[R-pkg-devel] try() in R CMD check --as-cran
Serguei Sokol
@ergue|@@oko| @end|ng |rom gm@||@com
Fri Jun 7 16:09:21 CEST 2019
On 07/06/2019 16:05, Jeff Newmiller wrote:
>>> 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 `||`.
You are right, I missed the second 'any()' at the first glance. I read
it as 'any(v1 || v2)'. My bad.
>
> 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
>>>>>>
>>>>>> ______________________________________________
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>>>>>>
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>>>>>>
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