[Bioc-devel] question regarding man pages

Dan Tenenbaum dtenenba at fredhutch.org
Wed Mar 2 23:21:15 CET 2016

#' @import(packageName) 

inserts an import statement into your NAMESPACE that looks like this:


It has nothing to do with the library() function.

And yes, unexported functions do not need to have man pages to be accepted into Bioconductor. However, they can have them.


----- Original Message -----
> From: "Krithika Bhuvaneshwar" <kb472 at georgetown.edu>
> To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Wednesday, March 2, 2016 2:18:14 PM
> Subject: Re: [Bioc-devel] question regarding man pages

> Thank you for the feedback - I have a follow up question (possibly a
> newbie question)
> So from what you are suggesting, the helper functions need not have man pages.
> I have to import some packages for the code to work in these helper
> functions. Before I used to have :
> #' @import(packageName) as part of the Roxygen header to indicate an import.
> I believe its not correct to have library(packageName) in the code. So
> how do I do this import ?
> Thanks,
> --Krithika
> On Tue, Mar 1, 2016 at 8:21 PM, Kasper Daniel Hansen
> <kasperdanielhansen at gmail.com> wrote:
>> Btw. a common (but not required) convention is that unexported helper
>> functions start with .  Personally I find that helpful.
>> On Tue, Mar 1, 2016 at 8:20 PM, Kasper Daniel Hansen
>> <kasperdanielhansen at gmail.com> wrote:
>>> You only need to document functions which are exported in the NAMESPACE
>>> file.  R CMD check will clearly warn about missing documentation.  I don't
>>> know how to deal with this in Rstudio.
>>> Best,
>>> Kasper
>>> On Tue, Mar 1, 2016 at 5:44 PM, Krithika Bhuvaneshwar
>>> <kb472 at georgetown.edu> wrote:
>>>> Hello,
>>>> We are working on our first  Bioconductor package and have a question
>>>> regarding man pages for helper functions
>>>> We have several .R files which are all helper functions.
>>>> 1)  I am using RStudio for package development, and it creates .Rd
>>>> files for all my .R files including helper files.
>>>> Do the helper .R files need man pages (i.e. .Rd files) ? IF NOT, can
>>>> you tell me how to prevent RStudio from creating these files ?
>>>> 2) If the answer to the above question is YES, then:
>>>> I'm not sure how to come up with working examples for the man pages in
>>>> these helper files. They are called in the middle of my code, and it
>>>> would be hard to provide an example for all these helper functions.
>>>> Any advise or tips for this ?
>>>> Besides, Since these helper functions are not "Exported" in the
>>>> Namespace, the end user will not see these helper functions. So are
>>>> examples necessary ?
>>>> Thanks,
>>>> --Krithika
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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