[Bioc-devel] Linking packages in man pages

[Sidharth Jain]

Huh, that would make a lot of sense.

But what's strange is that the dplyr package uses the same syntax (
https://github.com/tidyverse/dplyr/blob/master/man/reexports.Rd, line 39):
\item{magrittr}{\code{\link[magrittr]{\%>\%}}}
And the documentation for `%>%` is actually pipe.html.

I'll probably change the reference to be more vague as you suggested, but
I'm still curious why the documentation fails in this case, and why the
links fail only on tokay1 for the Windows build, but pass for all other
builds.

- Sid

On Mon, Jun 17, 2019 at 4:29 PM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> The problem is that the use of \link[]{} syntax requires that the help
> page is _named_ "%<>%.html" -- extremely unlikely! Actually the help page
> is named "compound.html". Again, avoid the problem of providing the name of
> the help page by letting R do the work for you `\code{\link{"\%<>\%"}}
> (I'm not sure about escaping those %; I think you could also say
> \code{\link[magrittr::compound]{"\%<>\%"}}, but that is fragile (breaking
> when magrittr decides to change the name of the page on which the function
> is defined).
>
> Martin
>
> On 6/17/19, 4:11 PM, "Sidharth Jain" <sidharthsjain using gmail.com> wrote:
>
>     Makes sense for mclapply, I'll remove the links in the documentation.
>
>     What about `%<>%` from magrittr? From my recollection, it should also
> be available on Windows machines.
>
>
>     Thanks,
>     Sid
>
>
>
>
>     On Mon, Jun 17, 2019 at 4:05 PM Martin Morgan <mtmorgan.bioc using gmail.com>
> wrote:
>
>
>     mclapply is not available or documented on Windows. I think the
> solution is actually to be vague, and replace
> \code{\link[parallel]{mclapply}}) with \code{\link{mclapply}} at
>
>
> https://github.com/sellerslab/gemini/blob/b1408bdce22df08d6950fee578eaac7665f54960/R/gemini_parallelization.R#L9
> <
> https://github.com/sellerslab/gemini/blob/b1408bdce22df08d6950fee578eaac7665f54960/R/gemini_parallelization.R#L9
> >
>
>     Martin
>
>     On 6/17/19, 3:52 PM, "Bioc-devel on behalf of Sidharth Jain" <
> bioc-devel-bounces using r-project.org on behalf of
>     sidharthsjain using gmail.com> wrote:
>
>         Hello,
>
>         I have been getting the following warnings upon package building
> on tokay1:
>
>         Found the following significant warnings:
>           Rd warning:
> C:/Users/pkgbuild/AppData/Local/Temp/RtmpwTSgiX/R.INSTALLe1c5c6b6ce1/gemini/man/gemini_parallelization.Rd:14:
>         file link 'mclapply' in package 'parallel' does not exist and so
> has
>         been treated as a topic
>           Rd warning:
> C:/Users/pkgbuild/AppData/Local/Temp/RtmpwTSgiX/R.INSTALLe1c5c6b6ce1/gemini/man/reexports.Rd:14:
>         file link '%<>%' in package 'magrittr' does not exist and so has
> been
>         treated as a topic
>
>         It seems that the problem is coming from links in my
> documentation. I
>         import functions from both packages.
>
>         I included the following in a function's roxygen2 skeleton:
>         \code{\link[parallel]{mclapply}})
>
>         I also added:@importFrom parallel mclapply
>         @importFrom magrittr `%<>%`
>
>         How should I indicate that these packages should be installed? Is
> this
>         a problem with my package, or a problem with the
> installation/tokay1?
>
>         Thanks,
>         Sid
>
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