[Bioperl-l] problem installing BioPerl

[Fields, Christopher J]

One problem is the BioPerl version is old; the latest CPAN release is 1.6.901 (May 2011).  Have you tried the latest version from CPAN?

chris

On Aug 25, 2013, at 12:22 PM, Scott Cain <scott at scottcain.net> wrote:

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