[R-pkg-devel] "invalid 'envir' argument" note from R-devel
John Fox
jfox at mcmaster.ca
Tue Jul 14 00:47:28 CEST 2015
Dear Duncan and Peter,
I've just arrived at more or less the same thing:
foo <- function() data(package="MASS")
bar <- function() data(package="MASS", envir=.GlobalEnv)
baz <- function() data(package="MASS", envir=globalenv())
all trigger the note when included with the Rcmdr sources:
* checking R code for possible problems ... NOTE
bar: Error while checking: invalid 'envir' argument
baz: Error while checking: invalid 'envir' argument
foo: Error while checking: invalid 'envir' argument
The envir argument to data() defaults to .GlobaEnv .
I hope this helps,
John
> -----Original Message-----
> From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
> Sent: July-13-15 6:32 PM
> To: John Fox; 'peter dalgaard'
> Cc: r-package-devel at r-project.org
> Subject: Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel
>
> On 13/07/2015 5:23 PM, John Fox wrote:
> > Dear Peter,
> >
> >> -----Original Message-----
> >> From: peter dalgaard [mailto:pdalgd at gmail.com]
> >> Sent: July-13-15 4:52 PM
> >> To: John Fox
> >> Cc: r-package-devel at r-project.org
> >> Subject: Re: [R-pkg-devel] "invalid 'envir' argument" note from R-
> devel
> >>
> >> Yes, there was a similar note from Alexandra Kuznetsova a couple of
> days
> >
> > Sorry, I didn't notice that.
> >
> >> ago. Look unintentional, but it is not easy to spot what triggers it.
> If
> >> someone could cook up a minimal example, or - maybe easier given the
> >> relatively short timeframe - bisect their way to the exact svn
> revision
> >> that triggered it, it might help in getting it fixed.
> >
> > I'm afraid that I'm not set up to build R-devel and I'm about to leave
> town
> > for three weeks. I'll see if I can produce a simpler example
> triggering the
> > error, however.
>
> Hana Sevcikova posted a simple example. I'll bisect on it.
>
> Here's her example:
>
> e <- new.env()
> data("mydataset", envir=e)
>
> I've substituted USArrests for "mydataset".
>
> Duncan Murdoch
>
> >
> > Thanks for this,
> > John
> >
> >>
> >> -pd
> >>
> >>> On 13 Jul 2015, at 22:31 , John Fox <jfox at mcmaster.ca> wrote:
> >>>
> >>> Dear list members,
> >>>
> >>> I'm getting a new note from R-devel that I haven't seen before when
> >> checking
> >>> the development version of the Rcmdr package:
> >>>
> >>> * checking R code for possible problems ... NOTE
> >>> readDataFromPackage: Error while checking: invalid 'envir' argument
> >>>
> >>> This note doesn't appear in R 3.2.1.
> >>>
> >>> My session info:
> >>>
> >>> -------- snip ----------
> >>>
> >>> R Under development (unstable) (2015-07-12 r68650)
> >>> Platform: x86_64-w64-mingw32/x64 (64-bit)
> >>> Running under: Windows 7 x64 (build 7601) Service Pack 1
> >>>
> >>> locale:
> >>> [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
> >>> LC_MONETARY=English_Canada.1252
> >>> [4] LC_NUMERIC=C LC_TIME=English_Canada.1252
> >>>
> >>> attached base packages:
> >>> [1] stats graphics grDevices utils datasets methods base
> >>>
> >>> loaded via a namespace (and not attached):
> >>> [1] tools_3.3.0
> >>>
> >>> -------- snip ----------
> >>>
> >>> I can't even localize the problem in readDataFromPackage(). There
> are
> >> only
> >>> two places in this function where there's a function call with an
> >> envir
> >>> argument, and I still get the note if I comment these out. As well,
> >>> readDataFromPackage() seems to work as intended -- there is no
> obvious
> >> error
> >>> in it.
> >>>
> >>> FWIW, here's readDataFromPackage(). The complete sources for the
> >> development
> >>> version of the Rcmdr package are on R-Forge.
