[BioC] crlmm error in Mac OS

[Hervé Pagès]

Hi Vince, Steven,

The error message is not helping but it seems that crlmm() won't
write to an output dir that already exists. So you just need to
delete the folder pointed by 'outputDir' (set by you to
'file.path(getwd(), "crlmmTest")'), or set it to another location.

H.


On 03/05/2011 12:56 PM, Vincent Carey wrote:
> 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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>>
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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