[Bioperl-l] problem installing BioPerl

Mon Aug 26 20:11:18 UTC 2013

Hi everyone,

Many thanks for your replies. It seems it's working now. I removed the BioPerl-1.6.1-6GLB93 directory and repeated the steps of installation:

>perl -MCPAN -e shell
cpan>d /bioperl/

cpan>install C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz

It went smoothly. The problem before was just my typo, it seems.

Best,
Daniela

From: Alexey Morozov [mailto:alexeymorozov1991 at gmail.com]
Sent: Sunday, August 25, 2013 7:59 PM
To: Fields, Christopher J
Cc: Scott Cain; Hartstern, Daniela; bioperl-l at bioperl.org<mailto:bioperl-l at bioperl.org>
Subject: Re: [Bioperl-l] problem installing BioPerl

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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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
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>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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--
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.