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<div>Hi Daniel,</div>
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<div>Try these installation instructions:</div>
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<div><a href="https://github.com/bioperl/bioperl-live/blob/master/INSTALL.md">https://github.com/bioperl/bioperl-live/blob/master/INSTALL.md</a></div>
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<div>We'll need to update the main bioperl.org instructions to reflect this updated version; this apparently fell through the cracks, though the main site’s installation procedure should still work. </div>
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<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>
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<div><a href="https://github.com/bioperl/bioperl-live/issues">https://github.com/bioperl/bioperl-live/issues</a></div>
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<div>To be honest I haven’t seen this pop up as an issue before.</div>
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<div>chris</div>
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<span style="font-weight:bold">From: </span><<a href="mailto:dancurtis87@gmail.com">dancurtis87@gmail.com</a>> on behalf of Daniel Curtis OU <<a href="mailto:dancurtis87@ou.edu">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">cjfields@illinois.edu</a>><br>
<span style="font-weight:bold">Subject: </span>BioPerl install failure OS X 10.11<br>
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Good morning Dr. Fields,</div>
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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="> Prokka</a> but
the installation fails. </div>
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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=">these
instructions</a> I got the following error-</div>
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<div class="gmail_default"><b>Test Summary Report</b></div>
<div class="gmail_default"><b>-------------------</b></div>
<div class="gmail_default"><b>t/SeqIO/Splicedseq.t (Wstat: 512 Tests: 1 Failed: 0)</b></div>
<div class="gmail_default"><b> Non-zero exit status: 2</b></div>
<div class="gmail_default"><b> Parse errors: Bad plan. You planned 19 tests but ran 1.</b></div>
<div class="gmail_default"><b>t/SeqIO/phd.t (Wstat: 65280 Tests: 2 Failed: 2)</b></div>
<div class="gmail_default"><b> Failed tests: 1-2</b></div>
<div class="gmail_default"><b> Non-zero exit status: 255</b></div>
<div class="gmail_default"><b> Parse errors: Bad plan. You planned 21 tests but ran 2.</b></div>
<div class="gmail_default"><b>t/Tools/Alignment/Consed.t (Wstat: 256 Tests: 15 Failed: 1)</b></div>
<div class="gmail_default"><b> Failed test: 1</b></div>
<div class="gmail_default"><b> Non-zero exit status: 1</b></div>
<div class="gmail_default"><b>t/Tools/SiRNA.t (Wstat: 65280 Tests: 5 Failed: 0)</b></div>
<div class="gmail_default"><b> Non-zero exit status: 255</b></div>
<div class="gmail_default"><b> Parse errors: Bad plan. You planned 11 tests but ran 5.</b></div>
<div class="gmail_default"><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 class="gmail_default"><b>Result: FAIL</b></div>
<div class="gmail_default"><b>Failed 4/334 test programs. 3/18602 subtests failed.</b></div>
<div class="gmail_default"><b> CJFIELDS/BioPerl-1.6.924.tar.<wbr>gz</b></div>
<div class="gmail_default"><b> ./Build test -- NOT OK</b></div>
<div class="gmail_default"><b>//hint// to see the cpan-testers results for installing this module, try:</b></div>
<div class="gmail_default"><b> reports CJFIELDS/BioPerl-1.6.924.tar.<wbr>gz</b></div>
<div class="gmail_default"><b>Failed during this command:</b></div>
<div class="gmail_default"><b> CJFIELDS/BioPerl-1.6.924.tar.<wbr>gz : make_test NO</b></div>
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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>
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I'd appreciate any guidance you have to offer.</div>
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Thank you,</div>
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<div><span style="font-family:"trebuchet ms",sans-serif"><font size="2"><b>Daniel Curtis<br>
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<div><span style="font-family:"trebuchet ms",sans-serif"><font size="2"><b>Dept. of Microbiology<br>
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<div><span style="font-family:"trebuchet ms",sans-serif"><font size="2"><b>Institute for Environmental Genomics<br>
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<div><span style="font-family:"trebuchet ms",sans-serif"><font size="2"><b>The University of Oklahoma<br>
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<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>
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