[Bioperl-l] Problem installing BioPerl

[Sophie]

Thank you!

On 1 June 2011 16:57, Chris Fields <cjfields at illinois.edu> wrote:

> 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
> >
>
>