[R-pkg-devel] Help Debugging Debian Error
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 G?bor Cs?rdi <csardi.gabor at 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 at gmail.com>
wrote:
On Fri, 15 May 2020 03:50:12 -0400 Paul Hibbing <paulhibbing at 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
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