[Bioperl-l] Problem installing BioPerl

[Chris Fields]

Just to note, you can also install locally if you do not want the distribution available for everyone (see local::lib on CPAN).  In fact, I suggest this in most cases for end users.

chris

On Jun 1, 2011, at 10:46 AM, Sophie wrote:

> Hi there,
> 
> I wrote this on the cpan shell:
> 
> o conf make_install_make_command 'sudo make'
> o conf mbuild_install_build_command 'sudo ./Build'
> o conf commit
> install CJFIELDS/BioPerl-1.6.901.tar.gz
> 
> and it seems like it installed, at least when I type perl -MBio::Seq -e 0  it gives me no error, and when I type   perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'    it gives me this  1.006901
> 
> Hopefully it worked, sorry to bother you,
> Thank you for your time,
> Best wishes,
> Sophie.
> 
> On 1 June 2011 16:39, Scott Cain <scott at scottcain.net> wrote:
> 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
>