[Bioc-devel] HAVE_ZLIB in affyio (breaking matchprobes)

Herve Pages hpages at fhcrc.org
Wed Apr 5 22:31:07 CEST 2006


I just "R CMD build/check" matchprobes on gopher5 (our main build machine)
with the last affyio version that Ben committed to svn today (v 0.99.1).
Since everything went fine, I conclude that the new affyio was automatically
installed with support for compressed files (with no manual 
configuration required).
So expect to see some green for the matchprobes result in tomorrow's
build/check report...

Ben Bolstad wrote:

>Sorry about that I'll fix up my part promptly. I do agree that
>supporting compressed CEL files is a good idea and should remain
>supported (though they have historically been used by only an extremely
>small part of the userbase).
>On Wed, 2006-04-05 at 18:17 +0100, Wolfgang Huber wrote:
>>Hi Ben, Herve,
>>can affyio be fixed such that the code that is conditionally compiled 
>>with #if defined(HAVE_ZLIB) preprocessor commands is indeed used if the 
>>machine does have zlib (which I think is standard on most modern systems).
>>Currently, this is breaking the build of matchprobes on the machines in 
>>since the example CEL files that the vignettes uses are gzipped, and 
>>affy::read.affybatch (via affyio/src/read_abatch.c) refuses to read it 
>>because it was apparently compiled without HAVE_ZLIB defined.
>>When I manually define HAVE_ZLIB in affyio/src/read_abatch.c, the 
>>matchprobes package passes R CMD check.
>>1. Can somebody (Ben?) add a configure.ac (or whatever helps) to affyio 
>>so that HAVE_ZLIB is defined?
>>2. Herve, can you make sure the build machines do install a version of 
>>affyio that supports compressed files?
>>Beyond fixing matchprobes, I think being able to read compressed CEL 
>>files is a good thing for everybody. Or am I missing sth?
>>Best regards
>>   Wolfgang
>>Wolfgang Huber
>>European Bioinformatics Institute
>>European Molecular Biology Laboratory
>>Cambridge CB10 1SD
>>Phone: +44 1223 494642
>>Fax:   +44 1223 494486
>>Http:  www.ebi.ac.uk/huber

Hervé Pagès
E-mail: hpages at fhcrc.org
 Phone: (206) 667-5791
   Fax: (206) 667-1319

More information about the Bioc-devel mailing list