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

[J C Nash]

Should try() not stop those checks from forcing an error?

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(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
>>>>
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>>>
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