[Bioperl-l] Re: Inline::C and io_lib

[Aaron J Mackey]

On Mon, 8 Jul 2002, Lincoln Stein wrote:

> The SCF-reading .XS module I sent out this morning got held by the
> mailing list program, so I'm sending it again directly to Aaron and
> Chad.

Excellent, will compare with my work to find improvement opportunities.

> Sounds like Aaron's got the situation all under control, however.

Pretty much, but a few questions for the policy authorities:

Currently, I'm taking the BEGIN/eval approach to check that Inline::C is
at all available, and if not, throwing an exception.  But there is this
bioperl-ext collection as well, which the staden::read.pm could go into
(and the various SeqIO::abi etc modules could just check to see if it was
available, and otherwise fail, or drop to a pure-perl solution if also
available).  I've discovered how to get the top-level Makefile.PL to deal
with individual deep subdirectory Makefile.PL, so it's no issue where to
put the Inline::C-requiring stuff, but I thought I'd provide an
opportunity for comment - in summary: bioperl-live or bioperl-ext?

Secondly, I'm going to be prompting during install whether or not the user
has the io_lib installed, and if so where the various lib/ and include/
directories are (is there some way to probe for these without making wild
guesses?  I guess I can look to see what directories the Perl lib/ and
include/'s are from Config.pm ... ?)  If they don't want to install the
io_lib stuff do we:
  a) not install the modules (abi.pm, etc) at all
  b) install them, but ensure that they fail immediately, without trying
to find Inline::C or io_lib themselves
  c) install them anyway, just don't ask about lib/include (use some
best-guess default).

I guess I'm aiming for a solution where if the user says no on the day the
install bioperl, they can later come back and install io_lib, and have
things Just Work (TM).  The lib/ include/ directory specification is a
niggly point though ...  Thoughts?

All that said, the basic "I have io_lib, I know where it's installed, and
I want it in BioPerl" is now working ... adding tests right now, and I
need some sample data files! (I can make them myself with bogus data, but
I'd prefer samples captured from the wild).

-Aaron


>
> Lincoln
>
>
> On Thursday 04 July 2002 10:05 pm, Aaron J Mackey wrote:
> > I have no issues - I knew that if *I* were going to do it, I'd use
> > Inline::C, out of habit, and ease of wrapping predefined libs.
> >
> > -Aaron
> >
> > On Thu, 4 Jul 2002, Chad Matsalla wrote:
> > > Hi All,
> > >
> > > I have some use for using io_lib from the Staden package as c-extensions
> > > for some work I am doing.
> > >
> > > I remembered a discussion in June with regards to this.
> > >
> > > Is anybody still interested in having this done? Does it have to use
> > > Inline::C ? I have done a bunch of work in XS. Can I just use XS?
> > >
> > > Regards,
> > >
> > > Chad Matsalla
>
>

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu