similar to: Compatibility issues caused by new simplify argument in apply function

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

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

? Sat, 17 Feb 2024 11:15:43 -0700 "Reed A. Cartwright" <racartwright at gmail.com> ?????: > I'm wrapping a function in R and I want to record all the arguments > passed to it, including default values and missing values. This is hard if not impossible to implement for the general case because the default arguments are evaluated in the environment of the function as it

Dear R-developers, in a new package, I'm currently working on, I tried to add a new method to function "t.test". The new class, on which the method is based, is called "speclib", so I defined the funcion for the new method as "t.test.speclib". R CMD check now gives always a warning, that S3 methods are not consistent, because R does not recognize that the

hsdar is back on CRAN We are very happy to announce that a new version of the hsdar-package (hyperspectral data analysis in R) is available on CRAN. The introductory vignette is available here: https://cran.r-project.org/web/packages/hsdar/vignettes/Hsdar-intro.pdf The main class "Speclib" has been changed in that the additional information is now stored in the SI slot (function

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

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

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

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, this is perhaps not so much an issue, but as you are currently working on the Rd parser anyway... When you want to document specific S4 methods for an S4 generic by \S4method{} within a \usage{} environment, and the second (signature_list) argument is "long", be it because you use multiple dispatch, be it because you use long class-names, (or both), one would probably like to be

(earlier I sent it as html by mistake). Hi, How can I get from C an object name used as a function argument? I have sample code in C that gives me access to the name of the function being called: SEXP xname(SEXP x) { const char *fun_name = CHAR(PRINTNAME(CAR(x))); x = CDR(x); const char *arg_name = isNull(TAG(x)) ? "" : CHAR(PRINTNAME(TAG(x)));

Hi, another Rd related issue I encountered is that if an error occurs in an \Sexpr in an Rd file, then on get the following error: * checking for portable compilation flags in Makevars ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking examples ... ERROR Error in paste(before, x, after, sep = "") : object 'exfile' not found Execution halted

# HG changeset patch # User Jim Fehlig <jfehlig@suse.com> # Date 1360861948 -3600 # Node ID 0f9c7503650fa1b1103b769e1129d66ff614b2ad # Parent cffb489a6df37d8d114e7d2d53a7a85d14e8f968 tools/xend: Only add cpuid and cpuid_check to sexpr once When converting a XendConfig object to sexpr, cpuid and cpuid_check were being emitted twice in the resulting sexpr. The first conversion writes

Hello, Here's an example that renders correctly using Rd2txt / Rd2latex / R CMD Rd2pdf, but has problems under Rd2HTML: \name{foo} \title{foo} \section{foo}{ This should be on a separate paragraph This should be on a separate paragraph This should be on a separate paragraph \Sexpr[stage=render,results=rd]{ paste( rep('Sexpr: This should be on a separate

Hi all, On FC5, using: Version 2.3.1 Patched (2006-08-06 r38829) and today's R version 2.4.0 alpha (2006-09-19 r39397) with the following .Rnw file: \documentclass[10pt]{article} \begin{document} This line should print '2': \Sexpr{1 + 1} %% This line should NOT print '2': \Sexpr{1 + 1} \end{document} The \Sexpr in the second line is processed even though the

Hi all, On FC5, using: Version 2.3.1 Patched (2006-08-06 r38829) and today's R version 2.4.0 alpha (2006-09-19 r39397) with the following .Rnw file: \documentclass[10pt]{article} \begin{document} This line should print '2': \Sexpr{1 + 1} %% This line should NOT print '2': \Sexpr{1 + 1} \end{document} The \Sexpr in the second line is processed even though the

I would like to create \examples{} in the manual dynamically, and while it is possible to do this with a \Sexpr at the top level, R CMD check issues a warning for it. (See below.) Is it intentional that \Sexpr is not allowed at the top level? The Rd grammar allows this, but R CMD check does not. Is there any other way to generate/modify the \examples{} section dynamically? Thanks, Gabor In

Hi, has anybody encountered and solved the following problem? I continued work now on a different computer where I have also used Sweave successfully before. I can run Sweave() and it generates a .tex file. All code chunks are processed and translated to Latex perfectly fine but somehow only the \Sexpr{} tags are not parsed. This is an example .Rnw: \documentclass{article} \usepackage{Sweave}

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