[R-pkg-devel] Mysterious "invalid z limit"

[Kevin R. Coombes]

A very helpful answer. For some reason (probably because I have an 
ancient perl script that automates the steps i take when building and 
checking packages), I keep forgetting that the "tools" package let's me 
do these things from within R.

I had already isolated the offending line ("plot(obj)") inside the chunk 
where the error occurred, and removed any additional arguments. I 
wrapped that line in a "try" command followed by a conditional 
"traceback()" to find the problem.  This allowed the package build to 
knit the vignette and provide some feedback about what was going on. It 
turned out that I had copied and pasted an assignment line of the form

main <- [compute the title]

from earlier in the code and pasted it directly as an argument to the 
call to image.default. And R did exactly what I told it to (not 
surprisingly), and interpreted the value of that assignment as the 
unnamed "zlim" option that would have been the corresponding positional 
argument that should have been there.

And yes, I still use "left arrow" <- instead of equals = as assignments. 
(Heck, I even use emacs and ESS with a leftover keybinding that uses the 
underscore key to insert the left arrow. Apparently, I'm ancient myself.)

   Kevin

On 1/8/2023 5:04 AM, Duncan Murdoch wrote:
> On 07/01/2023 8:43 p.m., Kevin R. Coombes wrote:
>> Hi,
>>
>> I am in the middle of developing a new package, which contains a
>> markdown-knitr-html vignette. When I try to run
>>
>> R CMD build [mypackagedirectory]
>>
>> I get an error message
>>
>> Quitting from lines 330-336
>> Error: processing vignette  failed with diagnostics:
>> invalid z limits
>>
>> If I run the same markdown script interactively inside R Studio, there
>> is no error.
>> If I knit the markdown script inside R Studio, it produces the correct
>> HTML output, with no error.
>>
>> The offending lines of code (the chunk at 330-336) invoke an "image"
>> method on an object of a class defined in the package, which in turn
>> computes a matrix from items inside the object and calls image.default,
>> which is presumably where the error is coming from.
>>
>> Two questions: (1) How is it possible that the same code works error
>> free in the RStudio contexts, but fails in the attempt to build the 
>> package?
>> (2) Any suggestions on how to debug something that only throws an error
>> from "R CMD build" would be most welcome.
>
> Debugging that sort of thing is hard.  Here's what I would try:
>
> From inside an R session, run
>
>   tools:::.build_packages("[mypackagedirectory]")
>
> That runs the code that R CMD build runs, so it might trigger the same 
> error.  If so, debug in the usual way, with traceback(), etc.
>
> If that doesn't trigger the error, try it using a different front-end, 
> e.g. running R at the command line instead of running it in RStudio.
>
> If you still can't trigger it, then start modifying the vignette to 
> find the exact line that causes the error (e.g. by commenting out the 
> second half of the code in that chunk; did the error go away? etc.).  
> Then modify it again to save all the inputs to the bad line in a file 
> before running it, and see if running that line in a different context 
> still triggers the error. Etc.
>
> Duncan Murdoch