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

[Wolfgang Huber]

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