[Bioc-devel] Linking packages in man pages

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Mon Jun 17 22:29:44 CEST 2019

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).


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. 
    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>
    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:
        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:
        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?
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