[Bioperl-l] Problem installing BioPerl

[Scott Cain]

Hi Sophie,

You need to use sudo to do the install.  Options include "sudo cpan"
to use the cpan shell, and "sudo ./Build install" to install from the
command line.

Scott


On Wed, Jun 1, 2011 at 11:17 AM, Sophie <alicarea at gmail.com> wrote:
> Hi Chris, Scott,
> Thank you for the quick response, I tried the latest version, and I get this
> on the terminal:
> ERROR: Can't create '/usr/local/bin'
> Do not have write permissions on '/usr/local/bin'
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>  at /Users/sophie/.cpan/build/BioPerl-1.6.901-yH47zc/Bio/Root/Build.pm line
> 853
>   CJFIELDS/BioPerl-1.6.901.tar.gz
>   ./Build install  -- NOT OK
> Warning (usually harmless): 'YAML' not installed, will not store persistent
> state
> Failed during this command:
>  CJFIELDS/BioPerl-1.6.901.tar.gz              : install NO
>
> I can't think of any other solution than to chmod 777 the /usr/local/bin but
> I really didn't want to do that.
> Thanks in advance for your help,
> Sophie
> On 1 June 2011 16:04, Chris Fields <cjfields at illinois.edu> wrote:
>>
>> I agree with Scott, in that you should use the latest version on CPAN.
>>  It's very possible it will fix some of the issues you are seeing, as the
>> build step has been simplified substantially to get around bioperl-specific
>> API conflicts with Module::Build.  So far, v 1.6.901 is installing on most
>> OS's, including darwin:
>>
>> http://matrix.cpantesters.org/?dist=BioPerl+1.6.901
>>
>> However, please let us know more details if you still run into problems.
>>
>> chris
>>
>> On Jun 1, 2011, at 9:40 AM, Scott Cain wrote:
>>
>> > Hi Sophie,
>> >
>> > If anything, I'd suggest a newer version (the current version is
>> > 1.6.901), and I'd also suggest indicating what the problem is; there
>> > might be a simple fix.
>> >
>> > Scott
>> >
>> >
>> > On Wed, Jun 1, 2011 at 10:32 AM, Sophie <alicarea at gmail.com> wrote:
>> >> Hi there,
>> >>
>> >> I've been trying to install BioPerl 1.6.1 on my Mac, (OS X), but no
>> >> matter
>> >> which method I use, CPAN, Buil.PL, etc, I can't install it, even when I
>> >> try
>> >> to force it. Should I try an older version of BioPerl?
>> >>
>> >> Thank you,
>> >> Best Regards,
>> >> Sophie.
>> >> _______________________________________________
>> >> 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
>>
>
>



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