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<div>My guess is that the errors below are fixed in 1.7.0, but the CPAN installation isn’t working correctly due to a CPAN indexing issue:</div>
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<div><a href="https://github.com/bioperl/bioperl-live/issues/87">https://github.com/bioperl/bioperl-live/issues/87</a></div>
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<div>This appeared to be fixed over the summer but cropped up again in the last release; I have a possible fix which will be pushed out this week (I’m also waiting on possible breakage with NCBI-related remote servers, so holding a bit until then).</div>
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<div>chris</div>
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<span style="font-weight:bold">From: </span>Liam Elbourne<br>
<span style="font-weight:bold">Date: </span>Thursday, October 27, 2016 at 6:00 PM<br>
<span style="font-weight:bold">To: </span>Chris Fields<br>
<span style="font-weight:bold">Cc: </span>Daniel Curtis OU, BioPerl List<br>
<span style="font-weight:bold">Subject: </span>Re: [Bioperl-l] BioPerl install failure OS X 10.11<br>
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Hi Daniel,
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<div class="">You won’t have any problems with Prokka, I’m using it with a forced installation on sierra currently, but I’ve run it with every version of the MacOS since it came out, all with forced installations of bioper (I’ve never run an unforced version
of bioperl, very rarely run into any problems, and never any that weren’t kludgeable).</div>
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<div class="">Regards,</div>
<div class="">Liam.</div>
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<div class="">On 28 Oct. 2016, at 12:08 am, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" class="">cjfields@illinois.edu</a>> wrote:</div>
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<div class="">Hi Daniel,</div>
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<div class="">Try these installation instructions:</div>
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<div class=""><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=cWGmX5jumvjiXANBu_Kj4tBhxn7Fs7O1K8XJwr_wnw8&s=y49pokQHAvJJDU1itmtzs4SmCzh2M3vFPSG-4jcy4w8&e=" class="">https://github.com/bioperl/bioperl-live/blob/master/INSTALL.md</a></div>
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<div class="">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=cWGmX5jumvjiXANBu_Kj4tBhxn7Fs7O1K8XJwr_wnw8&s=WWUlDJ9vRRoIkLLcYoVDOr9wLQ6lXHJsOvCtd1lBRPU&e=" class="">
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>
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<div class="">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 class=""><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=cWGmX5jumvjiXANBu_Kj4tBhxn7Fs7O1K8XJwr_wnw8&s=W_b0BDubksWUtITnlZZoU00cc1Jn-NAQOGVpycIbxE8&e=" class="">https://github.com/bioperl/bioperl-live/issues</a></div>
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<div class="">To be honest I haven’t seen this pop up as an issue before.</div>
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<div class="">chris</div>
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<span style="font-weight:bold" class="">From: </span><<a href="mailto:dancurtis87@gmail.com" class="">dancurtis87@gmail.com</a>> on behalf of Daniel Curtis OU <<a href="mailto:dancurtis87@ou.edu" class="">dancurtis87@ou.edu</a>><br class="">
<span style="font-weight:bold" class="">Date: </span>Thursday, October 27, 2016 at 7:40 AM<br class="">
<span style="font-weight:bold" class="">To: </span>Chris Fields <<a href="mailto:cjfields@illinois.edu" class="">cjfields@illinois.edu</a>><br class="">
<span style="font-weight:bold" class="">Subject: </span>BioPerl install failure OS X 10.11<br class="">
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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=" class=""> 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=" class="">these
instructions</a> I got the following error-</div>
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<div class="gmail_default"><b class="">Test Summary Report</b></div>
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<div class="gmail_default"><b class="">t/SeqIO/Splicedseq.t (Wstat: 512 Tests: 1 Failed: 0)</b></div>
<div class="gmail_default"><b class=""> Non-zero exit status: 2</b></div>
<div class="gmail_default"><b class=""> Parse errors: Bad plan. You planned 19 tests but ran 1.</b></div>
<div class="gmail_default"><b class="">t/SeqIO/phd.t (Wstat: 65280 Tests: 2 Failed: 2)</b></div>
<div class="gmail_default"><b class=""> Failed tests: 1-2</b></div>
<div class="gmail_default"><b class=""> Non-zero exit status: 255</b></div>
<div class="gmail_default"><b class=""> Parse errors: Bad plan. You planned 21 tests but ran 2.</b></div>
<div class="gmail_default"><b class="">t/Tools/Alignment/Consed.t (Wstat: 256 Tests: 15 Failed: 1)</b></div>
<div class="gmail_default"><b class=""> Failed test: 1</b></div>
<div class="gmail_default"><b class=""> Non-zero exit status: 1</b></div>
<div class="gmail_default"><b class="">t/Tools/SiRNA.t (Wstat: 65280 Tests: 5 Failed: 0)</b></div>
<div class="gmail_default"><b class=""> Non-zero exit status: 255</b></div>
<div class="gmail_default"><b class=""> Parse errors: Bad plan. You planned 11 tests but ran 5.</b></div>
<div class="gmail_default"><b class="">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 class="">Result: FAIL</b></div>
<div class="gmail_default"><b class="">Failed 4/334 test programs. 3/18602 subtests failed.</b></div>
<div class="gmail_default"><b class=""> CJFIELDS/BioPerl-1.6.924.tar.<wbr class="">gz</b></div>
<div class="gmail_default"><b class=""> ./Build test -- NOT OK</b></div>
<div class="gmail_default"><b class="">//hint// to see the cpan-testers results for installing this module, try:</b></div>
<div class="gmail_default"><b class=""> reports CJFIELDS/BioPerl-1.6.924.tar.<wbr class="">gz</b></div>
<div class="gmail_default"><b class="">Failed during this command:</b></div>
<div class="gmail_default"><b class=""> CJFIELDS/BioPerl-1.6.924.tar.<wbr class="">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 class="">
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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 class=""><span style="font-family:"trebuchet ms",sans-serif" class=""><font size="2" class=""><b class="">Daniel Curtis<br class="">
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<div class=""><span style="font-family:"trebuchet ms",sans-serif" class=""><font size="2" class=""><b class="">Dept. of Microbiology<br class="">
</b></font></span></div>
<div class=""><span style="font-family:"trebuchet ms",sans-serif" class=""><font size="2" class=""><b class="">Institute for Environmental Genomics<br class="">
</b></font></span></div>
<div class=""><span style="font-family:"trebuchet ms",sans-serif" class=""><font size="2" class=""><b class="">The University of Oklahoma<br class="">
</b></font></span></div>
<div class=""><b class=""><span style="font-family:georgia,serif" class=""><font size="2" class=""><span style="font-family:tahoma,sans-serif" class=""><span style="font-family:"trebuchet ms",sans-serif" class=""><a href="mailto:dancurtis87@ou.edu" target="_blank" class="">dancurtis87@ou.edu</a></span></span></font></span></b></div>
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