomic features</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed for DFSG-compliance of seqcluster</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="mosel"><span class="s1" style="color: #d14;">package cthreadpool (in new queue) (in crash space)</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/Pithikos/C-Thread-Pool/blob/master/thpool.h</span></span>
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<td class="diff-line-num old old_line" data-linenumber="48" 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="LC48" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed by ViennaRNA</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="mosel"><span class="s1" style="color: #d14;">Package MutliQC (in crash space) (in new queue)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/multiqc</span></span>
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<td class="diff-line-num old_line" data-linenumber="52" 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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<td class="diff-line-num new_line" data-linenumber="48" 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="LC48" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Addressed https://github.com/ewels/MultiQC/issues/800 by substuting</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" 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="50" 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">@@ -54,11 +50,25 @@ Package MutliQC (in crash space) (in new queue)</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The package was placed into contrib because of the dependency of its</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="mosel"><span class="s1" style="color: #d14;"> reports on external sources. For that reason and the remote depenency</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="mosel"><span class="s1" style="color: #d14;"> on ViennaRNA via seqcluster, also bcbio will be in contrib.</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"><span class="s1" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"><span class="s1" style="color: #d14;">package pyutilib (in new queue) (in crash space)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/PyUtilib/pyutilib</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/python-team/modules/pyutilib</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needed by pyomo for testing</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages just waiting for someone addressing the last mile for the upload</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="mosel"><span class="s1" style="color: #d14;">-------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="mosel"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="mosel"><span class="s1" style="color: #d14;">package viennarna (in crash space)</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/ViennaRNA/ViennaRNA</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/vienna-rna/blob/master/debian/changelog</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The package now has a custom license file - redistributable but non-free.</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed for testing seqcluster.</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Python and Perl packages are not tested, yet, not needed for seqcluster</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Package likely to be uploadable to non-free. Final checks needed.</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Documentation no longer builds with 2.4.14 would be nice to reactivate but not ultimately important for first upload.</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="mosel"></span>
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62
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="mosel"><span class="s1" style="color: #d14;">package pyomo (in crash space)</span></span>
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63
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/Pyomo/pyomo</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/science-team/pyomo</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" 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">@@ -66,11 +76,6 @@ package pyomo (in crash space)</td>
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66
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needed by optitype</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Status: Builds if errors in build time tests will be ignored</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="mosel"><span class="s1" style="color: #d14;">package pyutilib (in new queue) (in crash space)</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/PyUtilib/pyutilib</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/python-team/modules/pyutilib</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needed by pyomo for testing</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="mosel"><span class="s1" style="color: #d14;">package python-seqcluster (in crash space)</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/lpantano/seqcluster/</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/python-seqcluster</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="105" 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">@@ -100,17 +105,6 @@ package python-seqcluster (in crash space)</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="mosel"><span class="s1" style="color: #d14;"> apparently optional for bcbio: r-bioc-isomiRs - (needs r-bioc-DEGreport) all pre-depends except edgeR are in new</span></span>
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<td class="diff-line-num old_line" data-linenumber="101" 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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<td class="diff-line-num new_line" data-linenumber="106" 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="LC106" class="line" lang="mosel"><span class="s1" style="color: #d14;"> apparently optional for bcbio: install_github('</span><span class="n" style="color: #333;">rstudio</span><span class="p">/</span><span class="n" style="color: #333;">rmarkdown</span><span class="s1" style="color: #d14;">') -- this may be the same we have from CRAN - not checked</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="mosel"><span class="s1" style="color: #d14;">package viennarna (in crash space)</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/ViennaRNA/ViennaRNA</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/vienna-rna/blob/master/debian/changelog</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="mosel"><span class="s1" style="color: #d14;"> No idea about where exactly we stand with this.</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The package now has a custom license file - redistributable but non-free.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed for testing seqcluster.</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Steffen revisits ViennaRNA, will update to new upstream version this weekend</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Using current master not release because of erroneous commits of autogenerated files in 2.4.13 release source tree.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="111" 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="LC111" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Manual removal of folders along instructions in d/copyright</span></span>
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<td class="diff-line-num old old_line" data-linenumber="112" 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="LC112" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Python and Perl packages are not functional, yet, not needed for seqcluster</span></span>
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<td class="diff-line-num old old_line" data-linenumber="113" 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="LC113" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Waiting for acceptance of cthreadpool.</span></span>
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<td class="diff-line-num old_line" data-linenumber="114" 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="LC108" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages presumed easy to package</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="mosel"><span class="s1" style="color: #d14;">---------------------------------</span></span>
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