[BioC] crlmm error in Mac OS

[Steven Buechler]

Before using crlmm in the oligo package for a research project I executed the following commands copied from the vignette and received the error reported below. Any suggestions would be appreciated.

Steven Buechler
buechler.1 at nd.edi

*****

> library(oligo)
> library("hapmap100kxba")
> pathCelFiles <- system.file("celFiles", package = "hapmap100kxba")
> fullFilenames <- list.celfiles(path = pathCelFiles,
+ full.names = TRUE)
> outputDir <- file.path(getwd(), "crlmmTest")

> crlmm(fullFilenames, outputDir, verbose = FALSE)
Error: !(missing(tmpdir) | file.exists(tmpdir)) is not TRUE

> tempdir()
[1] "/var/folders/uA/uAFdydnnHIiHJBV4o2gC-E+++TI/-Tmp-//RtmpH9vgb7"
> traceback()
4: stop(paste(ch, " is not ", if (length(r) > 1L) "all ", "TRUE", 
       sep = ""), call. = FALSE)
3: stopifnot(!(missing(tmpdir) | file.exists(tmpdir)))
2: justCRLMMv3(filenames, outdir, batch_size = batch_size, recalibrate = recalibrate, 
       minLLRforCalls = minLLRforCalls, balance = balance, verbose = verbose)
1: crlmm(fullFilenames, outputDir, verbose = FALSE)
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets 
[7] methods   base     

other attached packages:
[1] pd.mapping50k.xba240_1.1.0 RSQLite_0.9-4             
[3] DBI_0.2-5                  hapmap100kxba_1.3.3       
[5] ff_2.2-1                   bit_1.1-6                 
[7] oligo_1.14.0               oligoClasses_1.12.2       
[9] Biobase_2.10.0            

loaded via a namespace (and not attached):
[1] affxparser_1.22.1     affyio_1.18.0        
[3] Biostrings_2.18.4     IRanges_1.8.9        
[5] preprocessCore_1.12.0 splines_2.12.2       
>