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PIMA on SGI

Brent Wiese brent at kite.imgen.bcm.tmc.edu
Thu Jan 28 12:10:45 EST 1993


In article <1993Jan27.081224.21491 at kakwa.ucs.ualberta.ca>, rndy at wimsey.mmid.ualberta.ca (Randy Read) writes:
> I've downloaded Smith & Smith's PIMA (Pattern Induced Multiple Alignment)  
> package (MBCRR-Package/pima-1.22.tar.Z on mbcrr.harvard.edu) by ftp as  
> suggested in their paper.  Attempts to install the package on either an SGI or  
> a NeXT lead to a number of compile-time warnings and fatal errors.  I still  
> only speak pidgin C, so I'm hoping that someone with a greater facility with  
> the language has sorted this out.
> 
> Has anyone out there succeeded in implementing this package on SGI hardware?   
> If so, is the revised version available, or is it just a matter of the right  
> compiler flags?  I would greatly appreciate any information, either by e-mail  
> or posted to this newsgroup.
> 
> Randy J. Read
> rndy at wimsey.mmid.ualberta.ca

     Yes, your errors can be resolved by a compiler setting.  Since the
code is not ansi but rather K&R C you should tell the compiler this.
The easiest way to do this would be to run ...

	setenv SGI_CC -cckr

... and then run the install.sh file.  Additionally you will want to make
as slight modification to the file make-cluster.sh .  Line number 258 of
make-cluster.sh should read ...

----------------------------------------------------------------
awk '{print NR,$0}' tmp-cluster.$$ | extract-cluster-loci | awk '{print $2}' |
----------------------------------------------------------------

... instead of ...

----------------------------------------------------------------
cat -n tmp-cluster.$$ | extract-cluster-loci | awk '{print $2}' |
----------------------------------------------------------------

     I don't have access to a NeXT system right now so I don't know how
you can tell the C compiler on your NeXT system to expect K&R C, or if
that is even possible.  If you don't have anybody around there that knows
how to tell the NeXT C compiler this, let me know and I will see what I can
do.  Please contact brent at bcm.tmc.edu or rsmith at bcm.tmc.edu if you are
having any further difficulties.

Thanks,
  Brent
-- 
Brent Wiese				Phone:	   713-798-6034
Institute for Molecular Genetics	Fax:	   713-798-5386
Baylor College of Medicine		Internet:  brent at bcm.tmc.edu
Houston, TX 77030  USA




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