[Bioperl-l] Problems with bioperl in Mac OS X 10.6 (Perl 5.10.0)

[Emanuele Osimo]

Hello Ryan,
unfortunately, if you upgraded to 10.6 without formatting, I have to tell
you that you'll be in big trouble with perl and with everything you
installed from the commandline... Because in the upgrade process everything
in the system folders, perl and bioperl being some of these things, is
erased without being uninstalled, so you'll find a lot of folders with the
same name but no contents.
I suggest you, as I did, to format your pc and reinstall 10.6 from scratch.
Then youl'll be able to install mysql (I had to install
mysql-5.4.3-beta-osx10.5, the only to work on 10.6), and, working with perl
5.10 that is already installed, you'll install bioperl with no effort.
Bye
Emanuele

On Mon, Nov 16, 2009 at 04:30, rbogard <ryan_bogard at hms.harvard.edu> wrote:

>
> In advance, any advice would be grealy appreciated! I have installed
> bioperl-588pm via fink but I am having difficulties calling the modules in
> script. The following is added to .profile (bash):
> PERL5LIB=/sw/lib/perl5/5.8.8:$PERL5LIB
>
> If I change this to /sw/lib/perl5 then I get an @INC error, as use
> Bio::PERL
> cannot be located.
>
> The environment variables are as follows:
>
>
> MANPATH=/sw/share/man:/usr/share/man:/usr/X11/man:/sw/lib/perl5/5.10.0/man:/usr/X11R6/man:/sw/lib/perl5-core/5.8.8/man:/sw/lib/perl5/5.8.8/man
>
> PERL5LIB=/sw/lib/perl5/5.8.8:/sw/lib/perl5:/sw/lib/perl5/darwin:/sw/lib/perl5/5.8.8
>
> PATH=/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin
> INFOPATH=/sw/share/info:/sw/info:/usr/share/info
>
>
> This is the perl script I'm attempting to run:
> #!/sw/bin/perl5.8.8
> use strict;
> use Bio::Perl;
> $seq_object = get_sequence('swiss',"ROA1_HUMAN");
> write_sequence(">roa1.fasta",'fasta',$seq_object);
>
> Here is the error output:
>
> dyld: lazy symbol binding failed: Symbol not found: _Perl_Tstack_sp_ptr
>  Referenced from:
> /sw/lib/perl5/5.8.8/darwin-thread-multi-2level/auto/IO/IO.bundle
>  Expected in: dynamic lookup
>
> dyld: Symbol not found: _Perl_Tstack_sp_ptr
>  Referenced from:
> /sw/lib/perl5/5.8.8/darwin-thread-multi-2level/auto/IO/IO.bundle
>  Expected in: dynamic lookup
>
> Trace/BPT trap
>
> I have looked through many forum postings and attempted the solutions
> offered in those instances, but none seem to work in my case. I'm not sure
> if it's because I have perl 5.10.0 installed while attempting to call
> bioperl 5.8.8; however, others seem to have it working just fine.
>
> Thank you, Ryan
> --
> View this message in context:
> http://old.nabble.com/Problems-with-bioperl-in-Mac-OS-X-10.6-%28Perl-5.10.0%29-tp26366421p26366421.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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