DECoN installation error

[anilkanthi]

"Failed to retrieve ExomeDepth package"

Please suggest how to resolve this issue and setup DECoN successfully.

[abernar-85]

I am having the same issue.

The version of ExomeDepth on CRAN is now 1.1.16. DECon should look for a more recent ExomeDepth.

Could you please fix this?

[emunte]

Hi,
I am facing the same... It would be very nice if you could fix it.
Meanwhile what I have done is changing version of ExomeDepth in renv.lock file.

I don't know the differences between ExomeDepth v1.1.15 and ExomeDepth v.1.1.16 so I don't know if the solution I came up with is correct or not... but at least it fixes this bug..

[abernar-85]

Thanks @emunte I could install DECoN

But then IdentifyFailures.R fails

This is my command:
Rscript IdentifyFailures.R --Rdata DECoN_summary.RData --out DECoN

The error:
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

Anyone knows how to solve this issue?

makeCNVcalls.R also fails with the same error

[fishcakess]

Thanks @emunte I could install DECoN

But then IdentifyFailures.R fails

This is my command: Rscript IdentifyFailures.R --Rdata DECoN_summary.RData --out DECoN

The error: 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

Anyone knows how to solve this issue?

makeCNVcalls.R also fails with the same error

you're giving the option as --Rdata but you need to put --RData (capital D)

[abernar-85]

Hi, thanks @fishcakess
In DECoN manual is written as --Rdata, but it should be --RData