<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
</head>
<body dir="auto">
<div>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. </div>
<div id="AppleMailSignature"><br>
</div>
<div id="AppleMailSignature">Try installing Bio::Root::Version instead of Bio::Perl, that should pull in the latest release which has most of these issues fixed.</div>
<div id="AppleMailSignature"><br>
</div>
<div id="AppleMailSignature">Chris<br>
<br>
Sent from my iPhone</div>
<div><br>
On Oct 27, 2016, at 2:45 PM, Daniel Curtis OU <<a href="mailto:dancurtis87@ou.edu">dancurtis87@ou.edu</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<div dir="ltr">
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
Good afternoon Chris,</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
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-</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<b>perlbrew use perl-5.25.6</b></div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<b><br>
</b></div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<b>perl -MCPAN -e shell</b></div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<b><br>
</b></div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<b>cpan>install Module::Build</b></div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<b>cpan>o conf prefer_installer MB</b></div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<b>cpan>o conf commit</b></div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<b>cpan>q</b></div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<b><br>
</b></div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<b>cpanm Bio::Perl</b></div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
At this point the installation failed once again.</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
I tried forcing the install with</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<b>cpanm -f Bio::Perl</b></div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
However the install failed again.</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
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=">
submission</a>. Do you know what the issue might be?</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
Thanks,</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr">
<div><span style="font-family:trebuchet ms,sans-serif"><font size="2"><b>Daniel Curtis<br>
</b></font></span>
<div><span style="font-family:trebuchet ms,sans-serif"><font size="2"><b>Dept. of Microbiology<br>
</b></font></span></div>
<div><span style="font-family:trebuchet ms,sans-serif"><font size="2"><b>Institute for Environmental Genomics<br>
</b></font></span></div>
<div><span style="font-family:trebuchet ms,sans-serif"><font size="2"><b>The University of Oklahoma<br>
</b></font></span></div>
<div><b><span style="font-family:georgia,serif"><font size="2"><span style="font-family:tahoma,sans-serif"><span style="font-family:trebuchet ms,sans-serif"><a href="mailto:dancurtis87@ou.edu" target="_blank">dancurtis87@ou.edu</a></span></span></font></span></b></div>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">On Thu, Oct 27, 2016 at 11:32 AM, Daniel Curtis OU <span dir="ltr">
<<a href="mailto:dancurtis87@ou.edu" target="_blank">dancurtis87@ou.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
Hi Chris,</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
I will follow the instructions on the github page you sent me and hopefully I can get Prokka running. </div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
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.</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
Thanks for your feedback.</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
Best,</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_default" style="font-family:monospace,monospace;font-size:small">
<br>
</div>
<div class="gmail_extra"><span class=""><br clear="all">
<div>
<div class="m_-1896261080836797892gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr">
<div><span style="font-family:trebuchet ms,sans-serif"><font size="2"><b>Daniel Curtis<br>
</b></font></span>
<div><span style="font-family:trebuchet ms,sans-serif"><font size="2"><b>Dept. of Microbiology<br>
</b></font></span></div>
<div><span style="font-family:trebuchet ms,sans-serif"><font size="2"><b>Institute for Environmental Genomics<br>
</b></font></span></div>
<div><span style="font-family:trebuchet ms,sans-serif"><font size="2"><b>The University of Oklahoma<br>
</b></font></span></div>
<div><b><span style="font-family:georgia,serif"><font size="2"><span style="font-family:tahoma,sans-serif"><span style="font-family:trebuchet ms,sans-serif"><a href="mailto:dancurtis87@ou.edu" target="_blank">dancurtis87@ou.edu</a></span></span></font></span></b></div>
</div>
</div>
</div>
</div>
<br>
</span>
<div>
<div class="h5">
<div class="gmail_quote">On Thu, Oct 27, 2016 at 8:08 AM, Fields, Christopher J <span dir="ltr">
<<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif">
<div>
<div>Hi Daniel,</div>
<div><br>
</div>
<div>Try these installation instructions:</div>