> >>>
> >>> -------- snip ----------
> >>>
> >>> readDataFromPackage <- function() {
> >>> env <- environment()
> >>> datasets <- NULL
> >>> initializeDialog(title=gettextRcmdr("Read Data From Package"))
> >>> dsname <- tclVar("")
> >>> package <- NULL
> >>> enterFrame <- tkframe(top)
> >>> entryDsname <- ttkentry(enterFrame, width="20",
> >> textvariable=dsname)
> >>> packages <- sort(.packages())
> >>> packages <- packages[! packages %in% c("base", "stats")]
> >>> packages <- packages[sapply(packages, function(package){
> >>> ds <-
> >>> data(package=package)$results
> >>> if (nrow(ds) == 0)
> >>> return(FALSE)
> >>> ds <- ds[, "Item"]
> >>> valid <- sapply(ds,
> >>> is.valid.name)
> >>> length(ds[valid]) > 0
> >>> })]
> >>> packageDatasetFrame <- tkframe(top)
> >>> packageFrame <- tkframe(packageDatasetFrame)
> >>> max.height <- getRcmdr("variable.list.height")
> >>> packageBox <- tklistbox(packageFrame, height=min(max.height,
> >>> length(packages)),
> >>> exportselection="FALSE",
> >>> selectmode="single", background="white")
> >>> packageScroll <- ttkscrollbar(packageFrame,
> >>> command=function(...) tkyview(packageBox, ...))
> >>> tkconfigure(packageBox, yscrollcommand=function(...)
> >>> tkset(packageScroll, ...))
> >>> for (p in packages) tkinsert(packageBox, "end", p)
> >>> datasetFrame <- tkframe(packageDatasetFrame)
> >>> datasetBox <- tklistbox(datasetFrame, height=max.height,
> >>> exportselection="FALSE",
> >>> selectmode="single", background="white")
> >>> datasetScroll <- ttkscrollbar(datasetFrame,
> >>> command=function(...) tkyview(datasetBox, ...))
> >>> tkconfigure(datasetBox, yscrollcommand=function(...)
> >>> tkset(datasetScroll, ...))
> >>> onPackageSelect <- function(){
> >>> assign("package",
> >>> packages[as.numeric(tkcurselection(packageBox)) + 1], envir=env)
> >>> datasets <<- data(package=package)$results[,3]
> >>> valid <- sapply(datasets, is.valid.name)
> >>> datasets <<- datasets[valid]
> >>> tkdelete(datasetBox, "0", "end")
> >>> for (dataset in datasets) tkinsert(datasetBox, "end",
> >>> dataset)
> >>> tkconfigure(datasetBox, height=min(max.height,
> >>> length(datasets)))
> >>> firstChar <- tolower(substr(datasets, 1, 1))
> >>> len <- length(datasets)
> >>> onLetter <- function(letter){
> >>> letter <- tolower(letter)
> >>> current <- 1 +
> >>> round(as.numeric(unlist(strsplit(tclvalue(tkyview(datasetBox) ), "
> >>> "))[1])*len)
> >>> mat <- match(letter, firstChar[-(1:current)])
> >>> if (is.na(mat)) return()
> >>> tkyview.scroll(datasetBox, mat, "units")
> >>> }
> >>> onA <- function() onLetter("a")
> >>> onB <- function() onLetter("b")
> >>> onC <- function() onLetter("c")
> >>> onD <- function() onLetter("d")
> >>> onE <- function() onLetter("e")
> >>> onF <- function() onLetter("f")
> >>> onG <- function() onLetter("g")
> >>> onH <- function() onLetter("h")
> >>> onI <- function() onLetter("i")
> >>> onJ <- function() onLetter("j")
> >>> onK <- function() onLetter("k")
> >>> onL <- function() onLetter("l")
> >>> onM <- function() onLetter("m")
> >>> onN <- function() onLetter("n")
> >>> onO <- function() onLetter("o")
> >>> onP <- function() onLetter("p")
> >>> onQ <- function() onLetter("q")
> >>> onR <- function() onLetter("r")
> >>> onS <- function() onLetter("s")
> >>> onT <- function() onLetter("t")
> >>> onU <- function() onLetter("u")
