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] question regarding man pages
3 messages · Krithika Bhuvaneshwar, Kasper Daniel Hansen
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
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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
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