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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Hi Daniel,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Just a note, please keep the bioperl-l mail list copied as someone else might chime in if I don’t immediately reply.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Judging by the installation it appears that the tools are already installed (note all the lines indicating that the installation is being skipped). You need to specify something
like ‘cpanm -f --reinstall Bio::Root::Version’ to make it reinstall everything. To be honest I would think a forced installation would suffice to overwrite the current one, but maybe this is a fail-safe to be more explicit if a full reinstallation is needed.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Also, I wouldn’t mess with CPAN settings while using perlbrew (I’ve never seen anyone need to adjust them prior to a run). Keep in mind that the cpan client and cpanm are not
the same thing, the latter is designed as a much simpler installer, akin to Python’s pip.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Also remember that odd-numbered perl releases are considered ‘developer’ releases, and may break. So far CPAN tests for this version seem fine though.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">chris<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">From: </span>
</b><span style="font-family:Calibri;color:black"><<a href="mailto:dancurtis87@gmail.com">dancurtis87@gmail.com</a>> on behalf of Daniel Curtis OU<br>
<b>Date: </b>Tuesday, November 1, 2016 at 3:31 PM<br>
<b>To: </b>Chris Fields<br>
<b>Subject: </b>Re: BioPerl install failure OS X 10.11<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Good afternoon Dr. Fields,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">I've tried the following for the installation <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">cpan>o conf prefer_installer MB</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">cpan>o conf prefer_installer commit</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">cpanm Bio::Root::Version</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">however the installation failed after running for a few minutes<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">I then tried forcing the installation with<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">cpamn -f Bio::Root::Version</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">however once again the installation failed. I've attached the .log file. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Should I try the installation with an older version of Perl? There was a suggestion on the GitHub discussion forum to do so, I'm still using 5.25.6. I can also just wait till you push out the
fix you have in the pipeline.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Thanks again for all your help.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Daniel Curtis</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Dept. of Microbiology</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Institute for Environmental Genomics</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">The University of Oklahoma</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black"><a href="mailto:dancurtis87@ou.edu" target="_blank">dancurtis87@ou.edu</a></span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">On Thu, Oct 27, 2016 at 3:31 PM, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Okay, that helps, I'll have a look. One thing that pops out is the version being installed (1.6.924) is not the latest, but this is a known bug that I recently pushed a fix
for and should be ready for the next release. Also, recent versions of Perl don't have CGI as part of the core install anymore. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Try installing Bio::Root::Version instead of Bio::Perl, that should pull in the latest release which has most of these issues fixed.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Chris<br>
<br>
Sent from my iPhone<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.5pt;font-family:Calibri;color:black"><br>
On Oct 27, 2016, at 2:45 PM, Daniel Curtis OU <<a href="mailto:dancurtis87@ou.edu" target="_blank">dancurtis87@ou.edu</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Good afternoon Chris,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">I followed the instructions on the
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl-2Dlive_blob_master_INSTALL.md&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=rsUdFdK6EF8fFM_5MHgSVidEznIVCGGrOVVV7t-dgpA&s=Y0sVSPQbXKhU7ROpz2ZUQd24Hc1r_1Gs4y35Rk1nf6c&e=" target="_blank">
Github page</a> and proceeded with the installation as follows-<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">perlbrew use perl-5.25.6</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">perl -MCPAN -e shell</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">cpan>install Module::Build</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">cpan>o conf prefer_installer MB</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">cpan>o conf commit</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">cpan>q</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">cpanm Bio::Perl</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">At this point the installation failed once again.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">I tried forcing the install with<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">cpanm -f Bio::Perl</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">However the install failed again.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">I've attached the log files and also made a
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl-2Dlive_issues&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=rsUdFdK6EF8fFM_5MHgSVidEznIVCGGrOVVV7t-dgpA&s=hfL4g7Z54wYy8JaenP1Ag4W7O9uZIkDprep-vnLDVhk&e=" target="_blank">
submission</a>. Do you know what the issue might be?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Thanks,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Daniel Curtis</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Dept. of Microbiology</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Institute for Environmental Genomics</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">The University of Oklahoma</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black"><a href="mailto:dancurtis87@ou.edu" target="_blank">dancurtis87@ou.edu</a></span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">On Thu, Oct 27, 2016 at 11:32 AM, Daniel Curtis OU <<a href="mailto:dancurtis87@ou.edu" target="_blank">dancurtis87@ou.edu</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Hi Chris,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">I will follow the instructions on the github page you sent me and hopefully I can get Prokka running. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Will upload the the test output as a bug report too. With regards to the test output, is there a log file that is generally created when such installations are taking place? If so where can
