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

[neha sanghi]

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
>