[Bioc-devel] ensemblVEP: 'fork' argument for 'VEPParam' should be integer

[Valerie Obenchain]

Thanks for catching this. A fix is checked in to 0.99.13.

It's great to have a tester for this package. Let me know if you have 
suggestions/feedback for the user interface, how the param options are 
specified etc.

Valerie


On 02/27/13 07:25, Julian Gehring wrote:
> Hi,
>
> 'VEPParam' allows to set the parameters for the ensembl VEP perl 
> script, and the documentation of 'ensemblVEP' specifies:
>
>
> """
> - fork: ‘logical’, default FALSE; enable forking
> """
>
>
> However, looking at the VEP documentation 
> (http://www.ensembl.org/info/docs/variation/vep/vep_script.html#forking) 
> and the example below, it should rather accept an integer than a 
> logical value:
>
>
> """
> library(ensemblVEP)
> file <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
>
> ## works ##
> vcf <- ensemblVEP(file, param=VEPParam())
>
> ## also works ##
> vcf <- ensemblVEP(file, param=VEPParam(basic=c(fork=FALSE)))
>
> ## is not valid, requires a logical ##
> vcf <- ensemblVEP(file, param=VEPParam(basic=c(fork=2L)))
> Error in validObject(.Object) :
>   invalid class “VEPParam” object: 2 must be TRUE or FALSE
>
> ## does not work ##
> vcf <- ensemblVEP(file, param=VEPParam(basic=c(fork=TRUE)))
> Value "--species" invalid for option fork (number expected)
> ERROR: Failed to parse command-line flags
> Error in .io_check_exists(path(con)) : file(s) do not exist:
>   '/tmp/RtmpjR3p8p/file7a4f5271f65c'
> """
>
>
> Best wishes
> Julian
>
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