Problem while running Rscript makeCNVcalls.R

[glbala87]

Dear All,

I have successfully installed Decon in my PC and encountering below mentioned error while executing Rscript makeCNVcalls.R command:

• The library is already synchronized with the lockfile.
  Loading required package: R.oo
  Loading required package: R.methodsS3
  R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following object is masked from ‘package:R.methodsS3’:

throw

The following objects are masked from ‘package:methods’:

getClasses, getMethods

The following objects are masked from ‘package:base’:

attach, detach, load, save

R.utils v2.11.0 (2021-09-26 08:30:02 UTC) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

timestamp

The following objects are masked from ‘package:base’:

cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
warnings

[1] "BEGIN makeCNVCalls.R"
Error in getopt_options(object, args) :
Error in getopt(spec = spec, opt = args) : long flag "Rdata" is invalid
Calls: parse_args -> parse_options -> getopt_options
Execution halted

Any solution for this problem?

Your help would be highly appreciated.

Thank you
Bala

[Sbird600]

Dear Bala, you have to use RData flag (capital D). There is a mistake in the respective examples in DECon v2.pdf file.

[glbala87]

I am using RData 'capital D', still I am getting this error.