Re: BioPerl install failure OS X 10.11

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.

Try installing Bio::Root::Version instead of Bio::Perl, that should pull in the latest release which has most of these issues fixed.

Chris

Sent from my iPhone

On Oct 27, 2016, at 2:45 PM, Daniel Curtis OU <[email protected]<mailto:[email protected]>> wrote:

Good afternoon Chris,

I followed the instructions on the Github page<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=> and proceeded with the installation as follows-

perlbrew use perl-5.25.6

perl -MCPAN -e shell

cpan>install Module::Build
cpan>o conf prefer_installer MB
cpan>o conf commit
cpan>q

cpanm Bio::Perl

At this point the installation failed once again.

I tried forcing the install with

cpanm -f Bio::Perl

However the install failed again.

I've attached the log files and also made a submission<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=>. Do you know what the issue might be?

Thanks,





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

On Thu, Oct 27, 2016 at 11:32 AM, Daniel Curtis OU <[email protected]<mailto:[email protected]>> wrote:
Hi Chris,

I will follow the instructions on the github page you sent me and hopefully I can get Prokka running.

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.

Thanks for your feedback.

Best,




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

On Thu, Oct 27, 2016 at 8:08 AM, Fields, Christopher J <[email protected]<mailto:[email protected]>> wrote:
Hi Daniel,

Try these installation instructions:

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

We'll need to update the main bioperl.org<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=> 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<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=>

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]>


<Fail2_build.log>
<Fail1_build.log>

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