I find it? I did save the terminal output as a text file since I'm still learning how to navigate the unix shell.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Thanks for your feedback.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Best,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Daniel Curtis</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Dept. of Microbiology</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Institute for Environmental Genomics</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">The University of Oklahoma</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black"><a href="mailto:dancurtis87@ou.edu" target="_blank">dancurtis87@ou.edu</a></span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">On Thu, Oct 27, 2016 at 8:08 AM, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Hi Daniel,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Try these installation instructions:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl-2Dlive_blob_master_INSTALL.md&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=rsUdFdK6EF8fFM_5MHgSVidEznIVCGGrOVVV7t-dgpA&s=Y0sVSPQbXKhU7ROpz2ZUQd24Hc1r_1Gs4y35Rk1nf6c&e=" target="_blank">https://github.com/bioperl/bioperl-live/blob/master/INSTALL.md</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">We'll need to update the main
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__bioperl.org&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=rsUdFdK6EF8fFM_5MHgSVidEznIVCGGrOVVV7t-dgpA&s=BbHUvgtYfXWSiyixeriNdaTAb6UkpCUvVNdXTybkISc&e=" target="_blank">
bioperl.org</a> instructions to reflect this updated version; this apparently fell through the cracks, though the main site’s installation procedure should still work. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">Based on the failures you shouldn’t have a problem with a forced installation, but it would be extremely helpful if you can post the complete test output as a bug report here:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl-2Dlive_issues&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=rsUdFdK6EF8fFM_5MHgSVidEznIVCGGrOVVV7t-dgpA&s=hfL4g7Z54wYy8JaenP1Ag4W7O9uZIkDprep-vnLDVhk&e=" target="_blank">https://github.com/bioperl/bioperl-live/issues</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">To be honest I haven’t seen this pop up as an issue before.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Calibri;color:black">chris<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">From: </span>
</b><span style="font-family:Calibri;color:black"><<a href="mailto:dancurtis87@gmail.com" target="_blank">dancurtis87@gmail.com</a>> on behalf of Daniel Curtis OU <<a href="mailto:dancurtis87@ou.edu" target="_blank">dancurtis87@ou.edu</a>><br>
<b>Date: </b>Thursday, October 27, 2016 at 7:40 AM<br>
<b>To: </b>Chris Fields <<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>><br>
<b>Subject: </b>BioPerl install failure OS X 10.11<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Good morning Dr. Fields,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">I'm trying to install BioPerl so as to be able to use<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tseemann_prokka&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=PyPCknQANCJDgVyMCzSzC4CVDkqF6joFM4rCMOnrDgw&s=Gy1o5DeoJfgiCP2vyQ96HucL3oLCnvbAi8vFf3ZYOnU&e=" target="_blank"> Prokka</a> but
the installation fails. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">I installed Perl 5.25.6 using perlbrew and after installation as per <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__bioperl.org_INSTALL.html&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=PyPCknQANCJDgVyMCzSzC4CVDkqF6joFM4rCMOnrDgw&s=VCQPF1u2oACUWmUfFZUMGr_3VCoL98dlWzWeZLwyxO8&e=" target="_blank">these
instructions</a> I got the following error-<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">Test Summary Report</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">-------------------</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">t/SeqIO/Splicedseq.t (Wstat: 512 Tests: 1 Failed: 0)</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> Non-zero exit status: 2</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> Parse errors: Bad plan. You planned 19 tests but ran 1.</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">t/SeqIO/phd.t (Wstat: 65280 Tests: 2 Failed: 2)</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> Failed tests: 1-2</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> Non-zero exit status: 255</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> Parse errors: Bad plan. You planned 21 tests but ran 2.</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">t/Tools/Alignment/Consed.t (Wstat: 256 Tests: 15 Failed: 1)</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> Failed test: 1</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> Non-zero exit status: 1</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">t/Tools/SiRNA.t (Wstat: 65280 Tests: 5 Failed: 0)</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> Non-zero exit status: 255</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> Parse errors: Bad plan. You planned 11 tests but ran 5.</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">Files=334, Tests=18602, 84 wallclock secs ( 2.42 usr 0.92 sys + 72.51 cusr 7.37 csys = 83.22 CPU)</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">Result: FAIL</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">Failed 4/334 test programs. 3/18602 subtests failed.</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> CJFIELDS/BioPerl-1.6.924.tar.gz</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> ./Build test -- NOT OK</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">//hint// to see the cpan-testers results for installing this module, try:</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> reports CJFIELDS/BioPerl-1.6.924.tar.gz</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black">Failed during this command:</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Courier;color:black"> CJFIELDS/BioPerl-1.6.924.tar.gz : make_test NO</span></b><span style="font-family:Courier;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Should I try forcing the install and see if Prokka will install correctly after that? Have you come across known issues with Prokka following a forced BioPerl 1.6.924 installation?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">I'd appreciate any guidance you have to offer.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Courier;color:black">Thank you,<o:p></o:p></span></p>
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<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Daniel Curtis</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Dept. of Microbiology</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">Institute for Environmental Genomics</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black">The University of Oklahoma</span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:Helvetica;color:black"><a href="mailto:dancurtis87@ou.edu" target="_blank">dancurtis87@ou.edu</a></span></b><span style="font-size:10.5pt;font-family:Calibri;color:black"><o:p></o:p></span></p>
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