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

[Duncan Murdoch]

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(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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