[Bioc-devel] HAVE_ZLIB in affyio (breaking matchprobes)
Hi, 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... Cheers, H.
Ben Bolstad wrote:
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 -------------------------------------
------------------------ Herv? Pag?s E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319