[Bioc-devel] Roxygen documentation under windows

2018-10-07 Thread Christian Mertes
Hey all, I have a question. My package builds perfectly on Linux and MacOS, but fails to link my documentation correctly on Windows, which results in a warning. The exact error which I get is: Rd warning:

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

2018-10-07 Thread Obenchain, Valerie
I forgot to add the .BBSoptions file should be located at the 'top' level of the package, e.g., MTseekerData/.BBSoptions. You might as well add that now instead of waiting until the packages are approved. I think the SPB was modified to be aware of the .BBSoptions file so it may require it too

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

2018-10-07 Thread Obenchain, Valerie
Hi Tim, As Michael said, the usual case is the data package 'Suggests' the software and the software 'Depends' or 'Imports' the data but this dependency could be reversed. When submitting a combo of packages to the SPB for review, the package that 'Suggests' is submitted first followed by the

Re: [Rd] Warning when calling formals() for `[`.

2018-10-07 Thread Peter Dalgaard
> On 7 Oct 2018, at 16:04 , Rui Barradas wrote: > > Hello, > > I don't see why you say that the documentation seems to be wrong: > > > class(args(`+`)) > #[1] "function" > > > args() on a primitive does return a closure. At least in this case it does. But in this case it doesn't: >

Re: [Rd] Warning when calling formals() for `[`.

2018-10-07 Thread Rui Barradas
Hello, This is because args(`[`) returns NULL and class(NULL) is NULL. So the question would be why is the return value of args(`[`) NULL? Rui Barradas Às 15:14 de 07/10/2018, Peter Dalgaard escreveu: On 7 Oct 2018, at 16:04 , Rui Barradas wrote: Hello, I don't see why you say that the

Re: [Rd] Warning when calling formals() for `[`.

2018-10-07 Thread Rui Barradas
Hello, This is the *third* time I send this, the first two I had a failure notice so if you have already received it please apologize. I believe this is consistent with the doc. From section Value: formals returns the formal argument list of the function specified, as a pairlist, or NULL

Re: [Rd] Warning when calling formals() for `[`.

2018-10-07 Thread Laurent Gautier
Note that having "function" in its class attribute does not make an object a primitive. For example: > class(`[`) [1] "function" > is.primitive(`[`) [1] TRUE > class(`rnorm`) [1] "function" > is.primitive(`rnorm`) [1] FALSE Le dim. 7 oct. 2018 à 10:04, Rui Barradas a écrit : > Hello, > > I

Re: [Rd] Warning when calling formals() for `[`.

2018-10-07 Thread Rui Barradas
Hello, I don't see why you say that the documentation seems to be wrong: class(args(`+`)) #[1] "function" args() on a primitive does return a closure. At least in this case it does. Rui Barradas Às 14:05 de 07/10/2018, Peter Dalgaard escreveu: There is more "fun" afoot here, but I don't

Re: [Rd] Warning when calling formals() for `[`.

2018-10-07 Thread Peter Dalgaard
There is more "fun" afoot here, but I don't recall what the point may be: > args(get("+")) function (e1, e2) NULL > args(get("[")) NULL > get("[") .Primitive("[") > get("+") function (e1, e2) .Primitive("+") The other index operators, "[[", "[<-", "[[<-" are similar The docs are pretty clear