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

[Spencer Graves]

	  If you use GitHub, I highly recommend using "GitHub Action" as 
described by Wickham and Bryan, R Packages:


https://r-pkgs.org/code.html#code-style


	  I'm not sure the best way to get it set up, but I have all my 
packages on GitHub configured so each "push" that changes anything has 
"R CMD Check" run on 5 different platforms:  The release version of R on 
the latest Windows, macOS, and Ubuntu plus the development version and 
the most recent old release on Ubuntu.  I rarely run R CMD check on my 
local machine anymore:  I just "git commit" and "git push".  Then GitHub 
Action manages testing on those 5 platforms.


	  To be precise, I do "git status" before "git push" to make sure I 
have "committed" everything I want to commit before I "git push".  And I 
do "git pull" to make sure a collaborator hasn't "pushed" something new 
I should look at before I "git push".


	  Finally, I want to thank again Gábor Csárdi who helped me greatly get 
past problems I hand with "GitHub Action" for my "sos" package.  He 
provided example workflows in:


https://github.com/r-lib/actions/blob/v2-branch/examples/check-standard.yaml


	  I also needed LaTeX support, for which Gábor suggested the following:


https://github.com/r-lib/actions/tree/v2/setup-tinytex#ctan-packages


	  Spencer Graves
	

On 1/8/23 9:11 AM, Kevin R. Coombes wrote:
> 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
> 
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