[Bioc-devel] affyILM build error on Windows computers

[Martin Morgan]

On 10/25/2011 05:36 AM, Henrik Bengtsson wrote:
> 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);

yes the trailing slash is the problem (also the trailing ;, but that's 
another story ;). system.file can also take a deconstructed file path

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

which allows R to make assumptions about path separators, in the same 
way as file.path.

Martin

>
> 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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