[Bioperl-l] Problems with Bioperl-ext package on WinVista?

[Smithies, Russell]

Dev-C++ http://www.bloodshed.net/devcpp.html is a good (i.e. free under GPL) Windows compiler I've used before.
Might save having to install Cygwin.

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Mark A. Jensen
> Sent: Wednesday, 12 August 2009 9:05 a.m.
> To: Jonny Dalzell; Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Problems with Bioperl-ext package on WinVista?
> 
> Jonny,
> It will run in Win/Vis but there are some caveats. The BioPerl package has
> some
> plain C components, as Rob pointed out. These need to be compiled, and the
> objects/libraries put in the right place. CPAN will cause this to happen when
> you have a compiler available; ActiveState .ppm will download the binaries
> directly from the repository (my understanding, anyway). CPAN is always
> available by doing
> 
> > perl -MCPAN -e shell
> 
> but you may not have a C compiler around. This is a little tricky. You can
> either explore Visual C/C++ options from MS here
> http://msdn.microsoft.com/en-us/library/ms950410.aspx, or you can do as I do,
> and install Cygwin (www.cygwin.com), which creates a linux-like environment
> with
> GNU compiler tools and many other (wonderful, IMHO) goodies. Not as wonderful
> as
> the real thing, I grant. Which bring me to a third possibility, that I haven't
> tried, which is an Ubuntu box running in a VM under Windows, or as a dual-boot
> system (https://help.ubuntu.com/community/WindowsDualBoot).
> MAJ
> ----- Original Message -----
> From: "Jonny Dalzell" <jdalzell03 at qub.ac.uk>
> To: <Bioperl-l at lists.open-bio.org>
> Sent: Tuesday, August 11, 2009 4:29 PM
> Subject: Re: [Bioperl-l] Problems with Bioperl-ext package on WinVista?
> 
> 
> >
> > Hi,
> >
> > thanks.  I did install HHMER from the site Mark suggested, and it is within
> > the directories that perl recognizes when reading the script...still I get
> >
> > "The C-compiled engine for Hidden Markov Model (HMM) has not been installed.
> > Please read the install the bioperl-ext package"
> >
> > Is it possible that this module simply won't run through windows?
> >
> > jonny
> >
> >
> >
> > Sendu Bala-2 wrote:
> >>
> >> Jonny Dalzell wrote:
> >>> Hi,
> >>>
> >>> I'm as sure as I can be.  I look in the HHMER folder and it contains
> >>> "Domain.pm", "Results.pm", and "Set.pm".  I thought perhaps it was
> >>> something
> >>> to do with @INC, but I put
> >>> "use lib "strawberry/per/lib C:/strawberry/perl/site/lib/Bio/Tools/";" at
> >>> the top of my script, which definately encompasses the directory it
> >>> should
> >>> be in, and I still get...
> >>>
> >>> "Can't locate Bio/Tools/HMM.pm in @INC (@INC contains: strawberry/per/lib
> >>> C:/strawberry/perl/site/lib/
> >>> Bio/Tools/ C:/strawberry/perl/lib C:/strawberry/perl/site/lib .) at
> >>> HMM.txt
> >>> line 5.
> >>> BEGIN failed--compilation aborted at HMM.txt line 5."
> >>>
> >>> I'm out of ideas.
> >>
> >> lib (or at least one entry in your PERL5LIB) needs to point to the
> >> directory that contains the Bio directory. So:
> >>
> >> use lib "strawberry/per/lib C:/strawberry/perl/site/lib/";
> >>
> >> Now it will be able to locate Bio::Tools::Hmm. You'll still get your
> >> original error because you don't have Hmmer installed. See Mark's reply.
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >
> > --
> > View this message in context:
> > http://www.nabble.com/Problems-with-Bioperl-ext-package-on-WinVista--
> tp24919498p24925178.html
> > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> 
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