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meyer-lab-cshl / plinkQC

R package for quality control of plink genetic datasets
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ERROR WHILE RUNNING PLINKQC IN RSTUDIO ON WINDOWS #26

Closed hkiran22 closed 4 years ago

hkiran22 commented 4 years ago

Hello, I am trying to run plinkQC on RStudio in Windows and I am getting the error below

Identification of related individuals
Identification of individuals of divergent ancestry
Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table    
Error in evaluate_check_ancestry(qcdir = qcdir, indir = indir, name = name,  :
  plink --pca output file: C:/Users/HP/AppData/Local/Temp/RtmpkhMIat/data.HapMapIII.eigenvec does not exist.

Kindly assist.

Thank you Mariam

twesigomwedavid commented 4 years ago

@hkiran22 @HannahVMeyer The problem seems to be on the preceding code chunk in the plinkQC tutorial:

system(paste("cp", file.path(package.dir, 'extdata/data.HapMapIII.eigenvec'),
             qcdir))

Windows OS does not seem to like that way of copying files. Perhaps using the line below instead can fix the problem?

file.copy(file.path(package.dir, 'extdata/data.HapMapIII.eigenvec'), qcdir)
HannahVMeyer commented 4 years ago

Mariam, did David's suggestion (thank you @twesigomwedavid) work? I will update the examples/vignette accordingly.

If not, Mariam, please provide more context. Which version of R and plinkQC are you using? can you please provide the output of sessionInfo().

hkiran22 commented 4 years ago

Dear Hannah, Yes. David’s suggestion worked for me. I am using R version 4.0.0 and 0.3.0 for plinkQC

Regards Mariam

On Mon, 1 Jun 2020 at 14:03, HannahVMeyer notifications@github.com wrote:

Mariam, did David's suggestion (thank you @twesigomwedavid https://github.com/twesigomwedavid) work? I will update the examples/vignette accordingly.

If not, Mariam, please provide more context. Which version of R and plinkQC are you using? can you please provide the output of sessionInfo().

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HannahVMeyer commented 4 years ago

Thanks for reporting back. I am closing this issue now.