[Bioperl-l] Re: [Bioperl-guts-l] BioPerl Installation failure--help!!!!!!!

[Jason Stajich]

I know that people "feel good" when tests pass, but they aren't necessary
to use the toolkit.  Did you try and run example scripts or do anything
with bioperl?  You can do quite a lot of things without any external
modules.

You need expat and libgd installed to install XML::Parser::PerlSAX and GD
respectively.  You only need these modules if you plan to parse XML or use
the Bio::Graphics tools.

To install bioperl and not worry about the tests passing.

CPAN> force install Bio::Seq

Quite a lot of things will run.
In the future we're making things more permissive and trying to remove
some external module dependancies -- understand there is a two-way pull
here, we want to focus on the biological question so why remake a
perfectly good module that exists already, and we want the toolkit to be
drag and drop easy to install.  CPAN should make that easier, but the
onous is on the writers of those modules as well.

Anyways, the SimpleAlign bug exposed in changes between perl 5.6 and perl
5.8.0.

Biblio/BioFetch/DB/EMBL_DB/Perl all need network access and or local
configuration of your env variables if your access is through a proxy.
Many mailings on the list about this use the htdig search tool on the
front page to find any of these good pointers.

-jason

On Mon, 23 Sep 2002, Mark Zhang wrote:

> Hi all,
>
>
>
> I am new to BioPerl. I spent more than one week to try to use CPAN to
> install Bundle::BioPerl with lots of frustrations. I would appreciate if you
> can point me to the right direction. Here is the relevant information:
>
>
>
> OS:      Compaq Tru64 v5.1a with latest patchkit
>
> perl installed:     perl-5.8.0 (perl is installed correctly and so is CPAN)
>
> perl modules failed to be installed based on BioPerl external dependencies:
>
> XML::Parser::PerlSAX
>
> SOAP::Lite
>
> GD
>
> All perl modules were installed with CPAN.
>
>
>
> I used the system mentioned above to install Bundle::BioPerl, what I found
> at the end was that there are make errors so that make install would not
> work. Not even a single Module related to Biology was installed!!! Here is a
> typical error summary produced by CPAN:
>
> Failed Test         Stat Wstat Total Fail  Failed  List of Failed^M
>
> ----------------------------------------------------------------------------
> ---^M
>
> t/Biblio_biofetch.t               13    1   7.69%  4^M
>
> t/BioFetch_DB.t                   27   ??       %  ??^M
>
> t/DB.t                            51    1   1.96%  2^M
>
> t/EMBL_DB.t                       15    1   6.67%  17^M
>
> t/Perl.t                           9    1  11.11%  3^M
>
> t/SimpleAlign.t                   53    1   1.89%  18^M
>
> 6 subtests skipped.^M
>
> Failed 6/94 test scripts, 93.62% okay. -6/3279 subtests failed, 100.18%
> okay.^M
>
> *** Exit 2^M
>
> Stop.^M
>
>   /sbin/make test -- NOT OK^M
>
> Running make install^M
>
>   make test had returned bad status, won't install without force^M
>
>
>
> My questions here are:
>
> (1)     are  these errors the result of lack of those 3 external modules?
>
> (2)     Can I do a force install?
>
> (3)     Are there any detailed steps that I can follow to install BioPerl(it
> seems to me that the steps are more complex than that outlined on bioperl
> webpage)
>
>
>
> Any of your comments are welcome!!!
>
>
>
> Mark Zhang
>
>
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu