similar to: some (minor) Rd issue: line breaking in \S4method within \usage{}

Dear developers, We want to use "\S4method" to document new S4-methods for "[" and "[<-". We use this for other functions/methods and it works without any problem, but in case of "[" and "[<-" we didn't manage to bring this to work. The problem occurs in the development version of our package "distrSim" which can be found

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Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Given S4 methods [ and [<-, how do I write the Rd-file usage clause for the latter one? What I have now is: \S4method{[}{TimeSeries,TimeDate,missing}(x, i, j, ..., drop) \S4method{[<-}{TimeSeries,TimeDate,missing,ANY}(x, i, j, ..., value) which results in the following output: ## S4 method for signature 'TimeSeries, TimeDate, missing': x[i, j, ..., drop]

Hi, I have seen several packages that with the most recent version of R are giving a warning like this: Assignments in \usage in documentation object 'marginalData-methods': marginalData(object) = value I assume that this is to prevent people from making assignments in their usage statements (which seems completely understandable). But what about the case above? This is a person

Dear R Developers, the new simplify argument in apply causes that my package (hsdar) does not pass the checks in R-devel. The workaround, Kurt Hornik send me, is working for the R-code: if("simplify" %in% names(formals(base::apply))) do something else do something else Unfortunately, I cannot conditionalize the man pages of the functions. I get the message that

Interesting problem. I'm very rusty on S4 but would one solution be to, already now, add 'simplify = TRUE' to the S4 method and document it; setMethod("apply", signature(X = "Speclib"), function(X, FUN, bySI = NULL, ..., simplify = TRUE) { ? Henrik On Fri, May 22, 2020 at 6:26

Dear list members, I have defined a binary operator %append% with methods for some S4 classes. In my documentation file, I want to list the methods explicitly by using e.g.: \S4method{\%append\%}{RecLinkData,RecLinkData}(x, y) In the HTML documentation this comes out right as ## S4 method for signature 'RecLinkResult,RecLinkResult' x %append% y , but R CMD check

What is the Rd file alias and usage syntax for an S4 assignment method? I have been trying variations on \alias{TSdoc<-,default-method} \usage{ \S4method{TSdoc}{default}(x) <- value but so far I have not got it right according to various codoc, etc, checks. Paul Gilbert ==================================================================================== La version fran?aise

I would like to add a class to the SparseM package. I have a class "matrix.csr" that describes a matrix in compressed sparse row format, now I would like a class matrix.diag.csr that describes such objects when they happen to be diagonal. The idea is that matrix.diag.csr objects should behave (later in life) exactly like matrix.csr objects, the distinction is only needed in order to

I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })

Hi, I do not know if everybody finds index pages of the html-formatted R help useful, but I know I am at least not the only one who uses them extensively to get the overview of functions and methods in a package (even for my own package). Problems arise, however, if a lot of S4 methods need to be documented blowing out the index with (generally irrelevant) entries like:

Hi, I'm documenting a package that makes heavy use of S4 methods at the moment, and I'm having a hard time from keeping the PDF output of Rd from looking really terrible. First of all, what is the preferred way to actually document S4 methods? When I use promptClass/promptMethod, I get a style that doesn't use the \S4method macro and puts the entire function signature into a \item.

You didn't explained what the error is. This is what it looks like to me, but I'm probably wrong in some details: 1. R-devel added an argument to the apply() function, so the header has changed from function (X, MARGIN, FUN, ...) to function(X, MARGIN, FUN, ..., simplify = TRUE) 2. Your package converted the function apply() to an S4 generic. 3. Now the signatures of your

Hi, Say we want to supply a generic plot() in a package with a simple class, like this: ---<--------------------cut here---------------start------------------->--- setClass("track", representation=representation(x="numeric", y="numeric")) if (!isGeneric("plot")) { setGeneric("plot", function(x, y, ...)

I get the following error from one of my Rd files in R CMD check (R 2-14.0) * checking Rd files ... WARNING Error in switch(attr(block, "Rd_tag"), TEXT = if (!grepl("^[[:space:]]* $", : EXPR must be a length 1 vector problem found in ?backsolve.Rd? This is likely something that will be glaringly obvious once it's pointed out, but without a line number I can't

If I call .S4methods(sd) I get the error ## Error in getGeneric(generic.function) : ## argument 'f' must be a string, generic function, or primitive: got an ordinary function By contrast, methods and .S3methods just state that no methods are found. methods(sd) ## no methods found S3methods(sd) ## no methods found It seems like the behavior of these functions ought to be consistent.

Hello R-List, ** This e-mail was initially bounced. Please forgive any duplicates.** I'm creating a new generic function and 3 associated methods, in which each of the methods only needs a subset of the arguments specified in the generic. So, I create the generic like so (with the signature defaulting to all of the args) ... setGeneric( name="myFunction", def =

Hi, I just figured out that I accidentally posted my message in HTML, so I am retrying in plain text only. Sorry. I am currently extending one of our CRAN packages and ran into an unexpected problem when checking the source package. I got some warnings in the step "* checking for code/documentation mismatches". I double checked everything and did not see anything that would