[R-pkg-devel] "invalid 'envir' argument" note from R-devel

peter dalgaard pdalgd at gmail.com
Tue Jul 14 09:40:42 CEST 2015 

The danger of minimal examples is that you risk working around only one aspect. 

The ones Alexandra had (from the sensR package) didn't (all?) involve data(). A couple of them were like the one below, in which the FORTRANesque style of naming the function the same as the variable with the eventual return value is a bit curious, but hardly illegal.

Then again, the version of sensR that she linked to hadn't had the namespace issues sorted, so there was quite a bit of "no visible global" messages as well. 

twoAFC <- function() {
  twoAFC <- binomial()
  twoAFC$link <- "Link for the 2-AFC test"
  twoAFC$linkinv <- function(eta) {
    ok <- eta > 0
    eta[!ok] <- 0.5
    eta[ok] <- pnorm(eta[ok] / sqrt(2))
    pmin(pmax(eta, 0.5), 1) ## restrict to [0.5, 1] - just to be sure
  }
  twoAFC$mu.eta <- function(eta) {
    ok <- eta >= 0
    eta[!ok] <- 0
    if(any(ok)) {
      sqrt.2 <- sqrt(1/2)
      eta[ok] <- dnorm(eta[ok] * sqrt.2) * sqrt.2
    }
    pmax(eta, 0) ## gradient cannot be negative.
  }
  twoAFC$linkfun <- function(mu) {
    ok <- mu > 0.5 & mu < 1
    mu[mu <= 0.5] <- 0
    mu[mu >= 1] <- Inf
    mu[ok] <- sqrt(2) * qnorm(mu[ok])
    pmax(mu, 0) ## delta cannot be negative
  }
  twoAFC
}

-pd

(In a hotel room in Aarhus, so not going to spend time on this for a couple of days.)


> On 14 Jul 2015, at 01:01 , Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
> 
> 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
>>>> 
>> 
>> 
>> ---
>> This email has been checked for viruses by Avast antivirus software.
>> https://www.avast.com/antivirus
>> 
> 

-- 
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

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