<div><br>
</div>
<div><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/bio<wbr>perl-live/blob/master/INSTALL.<wbr>md</a></div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>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:</div>
<div><br>
</div>
<div><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/bio<wbr>perl-live/issues</a></div>
<div><br>
</div>
<div>To be honest I haven’t seen this pop up as an issue before.</div>
<div><br>
</div>
<div>chris</div>
<div>
<div id="m_-1896261080836797892m_-6343563035915285416MAC_OUTLOOK_SIGNATURE"></div>
</div>
</div>
<div><br>
</div>
<span id="m_-1896261080836797892m_-6343563035915285416OLK_SRC_BODY_SECTION">
<div style="font-family:Calibri;font-size:12pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">
<span style="font-weight:bold">From: </span><<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>
<span style="font-weight:bold">Date: </span>Thursday, October 27, 2016 at 7:40 AM<br>
<span style="font-weight:bold">To: </span>Chris Fields <<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>><br>
<span style="font-weight:bold">Subject: </span>BioPerl install failure OS X 10.11<br>
</div>
<div>
<div class="m_-1896261080836797892h5">
<div><br>
</div>
<div>
<div>
<div dir="ltr">
<div style="font-family:monospace,monospace;font-size:small">Good morning Dr. Fields,</div>
<div style="font-family:monospace,monospace;font-size:small"><br>
</div>
<div style="font-family:monospace,monospace;font-size:small">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. </div>
<div style="font-family:monospace,monospace;font-size:small"><br>
</div>
<div style="font-family:monospace,monospace;font-size:small">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-</div>
<div style="font-family:monospace,monospace;font-size:small"><br>
</div>
<div style="font-family:monospace,monospace;font-size:small">
<div><b>Test Summary Report</b></div>
<div><b>-------------------</b></div>
<div><b>t/SeqIO/Splicedseq.t (Wstat: 512 Tests: 1 Failed: 0)</b></div>
<div><b> Non-zero exit status: 2</b></div>
<div><b> Parse errors: Bad plan. You planned 19 tests but ran 1.</b></div>
<div><b>t/SeqIO/phd.t (Wstat: 65280 Tests: 2 Failed: 2)</b></div>
<div><b> Failed tests: 1-2</b></div>
<div><b> Non-zero exit status: 255</b></div>
<div><b> Parse errors: Bad plan. You planned 21 tests but ran 2.</b></div>
<div><b>t/Tools/Alignment/Consed.t (Wstat: 256 Tests: 15 Failed: 1)</b></div>
<div><b> Failed test: 1</b></div>
<div><b> Non-zero exit status: 1</b></div>
<div><b>t/Tools/SiRNA.t (Wstat: 65280 Tests: 5 Failed: 0)</b></div>
<div><b> Non-zero exit status: 255</b></div>
<div><b> Parse errors: Bad plan. You planned 11 tests but ran 5.</b></div>
<div><b>Files=334, Tests=18602, 84 wallclock secs ( 2.42 usr 0.92 sys + 72.51 cusr 7.37 csys = 83.22 CPU)</b></div>
<div><b>Result: FAIL</b></div>
<div><b>Failed 4/334 test programs. 3/18602 subtests failed.</b></div>
<div><b> CJFIELDS/BioPerl-1.6.924.tar.g<wbr>z</b></div>
<div><b> ./Build test -- NOT OK</b></div>
<div><b>//hint// to see the cpan-testers results for installing this module, try:</b></div>
<div><b> reports CJFIELDS/BioPerl-1.6.924.tar.g<wbr>z</b></div>
<div><b>Failed during this command:</b></div>
<div><b> CJFIELDS/BioPerl-1.6.924.tar.<wbr>gz : make_test NO</b></div>
</div>
<div style="font-family:monospace,monospace;font-size:small"><br>
</div>
<div style="font-family:monospace,monospace;font-size:small"><br>
</div>
<div style="font-family:monospace,monospace;font-size:small">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?<br>
</div>
<div style="font-family:monospace,monospace;font-size:small"><br>
</div>
<div style="font-family:monospace,monospace;font-size:small">I'd appreciate any guidance you have to offer.</div>
<div style="font-family:monospace,monospace;font-size:small"><br>
</div>
<div style="font-family:monospace,monospace;font-size:small">Thank you,</div>
<br clear="all">
<div>
<div class="m_-1896261080836797892m_-6343563035915285416gmail_signature">
<div dir="ltr">
<div><span style="font-family:"trebuchet ms",sans-serif"><font size="2"><b>Daniel Curtis<br>
</b></font></span>
<div><span style="font-family:"trebuchet ms",sans-serif"><font size="2"><b>Dept. of Microbiology<br>
</b></font></span></div>
<div><span style="font-family:"trebuchet ms",sans-serif"><font size="2"><b>Institute for Environmental Genomics<br>
</b></font></span></div>
<div><span style="font-family:"trebuchet ms",sans-serif"><font size="2"><b>The University of Oklahoma<br>
</b></font></span></div>
<div><b><span style="font-family:georgia,serif"><font size="2"><span style="font-family:tahoma,sans-serif"><span style="font-family:"trebuchet ms",sans-serif"><a href="mailto:dancurtis87@ou.edu" target="_blank">dancurtis87@ou.edu</a></span></span></font></span></b></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</span></div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
<blockquote type="cite">
<div><Fail2_build.log></div>
</blockquote>
<blockquote type="cite">
<div><Fail1_build.log></div>
</blockquote>
</body>
</html>