Bundle::BioPerl under cygwin Was: [Bioperl-l] Ace failure

[Nash, John]

Bear with me, I am a novice at this, but a keen novice.

I am not sure if anybody is using cygwin here. (Cygwin is a "cost-less" (as
opposed to free) Unix-based environment which runs under Windows, without
having to deal with the hassle of dual boot.  It has a pretty good set of
features, including a full gcc and perl tool kit. I get my
corporate-mandated Outlook and bash shell under one roof).

I just tested Bundle::BioPerl under my stock standard cywin setup (from
www.cygwin.com) on a Toshiba Portégè laptop, using perl 5.6.1 built for
cygwin.  The Cpan module is tricky under cywin (libnet fails, of all things
with the "install Bundle::BioPerl" command, but it installs ok by hand), so
I loaded the modules one-by-one - doing "perl Makefile.PL", then "make",
then "make test" and "make install".

Most things loaded fine.  Nearly all tests passed.

SOAP::Lite needs you to chmod 777 its directory, or else MakeMaker pukes.
libxml-perl-0.07 fails one test (t/stream)
I only installed jpeg support wth GD

bioperl-1.2-alpha is puking badly as I speak... more details will come, if I
can figure them out, and if people are interested.

cheers,
John

---
John Nash, Research Officer, Pathogen Genomics Group, 
Institute for Biological Sciences, National Research Council of Canada
Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
Phone: (613) 990-0990, Fax: (613) 952-9092


-----Original Message-----
From: Chris Dagdigian [mailto:dag@sonsorol.org]
Sent: Wednesday, December 18, 2002 11:27 AM
To: Ewan Birney
Cc: Lincoln Stein; Chester Langin; bioperl-l@bioperl.org
Subject: Re: [Bioperl-l] Ace failure




I need to make Bundle::BioPerl sync up with the bioperl-1.2 release. I 
just uploaded a version to CPAN that added the XML::DOM dependency 
needed by SeqIO::bsml.

Let me know if anything else needs to be added before the 1.2 release.

FYI there are no Ace modules in the Bundle, the currently listed modules 
are viewable here:

http://search.cpan.org/author/CRAFFI/Bundle-BioPerl-2.04/BioPerl.pm

--Chris



Ewan Birney wrote:
> On Wed, 18 Dec 2002, Lincoln Stein wrote:
> 
> 
>>The test database is currently offline because it was being abused.  I'm
sure 
>>that you *don't* need the Ace module in order to install bioperl, and I 
>>wonder why it is part of Bundle::BioPerl.
> 
> 
> 
> I think we should probably drop it from Bundle::BioPerl
> 
> 
> the connections on your machine Lincoln means that lots of people must be 
> using the bundle to install extra dependancies. Probably a good thing.
> 
> 
> I have only had one test report BTW (from Jonathan Epstein - many thanks 
> Jonathan. It looks like "standard windows errors" in there).
> 
> 
> 
> Other reports. V. interested in Irix and Sun tests as I don't test on 
> those UNIXes myself regularly

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