[Bioc-devel] affyILM build error on Windows computers

[Henrik Bengtsson]

Add print() statements:

path <- system.file("rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/",
package="AffymetrixDataTestFiles");
print(path);file1 <- paste(path,"HG-Focus-1-121502.CEL", sep="")
print(file1);

and you most likely find the error(s).

My guess is that (i) you cannot have trailing slashes in system.file(), i.e. use

path <- system.file("rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin",
package="AffymetrixDataTestFiles");

and (ii) always use file.path() and never paste() to constructor paths, i.e.

file1 <- file.path(path,"HG-Focus-1-121502.CEL")

Also, in more recent versions of R, you can also do

path <- system.file("rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin",
package="AffymetrixDataTestFiles", mustWork=TRUE);

My $.02

/Henrik
On Tue, Oct 25, 2011 at 3:15 AM, Fabrice Berger
<fabrice.berger at gmail.com> wrote:
> 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
>
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