[Bioc-devel] affyILM build error on Windows computers

[Fabrice Berger]

Dear BioC developpers,

Checking the affyILM package on 
http://bioconductor.org/checkResults/2.9/bioc-LATEST/index.html ,
it appears that systematic errors are reported on Windows computers, 
leading to the following message :

* creating vignettes ... ERROR
Loading required package: Biobase

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'browseVignettes()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: AffymetrixDataTestFiles

Error: processing vignette 'affyILM.Rnw' failed with diagnostics:
  chunk 5
Error in ilm(file1) :
   Cannot read CEL files. Some files not found: HG-Focus-1-121502.CEL
Execution halted


Building/Checking/building binary with the other platforms does not lead 
to this error.

The code in the vignette, for that part of the process, is the following :

Load the library
<<>>=
library(affyILM)
@
and locate the test CEL-file
<<>>=
path <- system.file("rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/", 
package="AffymetrixDataTestFiles");
file1 <- paste(path,"HG-Focus-1-121502.CEL", sep="")
@

Calculation of the hybridization free energies for each probe, and 
estimation of concentrations using the Langmuir isotherm:
<<>>=
result <- ilm(file1);
@

Any idea to solve this issue?

Thanks,

Fabrice Berger