[Bioperl-l] problem installing BioPerl

Mon Aug 26 01:58:49 UTC 2013

By the way, would you please explain what's the difference (if any) between
installing bioperl via CPAN, by 'sudo apt-get install libbio-perl-perl' and
just 'sudo apt-get install bioperl'. It seems like CPAN install does not
carry along the external software dependencies (eg clustalw), but I'm not
sure.

2013/8/26 Fields, Christopher J <cjfields at illinois.edu>

> Um, that was strange; had an internet hiccup and seemed to have posted
> three times.  Apologies for that.
>
> -c
>
> On Aug 25, 2013, at 6:53 PM, "Fields, Christopher J" <
> cjfields at illinois.edu> wrote:
>
> > 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_WAYandran 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
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
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>
>
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-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.