[Bioperl-l] problems with a few packages

Michael Gooch gooch at student.uchc.edu
Wed Dec 15 17:00:52 EST 2010


noticed mention of optional packages not being installed and tried to 
install them.

can't install the following packages, cpan claims there is an error 
while running make. OS is mac snow leopard. I have installed several 
linux command line tools for various dependencies using macports. I 
couldn't possibly list them all from memory, but when I find that I need 
something normally found in linux that mac doesnt have, I try to get it 
with macports.

install Bio::Ext::Align
install Bio::SeqIO::staden::read

cpan[28]> force install Bio::Ext::Align
Running install for module 'Bio::Ext::Align'
Running make for B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
   Has already been unwrapped into directory 
/Users/gooch/.cpan/build/bioperl-ext-1.4-pmSEl7
   '/opt/local/bin/perl Makefile.PL' returned status 512, won't make
Running make test
   Make had some problems, won't test
Running make install
   Make had some problems, won't install

cpan[29]> force install Bio::SeqIO::staden::read
Running install for module 'Bio::SeqIO::staden::read'
Running make for B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
   Has already been unwrapped into directory 
/Users/gooch/.cpan/build/bioperl-ext-1.4-pmSEl7
   '/opt/local/bin/perl Makefile.PL' returned status 512, won't make
Running make test
   Make had some problems, won't test
Running make install
   Make had some problems, won't install



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