[Bioperl-l] problems with a few packages

Chris Fields cjfields at illinois.edu
Wed Dec 15 19:23:30 EST 2010


Michael,

Don't use the CPAN versions of these modules, they're no longer supported (note to self: ask Ewan to remove the old versions of bioperl off CPAN).  In fact, bioperl-ext is essentially abandonware.  The bioperl-ext code in github (https://github.com/bioperl/bioperl-ext) does work, but we can't make any promises re: bug fixes, as the authors of much of that code have long ago abandoned it.  

chris

On Dec 15, 2010, at 4:00 PM, Michael Gooch wrote:

> 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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