[Bioperl-l] BioPerl install failure OS X 10.11

Thu Nov 10 19:12:02 UTC 2016

Hi Daniel,

Just a note, please keep the bioperl-l mail list copied as someone else might chime in if I don’t immediately reply.

Judging by the installation it appears that the tools are already installed (note all the lines indicating that the installation is being skipped).  You need to specify something like ‘cpanm -f --reinstall Bio::Root::Version’ to make it reinstall everything.  To be honest I would think a forced installation would suffice to overwrite the current one, but maybe this is a fail-safe to be more explicit if a full reinstallation is needed.

Also, I wouldn’t mess with CPAN settings while using perlbrew (I’ve never seen anyone need to adjust them prior to a run).  Keep in mind that the cpan client and cpanm are not the same thing, the latter is designed as a much simpler installer, akin to Python’s pip.

Also remember that odd-numbered perl releases are considered ‘developer’ releases, and may break.  So far CPAN tests for this version seem fine though.

chris

From: <dancurtis87 at gmail.com<mailto:dancurtis87 at gmail.com>> on behalf of Daniel Curtis OU
Date: Tuesday, November 1, 2016 at 3:31 PM
To: Chris Fields
Subject: Re: BioPerl install failure OS X 10.11

Good afternoon Dr. Fields,

I've tried the following for the installation

cpan>o conf prefer_installer MB

cpan>o conf prefer_installer commit

cpanm Bio::Root::Version

however the installation failed after running for a few minutes

I then tried forcing the installation with

cpamn -f Bio::Root::Version

however once again the installation failed. I've attached the .log file.

Should I try the installation with an older version of Perl? There was a suggestion on the GitHub discussion forum to do so, I'm still using 5.25.6. I can also just wait till you push out the fix you have in the pipeline.

Thanks again for all your help.

Daniel Curtis
Dept. of Microbiology
Institute for Environmental Genomics
The University of Oklahoma
dancurtis87 at ou.edu<mailto:dancurtis87 at ou.edu>

On Thu, Oct 27, 2016 at 3:31 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:
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 <dancurtis87 at ou.edu<mailto:dancurtis87 at ou.edu>> 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
dancurtis87 at ou.edu<mailto:dancurtis87 at ou.edu>

On Thu, Oct 27, 2016 at 11:32 AM, Daniel Curtis OU <dancurtis87 at ou.edu<mailto:dancurtis87 at ou.edu>> 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
dancurtis87 at ou.edu<mailto:dancurtis87 at ou.edu>

On Thu, Oct 27, 2016 at 8:08 AM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> 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: <dancurtis87 at gmail.com<mailto:dancurtis87 at gmail.com>> on behalf of Daniel Curtis OU <dancurtis87 at ou.edu<mailto:dancurtis87 at ou.edu>>
Date: Thursday, October 27, 2016 at 7:40 AM
To: Chris Fields <cjfields at illinois.edu<mailto:cjfields at illinois.edu>>
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
dancurtis87 at ou.edu<mailto:dancurtis87 at ou.edu>

<Fail2_build.log>
<Fail1_build.log>

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