[R-pkg-devel] "invalid 'envir' argument" note from R-devel
Duncan Murdoch
murdoch.duncan at gmail.com
Tue Jul 14 01:01:06 CEST 2015
It happened in r68597. In my example, I hadn't imported the data()
function from utils; when I did that, it was fixed.
Not sure why the error is complaining about the envir argument.
Duncan Murdoch
On 13/07/2015 6:47 PM, John Fox wrote:
> 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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