Re: BioPerl install failure OS X 10.11

Hi Daniel,

Try these installation instructions:

https://github.com/bioperl/bioperl-live/blob/master/INSTALL.md

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.

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:

https://github.com/bioperl/bioperl-live/issues

To be honest I haven’t seen this pop up as an issue before.

chris

From: <[email protected]<mailto:[email protected]>> on behalf of Daniel Curtis OU <[email protected]<mailto:[email protected]>>
Date: Thursday, October 27, 2016 at 7:40 AM
To: Chris Fields <[email protected]<mailto:[email protected]>>
Subject: BioPerl install failure OS X 10.11

Good morning Dr. Fields,

I'm trying to install BioPerl so as to be able to use Prokka<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=> but the installation fails.

I installed Perl 5.25.6 using perlbrew and after installation as per these instructions<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=> I got the following error-

Test Summary Report
-------------------
t/SeqIO/Splicedseq.t                 (Wstat: 512 Tests: 1 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 19 tests but ran 1.
t/SeqIO/phd.t                        (Wstat: 65280 Tests: 2 Failed: 2)
  Failed tests:  1-2
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 21 tests but ran 2.
t/Tools/Alignment/Consed.t           (Wstat: 256 Tests: 15 Failed: 1)
  Failed test:  1
  Non-zero exit status: 1
t/Tools/SiRNA.t                      (Wstat: 65280 Tests: 5 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 11 tests but ran 5.
Files=334, Tests=18602, 84 wallclock secs ( 2.42 usr  0.92 sys + 72.51 cusr  7.37 csys = 83.22 CPU)
Result: FAIL
Failed 4/334 test programs. 3/18602 subtests failed.
  CJFIELDS/BioPerl-1.6.924.tar.gz
  ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports CJFIELDS/BioPerl-1.6.924.tar.gz
Failed during this command:
 CJFIELDS/BioPerl-1.6.924.tar.gz              : make_test NO


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?

I'd appreciate any guidance you have to offer.

Thank you,

Daniel Curtis
Dept. of Microbiology
Institute for Environmental Genomics
The University of Oklahoma
[email protected]<mailto:[email protected]>

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