[Rd] R CMD check --as-cran does not show all error messages.

[Mikko Korpela]

On 04.09.2014 18:15, Thalles wrote:

> I am writing a package with some R functions and try to submit it to CRAN.
> After build and check the package a number of times, I am struggling with
> the fact that the CRAN people responsible for checking  packages are
> replying me with some mistakes that I just do NOT get when I do the check in
> my computer. With the most recent R version, i.e. 3.1.1 and the command R
> CMD check --as-cran on my package I get:

(check log with no errors)

> However, the people from CRAN claim that there is a error:
> 
> * checking R code for possible problems ... NOTE
> PlotBgMap: no visible binding for global variable ‘canada.map’
> 
> This function 'PlotBgMap' loads this data set ‘canada.map’, that is part of
> the package. And the *LazyData: yes* is set in the DESCRIPTION file. I know
> that the cause of this error is because somehow, the package is not being
> loaded in the NAMESPACE, but it should be there because I am using LazyData.
> That is the code for the PlotBgMap function:
> 
> PlotBgMap <-function( traj, ... ) {
>     hySplitProj <- CRS(proj4string(traj))
>     canada <- spTransform(canada.map, hySplitProj)
>     plot(canada.map, border="white", col="lightgrey", ... )
> }
> 
> I'd like to know if I am missing something in the Checking process, or if I
> should do anything else to fix this error. Thanks.

It seems that this is the same issue as discussed recently on this
mailing list, with the title "no visible binding for global variable for
data sets in a package". I recommend reading the message thread.

Short story: There was a recent change to package checking in the
development version of R (R-devel). This more rigorous check is not
included in the current release version 3.1.1. You can use
opentraj::canada.map to access this particular data set, and a similar
approach for any other LazyData in your package. The :: technique was
suggested in the aforementioned message thread by professors Brian D.
Ripley and Peter Dalgaard.

Quoting "Changes in R-devel",
http://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html

> R CMD check now by default checks code usage directly on the package
> namespace without loading and attaching the package and its suggests
> and enhances. For good practice with packages in the Suggests field,
> see §1.1.3.1 of ‘Writing R Extensions‘.

The CRAN Repository Policy,
http://cran.r-project.org/web/packages/policies.html, suggests using the
most recent R-devel for package checking before submission.

-- 
Mikko Korpela
Aalto University School of Science
Department of Information and Computer Science