Wolfgang, 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). Ben
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 -------------------------------------