Fields, Christopher J | 15 Jun 18:55 2013

Re: Error in installing bioperl on CentOS 5.6

No, don't use CPANPLUS (it's no longer developed).  Use cpanminus:

https://metacpan.org/module/App::cpanminus

chris

On Jun 14, 2013, at 10:41 PM, Scott Cain <scott <at> scottcain.net> wrote:

> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Gmane