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

Wolfgang Huber huber at ebi.ac.uk
Wed Apr 5 19:17:42 CEST 2006

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 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

More information about the Bioc-devel mailing list