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

Ben Bolstad bmb at bmbolstad.com
Wed Apr 5 19:13:57 CEST 2006


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 
> Seattle:
> http://www.bioconductor.org/checkResults/1.8/html/gopher5/matchprobes.buildsrc.html
> 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
> England
> Phone: +44 1223 494642
> Fax:   +44 1223 494486
> Http:  www.ebi.ac.uk/huber
> -------------------------------------

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