[R-pkg-devel] [External] Re: try() in R CMD check --as-cran
Tomas Kalibera
tom@@@k@||ber@ @end|ng |rom gm@||@com
Fri Jun 14 16:01:24 CEST 2019
The advantage of "abort" (R_Suicide) over the default (R error) is that
it cannot be caught accidentally, so that one can detect more errors,
and it may be easier to find where the error happened. To make the
default behavior less surprising/more user friendly, and to allow
intentional catching of these errors, the default for R CMD check
--as-cran was changed in R-devel so that the normal R error is thrown,
and the documentation in R Internals updated accordingly. One thus has
to set the variable explicitly to get the stricter checks.
Best
Tomas
On 6/7/19 8:51 PM, Tierney, Luke wrote:
> A simplified version without a package:
>
> Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_"="abort,verbose")
> tryCatch(1:3 || 1, error = identity)
>
> Running this aborts the session since it calls R_Suicide without first
> signaling a condition to try any available handlers. Should be easy to
> change, but I don't know if there are any downsides for the CRAN
> workflow. I'll look into it.
>
> Best,
>
> luke
>
>
> On Fri, 7 Jun 2019, William Dunlap wrote:
>
>> I've attached a package, ppp_0.1.tar.gz, which probably will not get
>> through to R-help, that illustrates this.
>> It contains one function which, by default, triggers a condition-length>1
>> issue:
>> f <- function(x = 1:3)
>> {
>> if (x > 1) {
>> x <- -x
>> }
>> stop("this function always gives an error")
>> }
>> and the help file example is
>> try(f())
>>
>> Then
>> env _R_CHECK_LENGTH_1_CONDITION_=abort,verbose R-3.6.0 CMD check
>> --as-cran ppp_0.1.tar.gz
>> results in
>> * checking examples ... ERROR
>> Running examples in ‘ppp-Ex.R’ failed
>> The error most likely occurred in:
>>
>>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>>> ### Name: f
>>> ### Title: Cause an error
>>> ### Aliases: f
>>> ### Keywords: error
>>>
>>> ### ** Examples
>>>
>>> try(f())
>> ----------- FAILURE REPORT --------------
>> --- failure: the condition has length > 1 ---
>> --- srcref ---
>> :
>> --- package (from environment) ---
>> ppp
>> --- call from context ---
>> f()
>> --- call from argument ---
>> if (x > 1) {
>> x <- -x
>> }
>> --- R stacktrace ---
>> where 1: f()
>> where 2: doTryCatch(return(expr), name, parentenv, handler)
>> where 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>> where 4: tryCatchList(expr, classes, parentenv, handlers)
>> where 5: tryCatch(expr, error = function(e) {
>> call <- conditionCall(e)
>> if (!is.null(call)) {
>> if (identical(call[[1L]], quote(doTryCatch)))
>> call <- sys.call(-4L)
>> dcall <- deparse(call)[1L]
>> prefix <- paste("Error in", dcall, ": ")
>> LONG <- 75L
>> sm <- strsplit(conditionMessage(e), "\n")[[1L]]
>> w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
>> if (is.na(w))
>> w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
>> type = "b")
>> if (w > LONG)
>> prefix <- paste0(prefix, "\n ")
>> }
>> else prefix <- "Error : "
>> msg <- paste0(prefix, conditionMessage(e), "\n")
>> .Internal(seterrmessage(msg[1L]))
>> if (!silent && isTRUE(getOption("show.error.messages"))) {
>> cat(msg, file = outFile)
>> .Internal(printDeferredWarnings())
>> }
>> invisible(structure(msg, class = "try-error", condition = e))
>> })
>> where 6: try(f())
>>
>> --- value of length: 3 type: logical ---
>> [1] FALSE TRUE TRUE
>> --- function from context ---
>> function (x = 1:3)
>> {
>> if (x > 1) {
>> x <- -x
>> }
>> stop("this function always gives an error")
>> }
>> <bytecode: 0x4f413d0>
>> <environment: namespace:ppp>
>> --- function search by body ---
>> Function f in namespace ppp has this body.
>> ----------- END OF FAILURE REPORT --------------
>> Fatal error: the condition has length > 1
>> * checking PDF version of manual ... OK
>> * DONE
>>
>> Status: 1 ERROR, 1 NOTE
>> See
>> ‘/tmp/bill/ppp.Rcheck/00check.log’
>> for details.
