[R] Sweave: Incorporating warnings into a Sweave output chunck

[Thierry Onkelinx]

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 <dulcalma op 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, "\\.")[[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}", 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: mackay op northnet.com.au
>
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