[R-pkg-devel] CRAN packages suggesting other packages but not using them conditionally

[Ben Bolker]

   Apologies if I'm telling you something you already know:

   By default, fda::CRAN() uses the presence of environment variables 
matched by the regexp "^_R_" as a heuristic to decide whether it's being 
running on CRAN.

   testthat::skip_on_cran()  calls testthat::on_cran() to look for an 
environment variable called NOT_CRAN equal to "true". The 
devtools::check() machinery automatically sets this variable.


   So: fda::CRAN() depends on breakable assumptions, defaults to FALSE 
in an empty environment.  skip_on_cran() defaults to TRUE in an empty 
environment (but defaults to FALSE in a devtools::check() environment).


On 12/12/20 2:19 PM, Spencer Graves wrote:
>        I have tests in my code to detect when something like that is not 
> available.
> 
> 
>        I also have code in "\examples" to skip tests that would 
> encounter that.
> 
> 
>        Hadley's "testthhat:skip_on_cran" is supposed to suppress tests 
> like that on CRAN.  I have so far failed to understand how to use this 
> function that Hadley wrote.  Instead, I use things like the following:
> 
> 
> if(!fda::CRAN()){
> # Code that I want to run everyplace that's NOT CRAN
> 
> 
> }
> 
> 
>        When I wrote "fda::CRAN", I was told that I shouldn't do it, but 
> I didn't see a better option, and I've been using it for several years 
> now without being given a reason to discontinue using it or (better?) 
> being given an alternative that seems better to me.
> 
> 
>        Spencer
> 
> 
> On 2020-12-12 12:40, Michael L Friendly wrote:
>> Thanks, Dirk
>>
>> Just to clarify--
>> In my packages, candisc, heplots, vcdExtra I have mostly 2D graphic 
>> methods, but some 3D methods that use
>> rgl.  I therefore put rgl into Suggests:
>>
>> Could I solve this by making rgl a Depends: ?
>>
>> -Michael
>>
>>
>> -----Original Message-----
>> From: Dirk Eddelbuettel <edd using debian.org>
>> Sent: Saturday, December 12, 2020 12:46 PM
>> To: Michael L Friendly <friendly using yorku.ca>
>> Cc: r-package-devel using R-project.org; Prof Brian Ripley 
>> <ripley using stats.ox.ac.uk>
>> Subject: Re: [R-pkg-devel] CRAN packages suggesting other packages but 
>> not using them conditionally
>>
>>
>> On 12 December 2020 at 16:24, Michael L Friendly wrote:
>> | I got the email below concerning 3 of my packages but wonder if they
>> | are false alarms or if not, how to locate & fix the problem.
>> |
>> |     This concerns packages: ...
>> |
>> |     Suggested packages should be used conditionally: see  1.1.3.1 of 
>> 'Writing R Extensions'.  Some of these are hard to install on a 
>> platform without X11 such as M1 Macs: see the logs at 
>> https://www.stats.ox.ac.uk/pub/bdr/M1mac/.
>> |
>> |     You can check all of the suggested packages by setting 
>> environment variable _R_CHECK_DEPENDS_ONLY_=true  -- see 
>> https://cran.r-project.org/doc/manuals/r-devel/R-ints.html#Tools .
>> |
>> | Is this a false alarm?
>> |
>> | In each case, the outfile contains:
>> |
>> |     * checking package namespace information ... OK
>> |     * checking package dependencies ... NOTE
>> |     Package suggested but not available for checking: 'rgl'
>> |
>> | indicating that rgl is not avaiable on the testing machine.  Then,
>> | when checking examples an error is triggered when an example calls 
>> something that requires rgl.
>> |
>> |     >
>> |     > heplot3d(Adopted.mod, hypotheses=list("Reg"=c("AMED", "BMIQ")),
>> |     +         col = c("red", "blue", "black", "gray"), wire=FALSE)
>> |     Loading required namespace: rgl
>> |     Failed with error:  'there is no package called 'rgl''
>> |     Error in heplot3d.mlm(Adopted.mod, hypotheses = list(Reg = 
>> c("AMED", "BMIQ")),  :
>> |       rgl package is required.
>> |     Calls: heplot3d -> heplot3d.mlm
>> |     Execution halted
>> |
>> | Yet, heplot3d seems to contain the required way to refer to the 
>> suggested rgl package:
>> |
>> |                 if (!requireNamespace("rgl")) stop("rgl package is
>> | required.")
>> |
>> | So, I'm mystified.  Can anyone help?
>>
>> This is not conditional use in the sense of my reading of WRE.
>>
>> What you have here is essentially an "assert()" and equivalent to
>>    stopifnot(requireNamespace("rgl"))
>> which, in turn, is equivalent to a strong Depends or Imports as your 
>> package will experience a _critical error_ triggered by `stop()` if 
>> rgl is missing.
>>
>> The idea of a conditional use is to, well, be conditional. Below I 
>> make use of Rcpp if is present, but it is only a suggests:
>>
>>    ## see the source files in the snippets/ directory of the package
>>    ## check for (optional, only in Suggests:) Rcpp, and also wrapped in a
>>    ## dontrun as it takes 10s at CRAN (yet only 3.5 here) yielding a NOTE
>>    if (requireNamespace("Rcpp", quietly=TRUE)) {
>>        Rcpp::sourceCpp(system.file("snippets", "convolveExample.cpp", 
>> package="tidyCpp"))
>>    }
>>
>> If the _suggested_ package is present, it is used. If not we quietly 
>> move on.
>> (It's not the full story as the compilation occassionally takes 
>> longer, Windows complained so all this is now in a \dontrun{} block 
>> too. But the idea is generic and there are many more examples to be 
>> found.)
>>
>> Hope this helps,  Dirk
>>
>> -- 
>> https://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>> ______________________________________________
>> R-package-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
> 
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