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RahmanTeam / DECoN

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DECoN installation error #41

Open anilkanthi opened 1 year ago

anilkanthi commented 1 year ago

"Failed to retrieve ExomeDepth package"

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

Decon_setup_error

abernar-85 commented 1 year ago

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 commented 1 year ago

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. image

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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