[R-pkg-devel] try() in R CMD check --as-cran

[Sebastian Meyer]

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 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> 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]]
>>>
>>> ______________________________________________
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>>>
>>
> 
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