[R-pkg-devel] trivial package with R CMD check ERRORs that seem unrelated to package contents

[Duncan Murdoch]

On 28/05/2015 9:19 AM, Richard M. Heiberger wrote:
> I posted a package
>      trivial_3.1-18.tar.gz
> and the
>      00check-trivial.log
> from R-devel at
>
>       http://astro.temple.edu/~rmh/HH-test/
>
> The package contains one function
> trivial <- function(...) {}
> and a NAMESPACE that imports other packages.
>
> The 00check-trivial.log has many messages that look like they depend
> on aspects of the imported packages, including five of these
>      Error in validObject(.Object) :
>
> I need guidance on how to respond to these.
>
> My real package
>      HH_3.1-17.tar.gz
> is also there along with a clean check log from R-3.1.2 and a check log
> I don't understand from R-devel.

You're importing a lot of packages.  I think the first set of warnings

* checking whether package 'trivial' can be installed ... WARNING
Found the following significant warnings:
   Warning: replacing previous import by 'shiny::radioButtons' when loading 'trivial'
   Warning: replacing previous import by 'stats::dbinom' when loading 'trivial'
   Warning: replacing previous import by 'stats::pnorm' when loading 'trivial'
   Warning: replacing previous import by 'stats::dnorm' when loading 'trivial'
   Warning: replacing previous import by 'stats::dpois' when loading 'trivial'
   Warning: replacing previous import by 'latticeExtra::rootogram' when loading 'trivial'

could mean what they say: you already have a function called 
radioButtons imported,  and shiny::radioButtons is masking it, and 
similarly for the other warnings. Or it could be a bug in R-devel. If it 
really is a case of masking, the solution is probably to import less:  
just name the functions you really need, don't import everything.

The error

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
   there is no package called 'e1071'
Error: package or namespace load failed for 'trivial'
Execution halted


appears to be clear. You don't import e1071, but presumably one of your 
imports does,  and you don't have it.

I would guess the reason you didn't get the warnings previously is 
because it's a new check, and you didn't get the error because you did 
have e1071, or you were using different versions of the imported 
packages, and they didn't need it.

The errors like

Error in validObject(.Object) :
   invalid class "ObjectsWithPackage" object: superclass "atomicVector" not defined in the environment of the object's class
Execution halted


could be a bug in R-devel, or perhaps they are caused by using old 
versions of packages rather than reinstalling them for R-devel. I'm not 
sure what your response should be to these.   You could try 
install.packages() on all the dependencies just to be sure you have the 
latest builds; If they're an R-devel bug, they'll probably go away soon.

Duncan Murdoch