[Bioperl-l] problem installing BioPerl

[Scott Cain]

Hi Daniela,

I believe there is a Debian repository for BioPerl that you can use with
Ubuntu.  Just executing

  sudo apt-get install libbio-perl-perl

will probably do the trick.

If you don't want to do that, the most immiediate problem you have is that
IO::String isn't installed.  Try

  cpan> install IO::String

before installing BioPerl (it seems like it should have handled that
automatically and the fact that it didn't may indicate a deeper problem).

Scott



On Fri, Aug 23, 2013 at 5:44 PM, Hartstern, Daniela <
DANIELA.HARTSTERN at ucdenver.edu> wrote:

> Hello,
>
> I'm a beginner in Unix and programming. I'm trying to install BioPerl in
> Ubuntu-VMware following the instructions at
> http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAYand ran into problem by mistyping something. How can I fix it?
>
> Bellow in green are the points that need attention and my comments.
>
>
> .........
> cpan[3]> install C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
> Running make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
> Fetching with HTTP::Tiny:
>
> http://httpupdate18.cpanel.net/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
> Fetching with HTTP::Tiny:
> http://httpupdate18.cpanel.net/CPAN/authors/id/C/CJ/CJFIELDS/CHECKSUMS
> Checksum for
> /home/dhartstern/.cpan/sources/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
> ok
> Scanning cache /home/dhartstern/.cpan/build for sizes
>
> ............................................................................DONE
>
>   CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
>
> - ERROR: IO::String is not installed  <-- how can I fix this?
>
> (I think I'm being run by CPAN/CPANPLUS, so will rely on it to handle
> prerequisite installation)
>    I'll get CPAN to prepend the installation of this
> - ERROR: Data::Stag is not installed <-- how can I fix this?
>    I'll get CPAN to prepend the installation of this
> Install [a]ll optional external modules, [n]one, or choose
> [i]nteractively? [n]
> ^CWarning: No success on command[/usr/bin/perl Build.PL --installdirs
> site] <-- I meant to copy the text but pressed ctrl+C by mistake
>   CJFIELDS/BioPerl-1.6.1.tar.gz
>   /usr/bin/perl Build.PL --installdirs site -- NOT OK
> Running Build test
>   Make had some problems, won't test
> Running Build install
>   Make had some problems, won't install
> Could not read metadata file. Falling back to other methods to determine
> prerequisites
> Failed during this command:
> CJFIELDS/BioPerl-1.6.1.tar.gz                : writemakefile NO
> '/usr/bin/perl Build.PL --installdirs site' returned status 2
>
> cpan[3]> install C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
>      cpan[4]> d /bioperl/
> Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
> Distribution    CDRAUG/Dist-Zilla-PluginBundle-BioPerl-0.20.tar.gz
> Distribution    CJFIELDS/BioPerl-1.6.1.tar.gz
> Distribution    CJFIELDS/BioPerl-1.6.901.tar.gz
> Distribution    CJFIELDS/BioPerl-DB-1.006900.tar.gz
> Distribution    CJFIELDS/BioPerl-Network-1.006902.tar.gz
> Distribution    CJFIELDS/BioPerl-Run-1.006900.tar.gz
> Distribution    CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
> Distribution    RBUELS/Dist-Zilla-PluginBundle-Bioperl-0.01.tar.gz
> 9 items found
>
> cpan[5]> install C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
> Running Build for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
>   Has already been unwrapped into directory
> /home/dhartstern/.cpan/build/BioPerl-1.6.1-6GLB93
>   '/usr/bin/perl Build.PL --installdirs site' returned status 2, won't make
> Running Build test
>   Make had some problems, won't test
> Running Build install
>   Make had some problems, won't install
>
> cpan[6]> Caught SIGINT, trying to continue <--  I pressed ctrl+C again!
> cpan[6]>
>
>
>
>
> Thanks,
>
> Daniela Procopio Hartstern, PhD
> Clinical Molecular Genetics Fellow
> DNA Diagnostic Laboratory
> Denver Genetic Laboratories
> University of Colorado
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research