>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com
>>
>>
>> On Fri, Jun 7, 2019 at 10:21 AM Duncan Murdoch <murdoch.duncan using gmail.com>
>> wrote:
>>
>>> On 07/06/2019 12:32 p.m., William Dunlap wrote:
>>>> The length-condition-not-equal-to-one checks will cause R to shutdown
>>>> even if the code in a tryCatch().
>>> That's strange. I'm unable to reproduce it with my tries, and John's
>>> package is no longer online. Do you have an example I could look at?
>>>
>>> Duncan Murdoch
>>>
>>>> Bill Dunlap
>>>> TIBCO Software
>>>> wdunlap tibco.com <http://tibco.com>
>>>>
>>>>
>>>> On Fri, Jun 7, 2019 at 7:47 AM Duncan Murdoch <murdoch.duncan using gmail.com
>>>> <mailto:murdoch.duncan using gmail.com>> wrote:
>>>>
>>>> On 07/06/2019 9:46 a.m., J C Nash wrote:
>>>> > Should try() not stop those checks from forcing an error?
>>>>
>>>> try(stop("msg")) will print the error message, but won't stop
>>>> execution. Presumably the printed message is what is causing you
>>>> problems. If you want to suppress that, use
>>>>
>>>> try(stop("msg"), silent = TRUE)
>>>>
>>>> Duncan Murdoch
>>>>
>>>> >
>>>> > I recognize that this is the failure -- it is indeed the check
>>>> I'm trying to
>>>> > catch -- but I don't want tests of such checks to fail my package.
>>>> >
>>>> > JN
>>>> >
>>>> > On 2019-06-07 9:31 a.m., Sebastian Meyer wrote:
>>>> >> The failure stated in the R CMD check failure report is:
>>>> >>
>>>> >>> --- failure: length > 1 in coercion to logical ---
>>>> >>
>>>> >> This comes from --as-cran performing useful extra checks via
>>>> setting the
>>>> >> environment variable _R_CHECK_LENGTH_1_LOGIC2_, which means:
>>>> >>
>>>> >>> check if either argument of the binary operators && and || has
>>>> length greater than one.
>>>> >>
>>>> >> (see
>>>> https://cran.r-project.org/doc/manuals/r-release/R-ints.html#Tools)
>>>> >>
>>>> >> The failure report also states the source of the failure:
>>>> >>
>>>> >>> --- call from context ---
>>>> >>> fchk(x, benbad, trace = 3, y)
>>>> >>> --- call from argument ---
>>>> >>> is.infinite(fval) || is.na <http://is.na>(fval)
>>>> >>
>>>> >> The problem is that both is.infinite(fval) and is.na
>>>> <http://is.na>(fval) return
>>>> >> vectors of length 10 in your test case:
>>>> >>
>>>> >>> --- value of length: 10 type: logical ---
>>>> >>> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
>>> FALSE
>>>> >>
>>>> >> The || operator works on length 1 Booleans. Since fval can be of
>>>> length
>>>> >> greater than 1 at that point, the proper condition seems to be:
>>>> >>
>>>> >> any(is.infinite(fval)) || any(is.na <http://is.na>(fval))
>>>> >>
>>>> >> Best regards,
>>>> >>
>>>> >> Sebastian
>>>> >>
>>>> >>
>>>> >> Am 07.06.19 um 14:53 schrieb J C Nash:
>>>> >>> Sorry reply not quicker. For some reason I'm not getting
>>>> anything in the thread I started!
>>>> >>> I found the responses in the archives. Perhaps cc:
>>>> nashjc using uottawa.ca <mailto:nashjc using uottawa.ca> please.
>>>> >>>
>>>> >>> I have prepared a tiny (2.8K) package at
>>>> >>> http://web.ncf.ca/nashjc/jfiles/fchk_2019-6.5.tar.gz
>>>> >>>
>>>> >>> R CMD check --> OK
>>>> >>>
>>>> >>> R CMD check --as-cran --> 1 ERROR, 1 NOTE
>>>> >>>
>>>> >>> The error is in an example:
>>>> >>>
>>>> >>>> benbad<-function(x, y){
>>>> >>>> # y may be provided with different structures
>>>> >>>> f<-(x-y)^2
>>>> >>>> } # very simple, but ...
>>>> >>>>
>>>> >>>> y<-1:10
>>>> >>>> x<-c(1)
>>>> >>>> cat("test benbad() with y=1:10, x=c(1)\n")
>>>> >>>> tryfc01 <- try(fc01<-fchk(x, benbad, trace=3, y))
>>>> >>>> print(tryfc01)
>>>> >>>> print(fc01)
>>>> >>>
>>>> >>> There's quite a lot of output, but it doesn't make much sense
>>>> to me, as
>>>> >>> it refers to code that I didn't write.
