Re: BioPerl install failure OS X 10.11

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Re: BioPerl install failure OS X 10.11

Fields, Christopher J
Hi Daniel,

Try these installation instructions:


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:


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

chris

From: <[hidden email]> on behalf of Daniel Curtis OU <[hidden email]>
Date: Thursday, October 27, 2016 at 7:40 AM
To: Chris Fields <[hidden email]>
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 but the installation fails. 

I installed Perl 5.25.6 using perlbrew and after installation as per these instructions 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

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Re: BioPerl install failure OS X 10.11

Fields, Christopher J
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 <[hidden email]> wrote:

Good afternoon Chris,

I followed the instructions on the Github page 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. Do you know what the issue might be?

Thanks,





Daniel Curtis
Dept. of Microbiology
Institute for Environmental Genomics
The University of Oklahoma

On Thu, Oct 27, 2016 at 11:32 AM, Daniel Curtis OU <[hidden email]> 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

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

Try these installation instructions:


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:


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

chris

From: <[hidden email]> on behalf of Daniel Curtis OU <[hidden email]>
Date: Thursday, October 27, 2016 at 7:40 AM
To: Chris Fields <[hidden email]>
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 but the installation fails. 

I installed Perl 5.25.6 using perlbrew and after installation as per these instructions 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


<Fail2_build.log>
<Fail1_build.log>

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Re: BioPerl install failure OS X 10.11

Liam Elbourne-3
In reply to this post by Fields, Christopher J
Hi Daniel,

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).

Regards,
Liam.



On 28 Oct. 2016, at 12:08 am, Fields, Christopher J <[hidden email]> wrote:

Hi Daniel,

Try these installation instructions:


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:


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

chris

From: <[hidden email]> on behalf of Daniel Curtis OU <[hidden email]>
Date: Thursday, October 27, 2016 at 7:40 AM
To: Chris Fields <[hidden email]>
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 but the installation fails. 

I installed Perl 5.25.6 using perlbrew and after installation as per these instructions 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
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: BioPerl install failure OS X 10.11

Fields, Christopher J
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:


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).

chris

From: Liam Elbourne
Date: Thursday, October 27, 2016 at 6:00 PM
To: Chris Fields
Cc: Daniel Curtis OU, BioPerl List
Subject: Re: [Bioperl-l] BioPerl install failure OS X 10.11

Hi Daniel,

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).

Regards,
Liam.



On 28 Oct. 2016, at 12:08 am, Fields, Christopher J <[hidden email]> wrote:

Hi Daniel,

Try these installation instructions:


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:


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

chris

From: <[hidden email]> on behalf of Daniel Curtis OU <[hidden email]>
Date: Thursday, October 27, 2016 at 7:40 AM
To: Chris Fields <[hidden email]>
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 but the installation fails. 

I installed Perl 5.25.6 using perlbrew and after installation as per these instructions 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
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l