> >>> onV <- function() onLetter("v")
> >>> onW <- function() onLetter("w")
> >>> onX <- function() onLetter("x")
> >>> onY <- function() onLetter("y")
> >>> onZ <- function() onLetter("z")
> >>> for (letter in c(letters, LETTERS)){
> >>> tkbind(datasetBox, paste("<", letter, ">", sep=""),
> >>> get(paste("on", toupper(letter),
> >>> sep="")))
> >>> }
> >>> onClick <- function() tkfocus(datasetBox)
> >>> tkbind(datasetBox, "<ButtonPress-1>", onClick)
> >>> }
> >>> onDatasetSelect <- function(){
> >>> tclvalue(dsname) <-
> >>> datasets[as.numeric(tkcurselection(datasetBox)) + 1]
> >>> }
> >>> firstChar <- tolower(substr(packages, 1, 1))
> >>> len <- length(packages)
> >>> onLetter <- function(letter){
> >>> letter <- tolower(letter)
> >>> current <- 1 +
> >>> round(as.numeric(unlist(strsplit(tclvalue(tkyview(packageBox) ), "
> >>> "))[1])*len)
> >>> mat <- match(letter, firstChar[-(1:current)])
> >>> if (is.na(mat)) return()
> >>> tkyview.scroll(packageBox, mat, "units")
> >>> }
> >>> onA <- function() onLetter("a")
> >>> onB <- function() onLetter("b")
> >>> onC <- function() onLetter("c")
> >>> onD <- function() onLetter("d")
> >>> onE <- function() onLetter("e")
> >>> onF <- function() onLetter("f")
> >>> onG <- function() onLetter("g")
> >>> onH <- function() onLetter("h")
> >>> onI <- function() onLetter("i")
> >>> onJ <- function() onLetter("j")
> >>> onK <- function() onLetter("k")
> >>> onL <- function() onLetter("l")
> >>> onM <- function() onLetter("m")
> >>> onN <- function() onLetter("n")
> >>> onO <- function() onLetter("o")
> >>> onP <- function() onLetter("p")
> >>> onQ <- function() onLetter("q")
> >>> onR <- function() onLetter("r")
> >>> onS <- function() onLetter("s")
> >>> onT <- function() onLetter("t")
> >>> onU <- function() onLetter("u")
> >>> onV <- function() onLetter("v")
> >>> onW <- function() onLetter("w")
> >>> onX <- function() onLetter("x")
> >>> onY <- function() onLetter("y")
> >>> onZ <- function() onLetter("z")
> >>> for (letter in c(letters, LETTERS)){
> >>> tkbind(packageBox, paste("<", letter, ">", sep=""),
> >>> get(paste("on", toupper(letter), sep="")))
> >>> }
> >>> onClick <- function() tkfocus(packageBox)
> >>> tkbind(packageBox, "<ButtonPress-1>", onClick)
> >>> onOK <- function(){
> >>> datasetName <-
> >>> datasets[as.numeric(tkcurselection(datasetBox)) + 1]
> >>> dsnameValue <- tclvalue(dsname)
> >>> if (dsnameValue != "" && is.null(package)){
> >>> closeDialog()
> >>> if (is.element(dsnameValue, listDataSets())) {
> >>> if ("no" ==
> >>> tclvalue(checkReplace(dsnameValue, gettextRcmdr("Data set")))){
> >>> if (GrabFocus()) tkgrab.release(top)
> >>> tkdestroy(top)
> >>> readDataFromPackage()
> >>> return()
> >>> }
> >>> }
> >>> save.options <- options(warn=2)
> >>> check <- try(eval(parse(text=logger(paste("data(",
> >>> dsnameValue, ")", sep=""))),
> >>> envir=.GlobalEnv),
> >>> silent=TRUE)
> >>> options(save.options)
> >>> if (class(check) == "try-error"){
> >>> errorCondition(recall=readDataFromPackage,
> >>>
> >>> message=sprintf(gettextRcmdr("Data set %s does not exit"),
> >> dsnameValue))
> >>> return()
> >>> }
> >>> activeDataSet(dsnameValue)
> >>> tkfocus(CommanderWindow())
> >>> }
> >>> else{
> >>> if (is.null(package)) {
> >>> errorCondition(recall=readDataFromPackage,
> >>> message=gettextRcmdr("You must select a package."))
