[Bioc-devel] conditions on vectors of length > 1 Warning/ERROR

Charles Warden cwarden45 at gmail.com
Sun Jan 28 03:33:20 CET 2018


Hi Lori,

Thank you for pointing this out - I've added the any() function to the
function with the warning in the development version of COHCAP.

Thanks Again,
Charles

On Thu, Jan 25, 2018 at 9:44 AM, Shepherd, Lori <
Lori.Shepherd at roswellpark.org> wrote:

> Hello Bioconductor community,
>
> In a continued effort to better code, there have been efforts to identify problematic
> existing code in packages. The current issue at hand is identifying a
> conditional with a length greater than 1. This could either be an over site
> of not using any() or all() or could potential indicate problematic code
> with unexpected multiple output.
>
> dummy example:
>
> ```
> > check = c(1:5)
> > if (check > 3){
> +    FALSE
> + }
> Warning message:
> In if (check > 3) { :
>   the condition has length > 1 and only the first element will be used
> ```
>
> The following are packages that currently have code with this type of
> Warning/ERROR:
>
> cbaf
> COHCAP
> exomePeak
> ExtDist
> fabia
> gaia
> gCrisprTools
> GenVisR
> Guitar
> hapFabia
> KEGGlincs
> MassArray
> miRBaseVersions.db
> NOISeq
> pathview
> rHVDM
> SEPA
> sights
> support
> SVAPLSseq
>
>
> Please correct these issues as soon as possible. For a link to
> detailed output on what code is causing this, please see
>
> https://github.com/kalibera/rifcond
>
>
> We are implementing the check on incoming packages submitted to the
> Bioconductor tracker that will produce an ERROR and should be active by
> the end of next week.
>
> Thank you.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
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