[R] parsing error when using R CMD check

[Duncan Murdoch]

On 11-09-16 4:48 PM, Tarca, Adi wrote:
> Hi all,
>
> I am trying to run R CMD check on a package which passes R CMD INSTALL.
> The check stops because of a parsing problem in the example of a given function at this line:
>
> return(res[res$ID %in% list$targetGeneSets,])
>
> The code is ok, since it runs if I paste it in R.
> Is this a known parsing issue in R CMD check?

Percent signs in Rd files are comments unless they are escaped.  The 
parser sees your code as

return(res[res$ID

Rewrite it as

return(res[res$ID \%in\% list$targetGeneSets,])

Duncan Murdoch

> Thanks,
> Adi
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> Thanks,
>
>
>
> Adi Laurentiu TARCA, Ph.D.
> Assistant Professor (Research),
> Department of Computer Science&  Center for Molecular Medicine and Genetics, Wayne State University,
> Director, Bioinformatics and Computational Biology Unit,  Perinatology Research Branch (NICHD),
> 3990 John R., Office 4809,
> Detroit, Michigan 48201
> Tel: 1-313-5775305
>
>
> 	[[alternative HTML version deleted]]
>
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