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

Chris Fields cjfields at illinois.edu
Mon Nov 16 10:00:09 EST 2009

On Nov 16, 2009, at 1:04 AM, 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

Just starting from scratch isn't always the best solution (though it is the cleanest).  In this case I don't think anything you mention applies, as there are conflicting symbols being reported.  My guess is conflicting perl builds, probably between your system 5.10.0 (snow leopard) and your fink-installed perl 5.8.8 (they are binary incompatible).  Also, remember that snow leopard is primarily 64-bit, so it might be best to try working out whether your fink is attempting to compile 64- vs 32-bit.  

In this case, I would just uninstall the fink-based perl and either use the system one (snow leopard = 5.10.0), or roll your own and install 5.10.1 locally or in /usr/local.  Do NOT replace the system one, as that will likely break your OS.

In my experience, and not to bash on fink or MacPorts, I never had much luck with their perl installs.  Unless I plan on only using fink or macports for my OS (not likely in my case), I find they tend to cause problems in the long term unless one uses them to install packages with very few dependencies, and even then you need to make sure fink is configure to compile the correct binary.  For instance, they're fairly good for gd, libxml2, etc., but beyond that one may get into issues with odd, version-specific dependencies with some packages, such as relying on perl 5.8.8 (but not perl 5.10.x), db42 (instead of db44), etc.  I've ended up in the past with 2-3 different perl versions, berkeley db versions, etc. 


> 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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