[R] SNPRelate package error

[Joao Fadista]

Thanks for the reply. That was the problem. My getwd() was "C:/Windows/system32". I changed and now it works!

Best regards,
João Fadista, Ph.D.
Post Doc

Lund University Diabetes Centre
CRC, Malmö University Hospital
Jan Waldenströms gata 35, building 60, level 13
SE-205 02 Malmö, Sweden
Tel: +46 (0)40 391237
e-mail: joao.fadista at med.lu.se


-----Original Message-----
From: John Kane [mailto:jrkrideau at inbox.com] 
Sent: den 12 september 2012 15:13
To: Joao Fadista; r-help at r-project.org
Subject: RE: [R] SNPRelate package error

Are you sure that you have write permission to the directory that R is trying to write to?

John Kane
Kingston ON Canada


> -----Original Message-----
> From: joao.fadista at med.lu.se
> Sent: Wed, 12 Sep 2012 12:37:42 +0000
> To: r-help at r-project.org
> Subject: [R] SNPRelate package error
> 
> Dear all,
> 
> I am using the R package SNPRelate but I found an error when I run the 
> following command. Do you know what might be the problem? Thanks in 
> advance.
> 
> 
>> vcf.fn <- system.file("extdata", "sequence.vcf", package="SNPRelate") 
>> snpgdsVCF2GDS(vcf.fn, "test.gds")
> Start snpgdsVCF2GDS ...
>         Open
> C:/Users/med-jft/Documents/R/win-library/2.15/SNPRelate/extdata/sequence.vcf
>         Scanning ...
> Error in createfn.gds(outfn.gds) :
>   Can not create file 'test.gds'. Access is denied.
> 
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
> 
> locale:
> [1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252
> LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
> LC_TIME=Swedish_Sweden.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] SNPRelate_0.9.7 gdsfmt_0.9.10
> 
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
> 
> Best regards,
> João Fadista, Ph.D.
> Post Doc
> 
> Lund University Diabetes Centre
> CRC, Malmö University Hospital
> Jan Waldenströms gata 35, building 60, level 13
> SE-205 02 Malmö, Sweden
> Tel: +46 (0)40 391237
> e-mail: joao.fadista at med.lu.se
> 
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> PLEASE do read the posting guide
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