Hi Thierry
Thank you for your comments. I had considered it in the past but decided against it. May think again about switching but would have to change a lot of macros in my text editor. Regards Duncan From: Thierry Onkelinx [mailto:thierry.onkel...@inbo.be] Sent: Thursday, 5 January 2017 07:06 To: Duncan Mackay Cc: R Subject: Re: [R] Sweave: Incorporating warnings into a Sweave output chunck Dear Duncan, I'd recommend to switch from Sweave to knitr. Knitr has more options for handling warnings and errors than Sweave. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey 2017-01-04 4:07 GMT+01:00 Duncan Mackay <dulca...@bigpond.com>: Dear All There are some occasions I have run code in R without warning. After incorporating the code into an .Rnw file and running by Sweave I find there are warnings sent to the screen. On some occasions when I use Sweave(...) I would like to incorporate the warnings into the resulting tex file. Until now I have done it manually which is a bit of a pain. Does anyone know of a way? It would be nice to have a Sweave option to include it. The only reference I can find is https://stat.ethz.ch/pipermail/r-help/2006-December/121892.html which had no replies except this one on Nabble http://r.789695.n4.nabble.com/R-Sweave-and-warning-messages-td814182.html I have got the code from the attached Rnw file working in R version 3.3.1 But there are some problems with it. Below is the code including some of the options and setup with the function in one chunck <<redefwarning, echo=FALSE>>= options(warn = 1) cons <- showConnections(all = TRUE) # .CurFileName <- get("file", env = parent.frame(3)) # modified by next line .CurFileName <- as.vector(unlist( subset(data.frame(cons), class == "file" & nchar(description) > 0)[1]) ) .PrefixName <- strsplit(.CurFileName, "\\. <file:///\\.> ")[[1]][1] .LatexFileName <- paste(.PrefixName, "tex", sepo = ".") .LatexFileCon <- getConnection(what = as.integer(rownames(cons)[which(cons[,1] == .LatexFileName)])) sink(file = .LatexFileCon, append = TRUE, type = "message") warningbck <- warning warning <- function (..., call. = TRUE, immediate. = FALSE, domain = NULL){ args <- list(...) if (length(args) == 1 && inherits(args[[1]], "condition")) { cond <- args[[1]] message <- conditionMessage(cond) call <- conditionCall(cond) withRestarts({ .Internal(.signalCondition(cond, message, call)) .Internal(.dfltStop(message, call)) }, muffleWarning = function() NULL) invisible(message) } else { if (length(args) > 0) { args <- lapply(list(...), as.character) if (is.null(domain) || !is.na(domain)) args <- .Internal(gettext(domain, unlist(args))) message <- paste(args, collapse = "") } else{ message <- "" } writeLines(text = "\n\\end{Sinput}\n\\begin{Soutput}", con = .LatexFileCon) .Internal(warning(as.logical(call.), as.logical(immediate.), message)) writeLines(text = "\\end{Soutput}\n\\begin{Sinput} <file:///\\end%7bSoutput%7d\n\begin%7bSinput%7d> ", con = .LatexFileCon) } } This puts the warning into the input chunck directly after the R command e.g. as shown below \begin{Sinput} clust.hw <- svydesign(ids = ~Patient, data = hw.dat)Warning in svydesign.default(ids = ~Patient, data = hwd) : No weights or probabilities supplied, assuming equal probability \end{Sinput} I think that there also needs to be an argument about closing connections somewhere in the code. Regards Duncan Duncan Mackay Department of Agronomy and Soil Science University of New England Armidale NSW 2351 Email: home: mac...@northnet.com.au ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
