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

[Chris Fields]

Actually, why not just install via CPAN?  Any particular reason?

chris

On Nov 16, 2009, at 7:48 AM, Mark A. Jensen wrote:

> 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
>>>> --
>>>> 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.
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>> 
>> -- 
>> View this message in context: http://old.nabble.com/Problems-with-bioperl-in-Mac-OS-X-10.6-%28Perl-5.10.0%29-tp26366421p26372079.html
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l