[Bioperl-l] Error in installing bioperl on CentOS 5.6

[Scott Cain]

Hi Neha,

Sorry I didn't respond yesterday--I was out of the office.

It looks to me like you have something more fundamental wrong with your
cpan configuraiton.  Are you able to install anything via cpan?  You might
want to reconfigure it (using "o conf init" at the cpan prompt) or look
into a cpan shell replacement (I think cpanplus is popular with the cool
kids, but I don't use it).

Scott



On Thu, Jun 13, 2013 at 12:12 AM, neha sanghi <neha.sanghi86 at gmail.com>wrote:

> Hi Scott,
>
> I tried this also but again it failed with following error.*Basically it
> complains about gzip: yes/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz:
> * No such file or directory first and then subsequent steps fail.
>
> Reading '/share/apps/Metadata'
>   Database was generated on Tue, 11 Jun 2013 09:41:02 GMT
> Running install for module 'Bio::Perl'
> Running make for C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
> Fetching with HTTP::Tiny:
> http://cpan.mirror.ac.za/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
> Fetching with HTTP::Tiny:
> http://cpan.mirror.ac.za/authors/id/C/CJ/CJFIELDS/CHECKSUMS
> Checksum for yes/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz ok
> gzip: yes/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz: No such file or
> directory
> /bin/tar: yes/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz: Cannot
> open: No such file or directory
> /bin/tar: Error is not recoverable: exiting now
> Using Tar:/bin/tar xf
> "yes/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz":
> /bin/tar: yes/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz: Cannot
> open: No such file or directory
> /bin/tar: Error is not recoverable: exiting now
> Couldn't untar yes/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
> Directory 'yes/CJFIELDS-UBfyA6' has gone. Cannot continue.
> Failed during this command:
>  CJFIELDS/BioPerl-1.6.901.tar.gz              : unwrapped NO -- untar
> failed
>
>
>
>
> On Wed, Jun 12, 2013 at 7:42 PM, Scott Cain <scott at scottcain.net> wrote:
>
>> Hi Neha,
>>
>> I'm not sure Bundle::BioPerl is supported any more (which may explain why
>> it can't be found), but it doesn't matter since the only reason for
>> Bundle::BioPerl's existence was to install prereqs--it didn't install
>> BioPerl (which confused people).  Just install Bio::Perl via cpan instead.
>>
>> Scott
>>
>>
>>
>> On Wed, Jun 12, 2013 at 9:03 AM, neha sanghi <neha.sanghi86 at gmail.com>wrote:
>>
>>> Dear Sir/Ma'am,
>>>
>>> I am facing problem in installing bioperl. Below is teh error message:
>>>
>>>  perl -MCPAN -e 'install Bundle::BioPerl'
>>> CPAN::SQLite not installed, trying to work without
>>> Reading '/share/apps/Metadata'
>>>   Database was generated on Tue, 11 Jun 2013 09:41:02 GMT
>>> Fetching with HTTP::Tiny:
>>>
>>> http://cpan.mirror.ac.za/authors/id/C/CR/CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
>>> Fetching with HTTP::Tiny:
>>> http://cpan.mirror.ac.za/authors/id/C/CR/CRAFFI/CHECKSUMS
>>> Checksum for yes/authors/id/C/CR/CRAFFI/Bundle-BioPerl-2.1.8.tar.gz ok
>>> gzip: yes/authors/id/C/CR/CRAFFI/Bundle-BioPerl-2.1.8.tar.gz: No such
>>> file
>>> or directory
>>> /bin/tar: yes/authors/id/C/CR/CRAFFI/Bundle-BioPerl-2.1.8.tar.gz: Cannot
>>> open: No such file or directory
>>> /bin/tar: Error is not recoverable: exiting now
>>> Using Tar:/bin/tar xf
>>> "yes/authors/id/C/CR/CRAFFI/Bundle-BioPerl-2.1.8.tar.gz":
>>> /bin/tar: yes/authors/id/C/CR/CRAFFI/Bundle-BioPerl-2.1.8.tar.gz: Cannot
>>> open: No such file or directory
>>> /bin/tar: Error is not recoverable: exiting now
>>> Couldn't untar yes/authors/id/C/CR/CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
>>> Directory 'yes/CRAFFI-BVVKbJ' has gone. Cannot continue.
>>>
>>>         ...propagated at /usr/lib/perl5/5.8.8/CPAN/Shell.pm line 1699.
>>>
>>> Please help me in solving this issue
>>>
>>> Thanks and Regards,
>>> Neha
>>> _______________________________________________
>>> 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
>>
>
>


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