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)"?
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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