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

[Mark A. Jensen]

Ryan,
I'm not a mac person, but Koen has said (see 
http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink )
to use the unstable tree to get BioPerl 1.6.1, which is likely to be what you 
want.
cheers
Mark
----- Original Message ----- 
From: "rbogard" <ryan_bogard at hms.harvard.edu>
To: <Bioperl-l at lists.open-bio.org>
Sent: Monday, November 16, 2009 8:43 AM
Subject: Re: [Bioperl-l] Problems with bioperl in Mac OS X 10.6 (Perl 5.10.0)


>
> 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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> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
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