[Bioperl-l] Bioperl installation help

[Fields, Christopher J]

For some reason you are trying to install an older version of BioPerl; try installing Bio::Perl (or one of the core modules).  This should automatically install the latest version from CPAN.  My guess is this will address some of the issues.  However, w/o actually seeing what tests failed we can't help.

Also, if you are only interested in running local jobs, install BioPerl locally, or just grab the dist and add it to PERL5LIB.  There are instructions in the installation docs for that.  You can also use cpanm (cpanminus) to install things locally as well, it's highly recommended and much easier than cpan.

chris

On Nov 14, 2011, at 7:39 PM, Christel Chehoud wrote:

> Dear BioPerl,
> Thank you for creating such useful code. Unfortunately, every time I
> try to install Bioperl, it takes me a long time and is a challenging
> ordeal :( I am a new MAC user and was not able to download bioperl
> using CPAN. Here is the error I am getting:
> 
> ERROR: Can't create '/usr/local/bin'
> Do not have write permissions on '/usr/local/bin'
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> at /Users/Christel/.cpan/build/BioPerl-1.6.0-DiZ0rN/Bio/Root/Build.pm line 902
>  CJFIELDS/BioPerl-1.6.0.tar.gz
>  ./Build install  -- NOT OK
> ----
>  You may have to su to root to install the package
>  (Or you may want to run something like
>    o conf make_install_make_command 'sudo make'
>  to raise your permissions.Warning (usually harmless): 'YAML' not
> installed, will not store persistent state
> Failed during this command:
> CMUNGALL/Data-Stag-0.11.tar.gz               : make NO
> CJFIELDS/BioPerl-1.6.0.tar.gz                : make_test FAILED but
> failure ignored because 'force' in effect
> 
> 
> so I did:
> cpan> o conf make_install_make_command 'sudo make'
> followed by
> cpan> o conf commit
> 
> and started over..I got the same number of errors as last time (so I
> decided not to force install this time). do you have any suggestions:
> 
> 63 tests and 305 subtests skipped.
> Failed 11/329 test scripts. 981/17708 subtests failed.
> Files=329, Tests=17708, 127 wallclock secs (104.69 cusr + 12.51 csys =
> 117.20 CPU)
> Failed 11/329 test programs. 981/17708 subtests failed.
>  CJFIELDS/BioPerl-1.6.1.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module, try:
>  reports CJFIELDS/BioPerl-1.6.1.tar.gz
> Warning (usually harmless): 'YAML' not installed, will not store
> persistent state
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
> CMUNGALL/Data-Stag-0.11.tar.gz               : make NO
> FLORA/ExtUtils-Manifest-1.60.tar.gz          : make NO
> CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO
> 
> 
> Thanks a lot for your time and help.  I appreciate it.
> 
> Thank you,
> Christel
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l