[R-pkg-devel] Help Debugging Debian Error

[Paul Hibbing]

Thanks for the tips. It appears the error is indeed related to the
matchingMarkets package, but specifically an issue with rJava
configuration. Now I get the following (see
https://artifacts.r-hub.io/PAutilities_1.0.0.tar.gz-54a555386e924de6a53385479a1e199f/PAutilities.Rcheck/00check.log
):

VALIDATE...PREFS...MATCHES [*ignore this -- these are updates I printed
myself to pinpoint matchingMarkets as the culprit*]
WARNING: Initial Java 12 release has broken JNI support and does NOT work.
Use stable Java 11 (or watch for 12u if avaiable).
ERROR: Java exception occurred during rJava bootstrap - see stderr for Java
stack trace. Exception in thread "main"

* Is there a specification I can provide to get around this?

* Since the current CRAN version of my package depends on a recently
orphaned package, I am due to provide a new release by the 17th (per an
email from Prof. Brian Ripley). Is this a hard deadline, or can/should I
notify someone and/or request an extension? To complicate matters, I have a
publication coming out imminently, in which my package plays a central
role. So it's important that I avoid any lapse in its availability.

Paul

On Fri, May 15, 2020 at 5:06 AM Gábor Csárdi <csardi.gabor using gmail.com> wrote:

> You don't need to move the files around, though, just use a more
> verbose testthat reporter, e.g. in testthat.R use
>
> test_check("PAutilities", reporter = "summary")
>
> and then at least you'll know where it crashes. But to fix this,
> you'll probably need to debug it locally. You can do that in Docker if
> you don't have a local Linux machine.
>
> Gabor
>
> On Fri, May 15, 2020 at 10:00 AM Ivan Krylov <krylov.r00t using gmail.com>
> wrote:
> >
> > On Fri, 15 May 2020 03:50:12 -0400
> > Paul Hibbing <paulhibbing using gmail.com> wrote:
> >
> > > Complete output:
> > >   > library(testthat)
> > >   > library(PAutilities)
> > >   >
> > >   > test_check("PAutilities")
> >
> > It seems to me that the R process crashes while running your tests, but
> > since testthat::test_check captures everything to summarise it later,
> > you don't get to know where the crash occurs.
> >
> > Perhaps if you (temporarily) move your tests out of testthat/
> > subdirectory and remove the context() and testthat::test_that("...",
> > { ... }) calls, you would be able to see the exact location of the
> > crash in the *.Rout files?
> >
> > That said, it's probably one of your dependencies that's responsible
> > for the crash, not your package, since there is no compiled code.
> >
> > --
> > Best regards,
> > Ivan
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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