[Bioperl-l] Bioperl installation help

Dave Messina David.Messina at sbc.su.se
Wed Nov 16 12:01:49 EST 2011

Hi Christel,

Sorry to hear you're having trouble with the installation.

It looks like these modules aren't getting installed and are causing the
failed tests:
CMUNGALL/Data-Stag-0.11.tar.gz               : make NO
FLORA/ExtUtils-Manifest-1.60.tar.gz          : make NO

I would try installing those separately via CPAN first and then trying
again to install BioPerl.

Also, it was a good idea to set the make_install_make_command option to
CPAN, and that should have worked. Unfortunately, there's another
installation system called Module::Build that has its own option which may
need to be set:
cpan> o conf mbuild_install_build_command 'sudo ./Build'

That being said, I would suggest you grab the latest version of BioPerl
from github instead of using v1.6.1 from CPAN, which is fairly out of date
at this point.

And unless you're planning to use BioPerl with GBrowse or Bio::Graphics,
there's another, simpler way to get BioPerl up and running (assuming you
have all the prerequisites like Data::Stag installed):

See "Don't want to install BioPerl?" here:


On Tue, Nov 15, 2011 at 02:39, Christel Chehoud <cchehoud at gmail.com> 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
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