Thanks duncan. I fixed it by changing to depends and resubmitting my packages. But I changed from depends to imports for a very specific reason. namespace conflicts. There are work arounds for that so its not terminally broken, but IMPORT had the promise of just the elegance I was looking for.
Thanks for the explanation. Steve On Fri, Sep 23, 2011 at 11:44 AM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote: > On 23/09/2011 12:57 PM, steven mosher wrote: >> >> Duncan >> >> I have a related question. >> >> I need one function from R.utils. But R.utils depends on R.oo and >> R.methodsS3. >> so I made R.util an import and then used importFrom() in the namespace. >> >> The package passed the "check". However when it came to use the function >> it had not been loaded? do I need to add the upstream packages that >> R.util depends >> upon? also in the code do I need a library or require? > > Sounds exactly like the situation with sandwich below. The workaround > available to you is to Depend on R.utils. The author of R.utils could fix > the problem by importing R.oo and R.methodsS3, and the authors of R could > fix it by changing the behaviour of how R handles imports. > > Duncan Murdoch > >> A bit confused >> >> Steve >> >> On Mon, Sep 19, 2011 at 5:09 PM, Duncan Murdoch >> <murdoch.dun...@gmail.com> wrote: >> > 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 >> > >> > ______________________________________________ >> > R-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/r-devel >> > > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel