R devel - Sep 2011 - "could not find function" after import

I am trying to build a package (GWASTools, submitted to Bioconductor) 
that uses the "sandwich" package.  I have references to
"sandwich" in
DESCRIPTION:
Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy

and NAMESPACE:
import(sandwich)

In the code itself is a call to vcovHC:
Vhat <- vcovHC(mod, type="HC0")

I have sandwich version 2.2-7 installed.

When I run R CMD check on my package, I get the following error during 
checking of examples:
* using R Under development (unstable) (2011-08-29 r56828)
* using platform: x86_64-apple-darwin9.8.0 (64-bit)
...
* checking examples ... ERROR
...
Error in estfun.glm(x) : could not find function "is.zoo"
Calls: assocTestRegression ... meatHC -> rowMeans -> is.data.frame -> 
estfun -> estfun.glm

I import sandwich, sandwich depends on zoo, but a function in zoo cannot 
be found during execution.

I tried to get around this by explicitly including a "require"
statement
in assocTestRegression:
require(sandwich)

The example now runs, but I have a warning in R CMD check:
* checking for unstated dependencies in R code ... WARNING
?library? or ?require? call not declared from: ?sandwich?

I am not sure why this is a problem, as there is a "require" statement
(for a different package) in another function which does not cause any 
warnings.

Can anyone advise on how to get my package to successfully pass R CMD check?

thanks,
Stephanie Gogarten
Research Scientist, Biostatistics
University of Washington

On 11-09-19 4:48 PM, Stephanie M. Gogarten wrote:
> I am trying to build a package (GWASTools, submitted to Bioconductor)
> that uses the "sandwich" package.  I have references to
"sandwich" in
> DESCRIPTION:
> Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy
>
> and NAMESPACE:
> import(sandwich)
>
> In the code itself is a call to vcovHC:
> Vhat<- vcovHC(mod, type="HC0")
>
> I have sandwich version 2.2-7 installed.
>
> When I run R CMD check on my package, I get the following error during
> checking of examples:
> * using R Under development (unstable) (2011-08-29 r56828)
> * using platform: x86_64-apple-darwin9.8.0 (64-bit)
> ...
> * checking examples ... ERROR
> ...
> Error in estfun.glm(x) : could not find function "is.zoo"
> Calls: assocTestRegression ... meatHC ->  rowMeans ->  is.data.frame
->
> estfun ->  estfun.glm
>
> I import sandwich, sandwich depends on zoo, but a function in zoo cannot
> be found during execution.
>
> I tried to get around this by explicitly including a "require"
statement
> in assocTestRegression:
> require(sandwich)
>
> The example now runs, but I have a warning in R CMD check:
> * checking for unstated dependencies in R code ... WARNING
> ?library? or ?require? call not declared from: ?sandwich?
>
> I am not sure why this is a problem, as there is a "require"
statement
> (for a different package) in another function which does not cause any
> warnings.
>
> Can anyone advise on how to get my package to successfully pass R CMD
check?
>
If you said that your package Depends on sandwich, you'd probably pass 
checks, but this is arguably a bug in the sandwich package.

The problem is that since you only import sandwich, it never gets 
attached.  So it never attaches its dependency zoo.   It should import 
zoo (or import the functions in zoo that it uses) to work properly the 
way you are calling it.

You can see the same error as follows:

1.  Install sandwich, but don't attach it or zoo.

2.  Run

example(glm)

to create the "glm" object glm.D93.

Try to call

sandwich::estfun(glm.D93)

You'll get the same error as before because is.zoo() will not be loaded.

It's also arguably a design flaw in R.  For testing sandwich, zoo would 
generally end up being attached, because the testing of sandwich would 
attach it.  However, examples like the one above are never tested.

Duncan Murdoch