>>>> >>>
>>>> >>> The function fchk is attempting to check if functions provided
>>> for
>>>> >>> optimization do not violate some conditions e.g., character
>>>> rather than
>>>> >>> numeric etc.
>>>> >>>
>>>> >>> JN
>>>> >>>
>>>> >>>
>>>> >>> On 2019-06-07 8:44 a.m., J C Nash wrote:
>>>> >>>> Uwe Ligges ||gge@ @end|ng |rom @t using t|@t|k using tu-dortmund@de
>>>> >>>> Fri Jun 7 11:44:37 CEST 2019
>>>> >>>>
>>>> >>>> Previous message (by thread): [R-pkg-devel] try() in R
>>>> CMD check --as-cran
>>>> >>>> Next message (by thread): [R-pkg-devel] using package
>>>> data in package code
>>>> >>>> Messages sorted by: [ date ] [ thread ] [ subject ] [
>>>> author ]
>>>> >>>>
>>>> >>>> Right, what problem are you talking about? Can you tell us
>>>> which check
>>>> >>>> it is and what it actually complained about.
>>>> >>>> There is no check that looks at the sizes of x and y in
>>>> exypressions
>>>> >>>> such as
>>>> >>>> (x - y)^2.
>>>> >>>> as far as I know.
>>>> >>>>
>>>> >>>> Best,
>>>> >>>> Uwe
>>>> >>>>
>>>> >>>> On 07.06.2019 10:33, Berry Boessenkool wrote:
>>>> >>>>>
>>>> >>>>> Not entirely sure if this is what you're looking for:
>>>> >>>>>
>>>>
>>> https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R
>>>> >>>>> It does contain --as-cran a few times and there's the
>>>> change-history:
>>>> >>>>>
>>>>
>>> https://github.com/wch/r-source/commits/trunk/src/library/tools/R/check.R
>>>> >>>>>
>>>> >>>>> Regards,
>>>> >>>>> Berry
>>>> >>>>>
>>>> >>>>>
>>>> >>>>> ________________________________
>>>> >>>>> From: R-package-devel <r-package-devel-bounces using
>>>> r-project.org <http://r-project.org>> on behalf of J C Nash
>>>> <profjcnash using gmail.com <http://gmail.com>>
>>>> >>>>> Sent: Thursday, June 6, 2019 15:03
>>>> >>>>> To: List r-package-devel
>>>> >>>>> Subject: [R-pkg-devel] try() in R CMD check --as-cran
>>>> >>>>>
>>>> >>>>> After making a small fix to my optimx package, I ran my usual
>>>> R CMD check --as-cran.
>>>> >>>>>
>>>> >>>>> To my surprise, I got two ERRORs unrelated to the change. The
>>>> errors popped up in
>>>> >>>>> a routine designed to check the call to the user objective
>>>> function. In particular,
>>>> >>>>> one check is that the size of vectors is the same in
>>>> expressions like (x - y)^2.
>>>> >>>>> This works fine with R CMD check, but the --as-cran seems to
>>>> have changed and it
>>>> >>>>> pops an error, even when the call is inside try(). The irony
>>>> that the routine in
>>>> >>>>> question is intended to avoid problems like this is not lost
>>>> on me.
>>>> >>>>>
>>>> >>>>> I'm working on a small reproducible example, but it's not
>>>> small enough yet.
>>>> >>>>> In the meantime, I'm looking for the source codes of the
>>>> scripts for "R CMD check" and
>>>> >>>>> "R CMD check --as-cran" so I can work out why there is this
>>>> difference, which seems
>>>> >>>>> to be recent.
>>>> >>>>>
>>>> >>>>> Can someone send/post a link? I plan to figure this out and
>>>> provide feedback,
>>>> >>>>> as I suspect it is going to affect others. However, it may be
>>>> a few days or even
>>>> >>>>> weeks if past experience is a guide.
>>>> >>>>>
>>>> >>>>> JN
>>>> >>>>>
>>>> >>>>> ______________________________________________
>>>> >>>>> R-package-devel using r-project.org <http://r-project.org>
>>>> mailing list
>>>> >>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>> >>>>>
>>>> >>>>> [[alternative HTML version deleted]]
>>>> >>>>>
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>>>> >>>>>
>>>> >>>>
>>>> >>>
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>>>> >>
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>>>> >
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