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

[Jeff Newmiller]

>> any(is.infinite(fval)) || any(is.na(fval))
>
>a little typo here: it should be '|', not '||', right ?

Since `any` collapses the vectors to length 1 either will work, but I would prefer `||`.

On June 7, 2019 6:51:29 AM PDT, Serguei Sokol <serguei.sokol using gmail.com> wrote:
>On 07/06/2019 15:31, 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))
>a little typo here: it should be '|', not '||', right ?
>
>Best,
>Serguei.
>
>> 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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