Thanks Gabriel. Your explanation is very clear.
Seeing the example above, I made a mistake. If I export(timestwo) (and not
multiply), then calling timestwo in the package works fine.
However, in my real package I have a situation like the above:
contr.none <- function(n, contrasts) {
if (length(n) == 1)
contr.treatment(n, contrasts = n<=2)
else
contr.treatment(n, contrasts = length(unique(n))<=2)
}
The contr.none is called by another function named myfun(). myfun is
exported but not contr.none.
Then, when I try to use myfun() it complains as follows:
Error in get(ctr, mode = "function", envir = parent.frame()) :
object 'contr.none' of mode 'function' was not found
Thanks again,
Axel.
On Sat, Jan 25, 2014 at 9:37 PM, Gabriel Becker <gmbec...@ucdavis.edu>wrote:
> Axel,
>
> R CMD check and CRAN's submission guidelines do not allow undocumented
> *user facing* (i.e. exported) functions or objects in packages.
>
> If you want the users of your package to be able calling the timestwo
> function directly, it needs to be documented (and exported).
>
> If, on the other hand, the timestwo function is only used internally by
> other functions in your package, and there is no reason for the end user to
> be calling it, it does not need to be exported or documented. The flip side
> of this is that, as you saw, non-exported objects in packages are not
> visible to the user when your package is loaded (::: not withstanding, but
> there should "virtually never" be a situation where users using your
> package normally should need to be using :::).
>
> You can't have an undocumented function in your package which users can
> call directly from the commandline simply by typing its name at the prompt.
> Or rather, you absolutely can, but CRAN will reject the package.
>
> HTH,
> ~G
>
>
> On Sat, Jan 25, 2014 at 11:47 AM, Axel Urbiz <axel.ur...@gmail.com> wrote:
>
>> Thanks Dirk. Sorry...It's my misunderstanding about "export" in the
>> NAMESPACE then. Essentially, as I understand it now, I should export all
>> functions that are used in the package? Why would I not export a certain
>> function?
>>
>> In the example above, say I wanted to avoid documenting the function
>> "timestwo" in the foo package. Is there a way to do that? Otherwise in R
>> CMD check foo, I get this "Undocumented code objects: timestwo".
>>
>> Thanks again for all your help!
>> Axel.
>>
>>
>> On Sat, Jan 25, 2014 at 8:32 PM, Dirk Eddelbuettel <e...@debian.org>
>> wrote:
>>
>> >
>> > On 25 January 2014 at 20:26, Axel Urbiz wrote:
>> > | Dirk and Uwe, many thanks both for your responses. I'm still having
>> the
>> > same
>> > | issue. Here's in more detail:
>> > |
>> > | As Dirk suggested, I've done the following:
>> > |
>> > | * I've created a package named {foo}.
>> > |
>> > | * {foo} only has one file named test.R which includes exactly the
>> > following
>> > | code:
>> > |
>> > |
>> > | multiply <- function(x,y) x * y
>> > |
>> > | timestwo <- function(x) multiply(x, 2)
>> > |
>> > | * I've modified the NAMESPACE to include ONLY the following line:
>> > |
>> > | export(multiply)
>> > |
>> > | * I've successfully built and installed the foo package
>> > |
>> > | * Then in R I got this:
>> > |
>> > | > library(foo)
>> > |
>> > | > multiply(2,3)
>> > |
>> > | [1] 6
>> > |
>> > | > timestwo(2)
>> > |
>> > | Error: could not find function "timestwo"
>> > |
>> > | >
>> > |
>> > | * However, if in the NAMESPACE I write instead export(multiply,
>> > timestwo), then
>> > | I don't get the error above.
>> >
>> > That. Works. As. Designed. And. Documented.
>> >
>> > Case 1) You _export only multiply_. Hence timestwo is not found.
>> Hint:
>> > learn about the difference between '::' and ':::' as well.
