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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