[R-pkg-devel] R CMD Check: Tests running infinite

[Gábor Csárdi]

I don't think it is specific for testthat. R CMD check sets R_TESTS when it
runs the tests, so the separate R process it starts can have some special
startup options.

The problem happens if you start another R process from your R test, and
then R_TESTS confuses this process. (I am not sure how exactly.)

A lot of packages have to work around this:
https://github.com/search?q=user%3Acran+R_TESTS&type=Code

Most of these use testthat, but not all of them.

Gabor

On Mon, Feb 6, 2017 at 2:17 AM, Henrik Bengtsson <henrik.bengtsson at gmail.com
> wrote:

> In case someone else bumps into this later and finds this thread; can
> you confirm that this was a problem specific to using the testthat
> package for running the tests?
>
> /Henrik
>
> On Sun, Feb 5, 2017 at 11:28 AM, Patrick Schratz
> <patrick.schratz at gmail.com> wrote:
> > @gaborcsardi solved it :) See here:
> > https://github.com/hadley/testthat/issues/567#issuecomment-277536577
> >
> >
> > 2017-02-05 16:07 GMT+01:00 Patrick Schratz <patrick.schratz at gmail.com>:
> >>
> >> Thanks for the hint, Hendrik!
> >> However, this change did not make a difference :/
> >>
> >> I tried to use all cluster closing functions I came across but tests are
> >> still running infinite..
> >>
> >> cl <- makeCluster(par.args$par.units, outfile = out.progress)
> >> registerDoParallel(cl)
> >>
> >> foreach()
> >>
> >> parallel::stopCluster(cl)
> >> doParallel::registerDoSEQ()
> >> doParallel::stopImplicitCluster()
> >>
> >> 2017-02-05 15:04 GMT+01:00 Henrik Bengtsson <henrik.bengtsson at gmail.com
> >:
> >>>
> >>> Use
> >>>
> >>>   registerDoParallel(cl)
> >>>
> >>> The number of parallel workers is already contained in the 'cl' object,
> >>> so don't specify 'cores'!  (If you do that, I suspect you create yet
> another
> >>> cluster (a multicore one) which is used but never closed)
> >>>
> >>> registerDoParallel() should ideally give an error in your case. Author
> >>> BCC:ed.
> >>>
> >>> Henrik
> >>>
> >>> On Feb 5, 2017 03:56, "Patrick Schratz" <patrick.schratz at gmail.com>
> >>> wrote:
> >>>>
> >>>> Dear Uwe,
> >>>>
> >>>> thanks for the hint. My cluster is closed after the `foreach`call
> using
> >>>> `stopCluster()`.
> >>>>
> >>>> Before, I´ll do the following to init the cluster:
> >>>>
> >>>> *cl <- makeCluster(par.args$par.units, outfile = out.progress)*
> >>>> *registerDoParallel(cl, cores = par.args$par.units)*
> >>>>
> >>>> *foreach()*
> >>>>
> >>>> *stopCluster(cl)*
> >>>>
> >>>>
> >>>> Do you know of any other package which is using foreach in combination
> >>>> with
> >>>> tests and is hosted on Github? So I could compare settings.
> >>>>
> >>>> Best, Patrick
> >>>>
> >>>> 2017-02-02 0:01 GMT+01:00 Uwe Ligges <ligges at statistik.tu-dortmund.de
> >:
> >>>>
> >>>> > Check whether the parallel cluster is closed. Can it be that the
> >>>> > cluster
> >>>> > is still open and the check process waits for them to complete?
> >>>> >
> >>>> > Best,
> >>>> > Uwe Ligges
> >>>> >
> >>>> >
> >>>> >
> >>>> > On 31.01.2017 13:45, Patrick Schratz wrote:
> >>>> >
> >>>> >> Hello,
> >>>> >>
> >>>> >> when running R CMD check / devtools::check, section "running
> >>>> >> tests..." is
> >>>> >> not finishing (40 min+).
> >>>> >>
> >>>> >> *Checking tests only works:*
> >>>> >>
> >>>> >> *==> Sourcing R files in 'tests' directory*
> >>>> >>
> >>>> >> *testthat results
> >>>> >> ================================================================*
> >>>> >> *OK: 7 SKIPPED: 0 FAILED: 0*
> >>>> >>
> >>>> >> *Tests complete*
> >>>> >>
> >>>> >>
> >>>> >> As well as running tests line-by-line.
> >>>> >>
> >>>> >> How can I debug my tests to discover the problem during R CMD
> check?
> >>>> >>
> >>>> >> *Tests are using parallelization (foreach + doParallel)*
> >>>> >>
> >>>> >> Best, Patrick
> >>>> >>
> >>>> >>         [[alternative HTML version deleted]]
> >>>> >>
> >>>> >> ______________________________________________
> >>>> >> R-package-devel at r-project.org mailing list
> >>>> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>>> >>
> >>>> >>
> >>>>
> >>>>         [[alternative HTML version deleted]]
> >>>>
> >>>> ______________________________________________
> >>>> R-package-devel at r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >>
> >
>
> ______________________________________________
> R-package-devel at r-project.org mailing list
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