>> >
>> > Case 2) You _export both_. Both are found.
>> >
>> > No mystery. What other effect do you expect export() to have?
>> >
>> > Dirk
>> >
>> > |
>> > | * btw, here's my session info
>> > |
>> > | > sessionInfo()
>> > |
>> > | R Under development (unstable) (2014-01-17 r64821)
>> > |
>> > | Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> > |
>> > | locale:
>> > |
>> > | [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
>> > |
>> > | attached base packages:
>> > |
>> > | [1] stats graphics grDevices utils datasets methods base
>> > |
>> > |
>> > | other attached packages:
>> > |
>> > | [1] foo_1.0
>> > |
>> > |
>> > | Thanks,
>> > |
>> > | Axel.
>> > |
>> > |
>> > |
>> > |
>> > |
>> > |
>> > |
>> > |
>> > | On Sat, Jan 25, 2014 at 4:32 PM, Uwe Ligges <
>> > lig...@statistik.tu-dortmund.de>
>> > | wrote:
>> > |
>> > |
>> > |
>> > | On 25.01.2014 14:53, Dirk Eddelbuettel wrote:
>> > |
>> > |
>> > | On 25 January 2014 at 14:38, Axel Urbiz wrote:
>> > | | Hello,
>> > | |
>> > | | I'm building a package. My code is stored in foo.R. This
>> code
>> > has two
>> > | | functions FUN1 and FUN2. FUN1 calls FUN2. FUN1 is listed in
>> > export()
>> > | under
>> > | | the package NAMESPACE but NOT FUN2. After building the
>> package
>> > when I
>> > | call
>> > | | FUN1 is giving me an error that cannot find FUN2.
>> > |
>> > | Then you are doing something wrong in building, or possibly
>> > testing,
>> > | the package.
>> > |
>> > |
>> > |
>> > | I guess you have FUN1 in your Workspace and using that rather than
>> > the one
>> > | in your package.
>> > |
>> > | Uwe Ligges
>> > |
>> > |
>> > |
>> > |
>> > | "Everything within" can see everything else.
>> > |
>> > | | I solved this by adding FUN2 in the export() NAMESPACE.
>> > However, what
>> > | is
>> > | | puzzling me is that I have other examples similar to the
>> above
>> > (i.e.,
>> > | one
>> > | | function calling another but only one exported) in the same
>> > package
>> > | where I
>> > | | don't get the error message.
>> > | |
>> > | | Any idea of why that might be the case? My understanding is
>> > that
>> > | export
>> > |
>> > | We cannot tell without seeing the code.
>> > |
>> > | I suggest you spend two minutes with package.skeleton(),
>> create
>> > an
>> > | empty
>> > | package, put something like these two functions in
>> > |
>> > | multiply <- function(x, k) x * k
>> > |
>> > | timestwo <- function(x) multiply(x, 2)
>> > |
>> > | to convince yourself that timestwo() can in fact use
>> multiply().
>> > |
>> > | | only controls what is visible to the end user but functions
>> not
>> > | listed in
>> > | | export() are still "usable" within the package.
>> > | |
>> > | | In this case, the reason I'd like to avoid to export FUN2 is
>> > so I
>> > | don't
>> > | | have to add it in the package documentation.
>> > | |
>> > | |
>> > | | Any guidance is much appreciated.
>> > | |
>> > | | Regards,
>> > | | Axel.
>> > | |
>> > | | [[alternative HTML version deleted]]
>> > | |
>> > | | ______________________________________________
>> > | | R-devel@r-project.org mailing list
>> > | | https://stat.ethz.ch/mailman/listinfo/r-devel
>> > |
>> > |
>> > |
>> >
>> > --
>> > Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
>> >
>>
>> [[alternative HTML version deleted]]
>>
>>
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
>
> --
> Gabriel Becker
> Graduate Student
> Statistics Department
> University of California, Davis
>
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