> >>> return()
> >>> }
> >>> if (length(datasetName) == 0) {
> >>> errorCondition(recall=readDataFromPackage,
> >>> message=gettextRcmdr("You must select a data set.") )
> >>> return()
> >>> }
> >>> if (is.element(datasetName, listDataSets())) {
> >>> if ("no" ==
> >>> tclvalue(checkReplace(datasetName, gettextRcmdr("Data set")))){
> >>> if (GrabFocus()) tkgrab.release(top)
> >>> tkdestroy(top)
> >>> readDataFromPackage()
> >>> return()
> >>> }
> >>> }
> >>> closeDialog()
> >>> command <- paste("data(", datasetName, ',
> >>> package="', package, '")', sep="")
> >>> result <- justDoIt(command)
> >>> logger(command)
> >>> if (class(result)[1] != "try-error")
> >>> activeDataSet(datasetName)
> >>> tkfocus(CommanderWindow())
> >>> }
> >>> }
> >>> onDataHelp <- function(){
> >>> datasetName <- datasets[as.numeric(tkcurselection(datasetBox)) +
> 1]
> >>> dsnameValue <- tclvalue(dsname)
> >>> if (dsnameValue == "") dsnameValue <- datasetName
> >>> if (length(dsnameValue) == 0) Message(gettextRcmdr("No data
> >>> set selected."), type="warning")
> >>> else if (is.null(package)) doItAndPrint(paste('help("',
> >>> dsnameValue, '")', sep=""))
> >>> else doItAndPrint(paste('help("', dsnameValue, '",
> >>> package="', package, '")', sep=""))
> >>> }
> >>> OKCancelHelp(helpSubject="data")
> >>> dataHelpButton <- buttonRcmdr(top, text=gettextRcmdr("Help on
> >>> selected data set"), command=onDataHelp)
> >>> tkgrid(labelRcmdr(packageDatasetFrame, text=gettextRcmdr("Package
> >>> (Double-click to select)"), fg=getRcmdr("title.color"),
> >>> font="RcmdrTitleFont"),
> >>> labelRcmdr(packageDatasetFrame, text=" "),
> >>> labelRcmdr(packageDatasetFrame, text=gettextRcmdr("Data set (Double-
> >> click to
> >>> select)"),
> >>> fg=getRcmdr("title.color"),
> >>> font="RcmdrTitleFont"), sticky="w")
> >>> tkgrid(packageBox, packageScroll, sticky="nw")
> >>> tkgrid(datasetBox, datasetScroll, sticky="nw")
> >>> tkgrid(packageFrame, labelRcmdr(packageDatasetFrame, text=" "),
> >>> datasetFrame, sticky="nw")
> >>> tkgrid(packageDatasetFrame, sticky="w")
> >>> tkgrid(labelRcmdr(top, text=gettextRcmdr("OR"), fg="red"),
> >>> sticky="w")
> >>> tkgrid(labelRcmdr(enterFrame, text=gettextRcmdr("Enter name of data
> >>> set: "), fg=getRcmdr("title.color"), font="RcmdrTitleFont"),
> >> entryDsname,
> >>> sticky="w")
> >>> tkgrid(enterFrame, sticky="w")
> >>> tkgrid(dataHelpButton, sticky="w")
> >>> tkgrid(buttonsFrame, sticky="ew")
> >>> tkgrid.configure(packageScroll, sticky="ns")
> >>> tkgrid.configure(datasetScroll, sticky="ns")
> >>> tkbind(packageBox, "<Double-ButtonPress-1>", onPackageSelect)
> >>> tkbind(datasetBox, "<Double-ButtonPress-1>", onDatasetSelect)
> >>> dialogSuffix(focus=entryDsname)
> >>> }
> >>>
> >>> -------- snip ----------
> >>>
> >>> Any insight into the problem would be appreciated.
> >>>
> >>> Thanks,
> >>> John
> >>>
> >>> -----------------------------------------------
> >>> John Fox, Professor
> >>> McMaster University
> >>> Hamilton, Ontario, Canada
> >>> http://socserv.socsci.mcmaster.ca/jfox/
> >>>
> >>>
> >>>
> >>>
> >>> ---
> >>> This email has been checked for viruses by Avast antivirus software.
> >>> https://www.avast.com/antivirus
> >>>
> >>> ______________________________________________
> >>> R-package-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >> --
> >> Peter Dalgaard, Professor,
> >> Center for Statistics, Copenhagen Business School
> >> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> >> Phone: (+45)38153501
> >> Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
> >>
> >>
> >>
> >>
> >>
> >>
> >
> >
> >
> > ---
> > This email has been checked for viruses by Avast antivirus software.
> > https://www.avast.com/antivirus
> >
> > ______________________________________________
> > R-package-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
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