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

[rbogard]

The Mac OS X 10.6 was a fresh install on a new Mac Book Pro. Not sure if I
will have the same issues, but it's worth a shot as I have little on my
computer and reinstalling to start over wouldn't be too difficult. What
method did you use to install bioperl? I used fink and I am not sure the
available stable version is the one I need. I will install from the command
line this time around, and let you know how it turns out.

Thank you!



Emanuele Osimo wrote:
> 
> 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
>> --
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>>
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