[R-pkg-devel] gdb availability on r-devel-linux-x86_64-fedora-gcc

[Uwe Ligges]

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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