Hi Jim --
"James MacDonald" <jmac...@med.umich.edu> writes:
> Hi,
>
> Could someone point me to the relevant documentation that covers
> what should be in the DESCRIPTION file for packages that have
> functions imported via the NAMESPACE file? I have read the R
> Extensions manual, but I cannot find where it covers the DESCRIPTION
> file vis a vis importing from a namespace.
>
> An example:
>
> I have a package foo that uses two functions x and y from package
> bar. Both packages have namespaces, and I just want to import the
> functions from bar rather than attaching the package.
>
> I put
>
> Imports: bar
>
> in my DESCRIPTION file and
>
> importFrom(bar, x, y)
>
> in my NAMESPACE file.
>
> I have a vignette that uses both x and y from bar, and when I run R
> CMD build foo, at the vignette building step it errors out because
> it cannot find function x. If I add
>
> Depends: bar
>
> to my DESCRIPTION file it all works, but bar is attached and it
> seems I have not accomplished what I wanted. I am obviously
> misunderstanding something but I don't know what.
If I'm reading correctly, you have a vignette chunk that does
<<>>=
x()
@
This corresponds to use of x _outside_ your package name space -- the
vignette is being processed like any R session.
You already have Imports: foo in your DESCRIPTION file (because you're
using x _within_ your package name space), so you know the user will
have foo installed. The vignette just needs to
library(foo)
before calling x -- i.e., attach foo to the search path, so that x can
be found in a normal R session.
A slightly different scenario is when your vignette uses a package
that it is not meaningful to Import: or Depend: on, in which case
you'll want to mention the package in the Suggests: field of
DESCRIPTION. In this case I think you also want to add a line
%\VignetteDepends{foo}
to the vignette. Suggests: is a little problematic because the default
for install.packages does NOT install packages mentioned in Suggests:
so users may be unable to build your vignette without first installing
additional packages.
Back to the case where the package Imports: foo. This is still
helpful, as it keeps from cluttering the user search path and allows
you to be confident that references to x within your package find the
appropriate x, regardless of what the user is doing to their search
path.
Hope that helps.
Martin
> Best,
>
> Jim
>
>
>
> James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
> 8220D MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor MI 48109-0646
> 734-936-8662
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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