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

Dear Duncan,

On Mon, 13 Jul 2015 20:00:02 -0400
 Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
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.
If you mean an unexported function named data() in the Rcmdr package, then I'm pretty sure that there is none -- and I just checked all of the many uses of the word "data" in the Rcmdr sources. Of course, I may have missed something or, more likely, misunderstood what you're suggesting.
I tracked it down to a bug in codetools.  The "envir" it is talking
about is an argument to a different function, nothing to do with the
argument to data().

I've passed it on to Luke Tierney, author of codetools.

Duncan Murdoch
Best,
 John

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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______________________________________________
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

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------------------------------------------------
John Fox, Professor
McMaster University
Hamilton, Ontario, Canada
http://socserv.mcmaster.ca/jfox/

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

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