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

[Shepherd, Lori]

Thank you for your quick response and your contribution to Bioconductor!


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Charles Warden <cwarden45 at gmail.com>
Sent: Saturday, January 27, 2018 9:33:20 PM
To: Shepherd, Lori
Cc: Martin Morgan
Subject: Re: conditions on vectors of length > 1 Warning/ERROR

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<mailto: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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