[Bioperl-l] problem installing BioPerl

[Hartstern, Daniela]

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_WAY and 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