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[Bioc-devel] warning in R CMD check

3 messages · ALEXANDRE SANCHEZ PLA, Joern Toedling

Original
ALEXANDRE SANCHEZ PLA
# 
Hello

I am trying to build a package to upload it to Bioconductor-
The package builds correctly using R-2.6.2 and Bioconductor 2.1 but R CMD check
issues the following warning: 

--------------------------------------------------------------
* checking for unstated dependencies in R code ... WARNING

'library' or 'require' calls not declared from:

  anotPkg anotPack

See the information on DESCRIPTION files in the chapter 'Creating R

packages' of the 'Writing R Extensions' manual.

---------------------------------------------------------------

'anotPkg' or 'anotPack' are not package names indeed. I use them as argument
to pass any annotation package names to a function which will load them in
execution time.

It is as if I wanted to have a 'loadAnnotations' function in my package which
could be as follows:

loadAnnotations <- function (anotPack){
  if (!require(anotPack, character.only=T))
     cat("Could not load the package")
}


So my question is: what should I do if I wanted to include such a function in my
package to avoid the warning?

Thanks for any suggestions

Alex Sanchez
Departament d'Estadistica. Universitat de Barcelona
Joern Toedling
# 
Hi Alex,

use the function's argument 'quietly' to suppress the warning.

require(anotPack, character.only=TRUE, quietly=TRUE)

btw, I would suggest to spell out TRUE in functions, since some users
might unwisely have used 'T' as a variable name.

Regards,
Joern
ALEXANDRE SANCHEZ PLA wrote:
Joern Toedling
# 
Actually the remark about spelling out TRUE instead of T is even more
relevant to your question than I thought. You may want to use 'quietly',
but the reason for your warning in check is really the 'T'. Put
character.only=TRUE and the warning should be gone.
Joern Toedling wrote: