[R-pkg-devel] try() in R CMD check --as-cran
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(fval)
The problem is that both is.infinite(fval) and 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(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 at 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 at t|@t|k at tu-dortmund@de
Fri Jun 7 11:44:37 CEST 2019
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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> on behalf of J C Nash <profjcnash using 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 mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] ______________________________________________ R-package-devel using r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
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