Re: [Rd] "could not find function" after import

From: steven mosher <moshersteven_at_gmail.com>
Date: Fri, 23 Sep 2011 12:13:59 -0700

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.duncan_at_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.duncan_at_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_at_r-project.org mailing list
>> >  https://stat.ethz.ch/mailman/listinfo/r-devel
>> >
>
>



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