On 12.08.2023 15:10, Jamie Lentin wrote:
Hello list,
Our package gadget3[0] has just started failing the "donttest"
additional check[1] on r-devel-linux-x86_64-fedora-gcc, specifically:-
> # Build the model in an isolated R session w/debugger
> writeLines(TMB::gdbsource(g3_tmb_adfun(cpp, compile_flags = "-g",
output_script = TRUE)))
Error in system(cmd, intern = TRUE, ignore.stdout = FALSE,
ignore.stderr = TRUE) :
error in running command
Calls: writeLines -> <Anonymous> -> system
Execution halted
The system call in question is done by the TMB package[2], and not ours
to tinker with:
cmd <- paste("R --vanilla < ",file," -d gdb --debugger-args=\"-x",
gdbscript,"\"")
txt <- system(cmd,intern=TRUE,ignore.stdout=FALSE,ignore.stderr=TRUE)
My only vaguely reasonable guess is that gdb isn't available on the host
in question (certainly R will be!). How likely is this? Is it worth
trying to resubmit with the call wrapped with an "if (gdb is on the path)"?
I guess it is really not available as that system got an update.
Note that you package does not declare any SystemRequirements. Please do
so and mention gdb.
Wrapping it in "if (gdb is on the path)" seems a good solution.
Best,
Uwe Ligges
If this is a silly idea, which I suspect it is, would a resubmission
removing the example be accepted or just raise red flags? This is
obviously cheating---and it's a useful example I'd rather keep---but I'm
not sure we have many other options available to us.
This example isn't a problem when run elsewhere. The TMB package itself
isn't failing[3], but there doesn't seem to be any examples exercising
TMB::gdbsource() there.
Thanks for any help!
[0] https://CRAN.R-project.org/package=gadget3
[1] https://www.stats.ox.ac.uk/pub/bdr/donttest/gadget3.out
[2] https://github.com/kaskr/adcomp/blob/master/TMB/R/gdbsource.R#L40-L42
[3] https://cran.r-project.org/web/checks/check_results_TMB.html
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