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

getAnywhere("data")

On 13/07/2015 7:35 PM, John Fox wrote:

Dear Duncan,

-----Original Message-----
From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
Sent: July-13-15 7:01 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

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.

Yes, importing data works for me too! It's odd that the problem didn't show
up as an undefined global symbol rather than as a note about the envir
argument. (I was fixing imports from standard packages when the problem
arose.)

I'd guess that it's finding some other private function called data();
that's probably worth fixing.

Duncan

Thanks for tracking this down.

John

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/




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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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