[Rd] Conditional importFrom (roxygen?)
Folks:
I am getting a build failure when I:
#' @importFrom utils shortPathName
which roxygenizes it to the NAMESPACE.
I suspect this is because this particular function is Windows-only, but I'm
a bit confused how I should "properly" importFrom a function like this so
it doesn't cause a build failure, but I don't get a note in my R CMD CHECK
if I DON'T have it:
gdal_setInstallation : correctPath: no visible global function
definition for 'shortPathName'
gdalinfo: no visible global function definition for 'glob2rx'
gdallocationinfo: no visible global function definition for
'write.table'
gdaltransform: no visible global function definition for 'write.table'
get_subdatasets: no visible global function definition for 'glob2rx'
mosaic_rasters: no visible global function definition for 'write.table'
Undefined global functions or variables:
glob2rx shortPathName write.table
Consider adding
importFrom("utils", "glob2rx", "shortPathName", "write.table")
to your NAMESPACE.
I'll note my function actually first checks to see what OS is running, and
doesn't use this function on non-Windows machines, so having this function
does not cause any actual errors:
...
if (.Platform$OS.type=="windows")
{
x <- shortPathName(x)
} else
{
x <- path.expand(x)
}
...
Is there a way to do a conditional importFrom based on the OS? Or can I
safely ignore this (I'm trying to submit to CRAN).
--j
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Re: [Rd] Conditional importFrom (roxygen?)
On 04/10/2015 10:10 AM, Jonathan Greenberg wrote:
> Folks:
>
> I am getting a build failure when I:
> #' @importFrom utils shortPathName
>
> which roxygenizes it to the NAMESPACE.
>
> I suspect this is because this particular function is Windows-only, but I'm
> a bit confused how I should "properly" importFrom a function like this so
> it doesn't cause a build failure, but I don't get a note in my R CMD CHECK
> if I DON'T have it:
>
> gdal_setInstallation : correctPath: no visible global function
> definition for 'shortPathName'
> gdalinfo: no visible global function definition for 'glob2rx'
> gdallocationinfo: no visible global function definition for
> 'write.table'
> gdaltransform: no visible global function definition for 'write.table'
> get_subdatasets: no visible global function definition for 'glob2rx'
> mosaic_rasters: no visible global function definition for 'write.table'
> Undefined global functions or variables:
> glob2rx shortPathName write.table
> Consider adding
> importFrom("utils", "glob2rx", "shortPathName", "write.table")
> to your NAMESPACE.
>
> I'll note my function actually first checks to see what OS is running, and
> doesn't use this function on non-Windows machines, so having this function
> does not cause any actual errors:
>
> ...
>
> if (.Platform$OS.type=="windows")
>
> {
>
> x <- shortPathName(x)
>
> } else
>
> {
>
> x <- path.expand(x)
>
> }
>
>
> ...
>
> Is there a way to do a conditional importFrom based on the OS? Or can I
> safely ignore this (I'm trying to submit to CRAN).
>
Yes, you can put conditionals into the NAMESPACE file. Apparently
roxygen2 doesn't support this feature, so you'll have to do it by hand.
Duncan Murdoch
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Re: [Rd] Conditional importFrom (roxygen?)
Duncan Murdoch gmail.com> writes: > > On 04/10/2015 10:10 AM, Jonathan Greenberg wrote: > > Folks: > > [snip snip snip] > > > > Is there a way to do a conditional importFrom based on the OS? Or can I > > safely ignore this (I'm trying to submit to CRAN). > > > > Yes, you can put conditionals into the NAMESPACE file. Apparently > roxygen2 doesn't support this feature, so you'll have to do it by hand. > > Duncan Murdoch > > This has been submitted as an issue at https://github.com/klutometis/roxygen/issues/378 closely related: https://github.com/klutometis/roxygen/issues/371 my current hacky solution to this is to use a Makefile that post-processes the NAMESPACE after it's roxygenized, e.g. search for "getRversion" in https://github.com/glmmTMB/glmmTMB/blob/master/Makefile __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Conditional importFrom (roxygen?)
On 04/10/2015 7:34 PM, Ben Bolker wrote: > Duncan Murdoch gmail.com> writes: > >> >> On 04/10/2015 10:10 AM, Jonathan Greenberg wrote: >>> Folks: >>> > > [snip snip snip] > >>> >>> Is there a way to do a conditional importFrom based on the OS? Or can I >>> safely ignore this (I'm trying to submit to CRAN). >>> >> >> Yes, you can put conditionals into the NAMESPACE file. Apparently >> roxygen2 doesn't support this feature, so you'll have to do it by hand. >> >> Duncan Murdoch >> >> > > This has been submitted as an issue at > > https://github.com/klutometis/roxygen/issues/378 > > closely related: > > https://github.com/klutometis/roxygen/issues/371 > > my current hacky solution to this is to use a Makefile that > post-processes the NAMESPACE after it's roxygenized, e.g. search > for "getRversion" in > > https://github.com/glmmTMB/glmmTMB/blob/master/Makefile Hadley has the right idea (allow roxygen to specify some uninterpreted text to drop into the NAMESPACE file), but it doesn't go far enough. Really this is a design flaw in roxygen: being able to enter NAMESPACE and help page info in source files is a great feature, but being forced to go all or nothing is a flaw. If base R adds something new to the NAMESPACE or .Rd files (or has some obscure feature that roxygen authors didn't notice), it's really hard for roxygen users to make use of it. A better design would be to allow content from both sources: some manually entered NAMESPACE stuff, and some automatically generated stuff. A really nice design would be to read the manually entered stuff and show (some of?) it in the .R files, but that would be really tricky to get right. I think it would need to be supported by a GUI, it wouldn't be reasonable to expect people to type it all properly in a dumb editor. Maybe Hadley knows someone who has written a GUI? Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
