It looks like a bug in codetools. It handles a number of functions
specially; data() is one, binomial() is another. I think there are some
implicit assumptions in it that stats and utils are on the search path,
but in the new tests, they aren't.
Duncan Murdoch
On 14/07/2015 3:40 AM, peter dalgaard wrote:
> 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.dun...@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.dun...@gmail.com]
>>>> Sent: July-13-15 6:32 PM
>>>> To: John Fox; 'peter dalgaard'
>>>> Cc: r-package-devel@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: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/
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ---
>>>>>>> This email has been checked for viruses by Avast antivirus software.
>>>>>>> https://www.avast.com/antivirus
>>>>>>>
>>>>>>> ______________________________________________
>>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ---
>>>>> This email has been checked for viruses by Avast antivirus software.
>>>>> https://www.avast.com/antivirus
>>>>>
>>>>> ______________________________________________
>>>>> R-package-devel@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
>>>
>>
>
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