[Bioperl-l] Budle::BioPerl dependency issues

gang wu gwu at molbio.mgh.harvard.edu
Mon Nov 20 13:31:34 EST 2006


Hi Sendu,

I think the package was not installed at all. The only thing I saw in 
the Bio folder is ANS1 which was another package(I mistakenly thought 
it's the only package installed by Bundle-BioPerl 2.1.16). I did not 
force install with CPAN. So is it possible that the three typos forbid 
bioperl be installed?

Thanks.

Gang

Sendu Bala wrote:
> gang wu wrote:
>> It turned out that most of the modules of BioPerl were not installed 
>> at all. And none of the scripts were installed. I had to download and 
>> install bioperl-1.5.2-RC3.tar.gz 
>> <http://bioperl.org/DIST/bioperl-1.5.2-RC3.tar.gz> again. A similar 
>> problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually 
>> copied all stuff under Bio folder to the corresponding Perl library 
>> folder. Is it Ok to do it in this way?
>
> It will work, but is hardly good enough from our point of view (you 
> shouldn't have to do that).
>
> Can you tell me exactly what you mean by 'were not installed'? What 
> did you do to try and install? How did you determine that installation 
> had failed?
>
> With CPAN, if you were still getting errors during testing, what were 
> those remaining errors, and did you do a forced install to ignore the 
> errors? If a forced install didn't actually install anything, what 
> message did CPAN give you about that, if any?
>
> With the manual download, after doing "perl Makefile.PL", what is your 
> output of "make install"?
>
>
> Thank you,
> Sendu.



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