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,
Jo?o Fadista, Ph.D.
Post Doc

Lund University Diabetes Centre
CRC, Malm? University Hospital
Jan Waldenstr?ms gata 35, building 60, level 13
SE-205 02 Malm?, Sweden
Tel: +46 (0)40 391237
e-mail: joao.fadista at med.lu.se
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,
Jo?o Fadista, Ph.D.
Post Doc

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

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Thanks for the reply. That was the problem. My getwd() was "C:/Windows/system32". I changed and now it works!

Best regards,
Jo?o Fadista, Ph.D.
Post Doc

Lund University Diabetes Centre
CRC, Malm? University Hospital
Jan Waldenstr?ms gata 35, building 60, level 13
SE-205 02 Malm?, 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,
Jo?o Fadista, Ph.D.
Post Doc

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

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
____________________________________________________________
FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family!
Visit http://www.inbox.com/photosharing to find out more!