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

Mon Nov 16 16:57:16 UTC 2009

I read that posting by Koen and used the unstable tree after the first
attempt; however, the errors still persisted. I just finished a fresh
install and I will just follow Mr. Fields advice and use CPAN. 
Thank you all for the help!

Chris Fields-5 wrote:
> 
> 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.
>>>>> 
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