similar to: Rcmd check does not recognize formal generic function as code object

1. I'm putting together my first package that uses S4 classes and objects. I'd like to document them, but I'm not sure what the documentation should look like, and package.skeleton doesn't produce any at all for the classes or methods. Are there any good examples to follow? 2. How do I do the equivalent of debug(foo), when foo is an anonymous function being used as a method?

Should R CMD check consider it an error to define a new method using setMethod for a class which is not currently defined? It seems to me that it would be best not to consider this an error. What currently happens in that setMethod issues a warning, quite correctly. This warning produces an object 'last.warning'. Then R CMD check issues a WARNING that 'last.warning' is an

Martin Maechler has suggested that I post this comment to r-devel. It was originally posted to bioconductor. --------------------------------- I'd like to raise the issue of a capitalization convention for naming objects in R. Almost everything in R used to be lowercase but recently there is increasing use of mixed upper/lower case to define names. There is potential for using the

I am another person who has had trouble documenting S4 classes and (particularly) methods. The methods package itself is pretty cool by the way, but it is a pity that there are as yet no guidelines on S4 in the "Writing R Extensions" document. I have actually put together a guide on S4 documentation myself for the use of my own lab which is at

I've had repeated problems with promptClass missing methods, usually telling me a class has no methods when it does. In my current case, I've defined an S4 class "mspathCoefficients" with a print method setMethod("print", signature(x="mspathCoefficients"), function(x, ...) { # etc The file promptClass creates has no methods in it. >

please see the code below. foo2 fails to dispatch correctly, but foo does fine. i have tried 'cacheMetaData(1)' and a number of different variants of 'cacheGenericsMetaData', on the possibility there is a caching issue. but i still can't sort it out. also one general question: does it really matter what's in the body of the function definition in a

Dear all, I'm writing to ask for advice as to best practice. A PhD student working with me is writing C++ code that we hope to make public as src code in our Bioconductor package edgeR. He wants to call the function fmm_spline, which is part of the source code for the stats package http://svn.r-project.org/R/trunk/src/library/stats/src/splines.c, from his C++ code. This function

Hi! Have written some functions with signature "numeric". eg. setGeneric("foo", function(object,...) standardGeneric("foo")) setMethod("foo",signature(object="numeric"),def = .... To generate the Rd file sceleton i use > promtClass("numeric") A shell of class documentation has been written to the file

Hello all, I was checking the newest update of my library before submitting it to CRAN, using R 2.15.0 and Rtools for Windows 215 using Rcmd in the Command Prompt, on my x64 Windows7 laptop. I recently heard that for checking packages for CRAN submission one should use the option --as-cran; previously I was submitting packages, so I was trying that for the first time. The check proceeds fine

In R 2.1.1, the default behaviour of scan() was changed to process all C-style escapes, even when a delimiter was specified using the 'sep' argument. A new argument 'allowEscapes' was introduced to turn this processing off. Because read.table() calls scan(), read.table() inherits the new default behaviour of scan() but without a way to turn it off. For example, reading a file

My question has two parts. The first is with regard to the frame or environment in which generic functions are defined in packages. It seems as though they are defined (i.e. exist as objects) in frame 1, even when defined in a package. The following is a short example: setClass("track",representation(x="numeric",y="numeric")) plotTrack <- function(x,y,...)

Hi the devel list. I am adapting the package.skeleton to S4 classes and methods I would have been very proud to post a new working function on this list. Unfortunately, I do not manage to solve all the problems. Mainly - sys.source does not compile a file with setClass - dumpMethod does not exists yet In the following code, thise two problems are notified by a line ################# Still

This is just a suggestion/wish that it would be nice for the F-distribution functions to recognize limiting cases for infinite degrees of freedom, as the t-distribution functions already do. The t-distribution functions recognize that df=Inf is equivalent to the standard normal distribution: > pt(1,df=Inf) [1] 0.8413447 > pnorm(1) [1] 0.8413447 On the other hand, pf() will accept Inf

The R Journal home page doesn't make any promises about how frequently the journal will be published. Historically, though, there have been issues in June and December of each year. The June issue has always appeared by this time (6 August) in previous years. Has there been a change in the publication schedule? Are there still plans for a June 2016 issue? Thanks Gordon

I am building R packages using R 1.7.0pat under Windows 2000 Professional. All works fine except that I haven't been able to figure out how to use the --docs=TYPE option. I would like to optionally turn off building chm help. I have tried build commands like rcmd build --binary --docs=TYPE mypackagename In place of "TYPE" I have tried things like "html",

I do lots of analyses on large microarray data sets so memory use and speed and both important issues for me. I have been trying to estimate the overheads associated with using formal S4 data objects instead of ordinary lists for large data objects. In some simple experiments (using R 1.7.1 in Windows 2000) with large but simple objects it seems that giving a data object a formal class

Hi! I have renamed some functions and deleted others. I have noticed that R CMD check complains only about newly added functions, but documented non-anymore-existing functions seem not to matter. I knew about prompt and promptMethods promptClass. They are extremely useful if you are starting to write a package. But what with existing packages that have to be rewritten? Having code and

Hi Peter and others, If it helps, I wrote a small function glm.scoretest() for the statmod package on CRAN to compute score tests from glm fits. The score test for adding a covariate, or any set of covariates, can be extracted very neatly from the standard glm output, although you probably already know that. Regards Gordon --------------------------------------------- Professor Gordon K

I'm writing functions that need to behave differently for GLMs like binomial and Poisson with fixed deviance, and those like normal or gamma or quasi where the deviance is estimated from the data. Given a glm object, is there a simple way to tell this directly, or do I have to look at the name of the family? Duncan Murdoch

I've noticed a curious interpretation of escaped characters in \examples{} in .Rd files. For example, if I type files <- dir(pattern="\\.txt") at the R prompt, I will get a vector containing all file names in the current directory containing the string ".txt". If I put \examples{ files <- dir(pattern="\\.txt") } in an .Rd file of a package,