On 13/07/2015 5:23 PM, John Fox wrote:
> Dear Peter,
>
>> -----Original Message-----
>> From: peter dalgaard [mailto:pda...@gmail.com]
>> Sent: July-13-15 4:52 PM
>> To: John Fox
>> Cc: r-package-devel@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 <j...@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/
>>>
>>>
>>>
>>>
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>>>
>>> ______________________________________________
>>> R-package-devel@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....@cbs.dk Priv: pda...@gmail.com
>>
>>
>>
>>
>>
>>
>
>
>
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