ERROR WHILE RUNNING PLINKQC IN RSTUDIO ON WINDOWS

[hkiran22]

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]

@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]

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]

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 ***@***.***> 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(). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#26 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APY5MLQGEBFXZ4YQVHPVW23RUODHLANCNFSM4NOZZOZA> .

-- Is 45:25

[HannahVMeyer]

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