[BioC] crlmm error in Mac OS

[Vincent Carey]

I cannot confirm this with the sessionInfo shown below.

[code from vignette...]
> crlmm(fullFilenames, outputDir, verbose = FALSE)
Loading required package: DBI
Removing temporary files ... OK.
> sessionInfo()
R version 2.12.2 Patched (2011-03-03 r54672)
Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] 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] oligo_1.14.0               oligoClasses_1.12.1
 [7] Biobase_2.10.0             weaver_1.16.0
 [9] codetools_0.2-5            digest_0.4.2

loaded via a namespace (and not attached):
[1] Biostrings_2.18.2     IRanges_1.8.7         affxparser_1.22.0
[4] affyio_1.18.0         preprocessCore_1.12.0 splines_2.12.2


On Sat, Mar 5, 2011 at 2:16 PM, Steven Buechler <buechler.1 at nd.edu> wrote:
> 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
>>
>
>
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