similar to: package vignettes, suggests and R CMD check

Hi r-devels, I am stuck in some S4 inheritance problem: setClass("A",representation(a="numeric")) setClass("A1",representation(b="numeric"),contains="A") setClass("A2",representation(c="numeric"),contains="A1") if(!isGeneric("foo")){ setGeneric("foo", function(x,y,z, ...)

Hi R-devels, I noticed that for the scheduled R 2.3.0, there is still no function df() for non-centrality != 0. Easter is quickly approaching, so as my little gift, I would like to offer you some code to fill this gap: After excluding some "unusual" cases, it amounts to differentiating the corresponding function pnf() --- which in turn leads to the function dnbeta() already available

Hi R-devels, in "Writing R extensions" as well as in the help to .onAttach(), you mention that one could use this function to issue a start-up message/banner for the package. My little wish for Easter: a 'quietly'-type argument for .onAttach() / .First.lib() which is passed through by functions require() and library() respectively, and by means of which one could optionally

Dear all, I have a question regarding setIs and method dispatch in S4 classes: Consider the following example: ##################################################### ## A02 "contains" A01 by setIs: setClass("A01", representation(a="numeric",b="numeric")) setClass("A02", representation(a="numeric",d="numeric"))

Hello, after some discussions with Martin Maechler and Josef Leydold (WU Wien), we have felt the need for some package that should allow for an object-orientated approach to distributions. Our small group at Bayreuth now has developed a package "distr" which tries to fill this gap, implementing distributions by means of S4--classes. A mother class "Distribution" is

Hi R-devels, recently, we have seen a new warning by "R CMD check" appearing for the devel-version of our package distrEx available on r-forge, e.g. as *|install.packages("/distrEx/",repos="http://r-forge.r-project.org")|* Here is the warning: %--------------------- [...snip ...] * checking for unstated dependencies in R code ... WARNING .get_S4_methods_list():

Hello, I'm trying to rebuild a package (using R version 3.3.2 (2016-10-31)) that has not seen any changes since it was last built without problems in previous R versions. It fails during vignette building with: ---<--------------------cut here---------------start------------------->--- $ R CMD build diveMove * checking for file ?diveMove/DESCRIPTION? ... OK * preparing ?diveMove?: *

A package uses VignetteEngine: knitr; the package itself does not Suggests: knitr, but it Suggests: BiocStyle which in turn Suggests: knitr. Nonetheless, R CMD check fails indicating that a package required for checking is not declared. Is it really the intention that the original package duplicate Suggests: knitr? This is only with a recent R. In detail, with $ Rdev --version|head -3 R Under

Hi, Does anyone know what the distribution for the product of two correlated normal? Say I have X~N(a, \sigma1^2) and Y~N(b, \sigma2^2), and the \rou(X,Y) is not equal to 0, I want to know the pdf or cdf of XY. Thanks a lot in advance. yu [[alternative HTML version deleted]]

Hi all, I have a question regarding how to properly analyze a data set and then how to perform the analysis in R. First, I have data that I would like to analyze using a mixed GLM (I think this is the most appropriate method, but I am unsure). In a mixed model (y = X*beta+Z*gamma+epsilon), I would like to structure the variance matrices of gamma, G, and the error, R, to take advantage of all my

Hello, I have a question on how to tabulate the time series data. I use RStudio, but if can be done in any other R editor, it should work in RStudio as well. > a1<-11:22 > a1ts<-ts(a1, frequency=4, start=c(1978,1)) > a1ts Qtr1 Qtr2 Qtr3 Qtr4 1978 11 12 13 14 1979 15 16 17 18 1980 19 20 21 22 If I click the variable "a1ts" on the

Hi, I have a package that contains two vignettes that both use saved objects in the examples directory of the package. With previous versions of R I could have a code chunk in the vignette like this: <<echo=false>>= load("../examples/somedata.Rdata") @ followed by a code chunk like <<eval=false>>= foo <- bar("data") @ that simulated the actual

Hi R-devels, I encounter the following problem when I want to build a vignette in the package building process under Windows platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor

Hi, Recently I saw a couple of cases in which the package vignettes were somewhat complicated so that Stangle() (or knitr::purl() or other tangling functions) can fail to produce the exact R code that is executed by the weaving function Sweave() (or knitr::knit(), ...). For example, this is a valid document that can pass the weaving process but cannot generate a valid R script to be source()d:

Hi, I was not able to find a way such that R CMD build run Sweave with eval=FALSE. I have a package where I want the R code in the vignettes to run only during R CMD check but not on R CMD build. Is there any way to achieve this ? thank you. ____________________________________________________________________________________Got a little couch potato? Check out fun summer activities

Dear R-helpers, www.statistik.lmu.de/~*leisch*/*Sweave*/*Sweave*-Rnews-2003-2.pdf says that R CMD build creates the pdf from a .Rnw file. But when I do R CMD build followed by R CMD check it gives me a warning that there is a vignette without a PDF. My query is : when R CMD build works it creates a pdf in the doc subdirectory of the directory returned by system.file(package = mypackage) and not

Dear all, I have a data.frame with a column like the x shown below myDF<-data.frame(cbind(x=c("[[1, 0, 0], [0, 1]]", "[[1, 1, 0], [0, 1]]","[[1, 0, 0], [1, 1]]", "[[0, 0, 1], [0, 1]]"))) > myDF x 1 [[1, 0, 0], [0, 1]] 2 [[1, 1, 0], [0, 1]] 3 [[1, 0, 0], [1, 1]] 4 [[0, 0, 1], [0, 1]] As you can see my x column is composed of

Hi, as a starting point for using Tcl/Tk in R, I used to refer to James Wettenhall's nicely presented TclTk Examples formerly hosted at http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/ These days I have been trying to reach these pages but without success. Does anyone know (James, himself, perhaps ;-) whether they are / will be available at some other location --- it would be a pity

Hi, I noticed a minor flaw in integrate() from package stats: Taking up arguments lower and upper from integrate(), if (lower == Inf) && (upper == Inf) or if (lower == -Inf) && (upper == -Inf) integrate() calculates the value for (lower==-Inf) && (upper==Inf). Rather, it should return 0. Quick fix: ### old code ### ### [snip] else {

Hi, I found the following problem with recent R-devel (2010-08-26 r52817) on Windows (32-bit and 64-bit): 'R CMD build <pkg>' gets stalled during vignette creation for packages that have a Makefile in <pkg>/inst/doc. It seems that the problem is that the commands used in the Makefile for converting .tex to .pdf are not able to locate the Sweave.sty file anymore (if I drop