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

[Patrick Schratz]

>
> Nevertheless, putting an empty startup.Rs file in tests/testthat fixes the
> testParallel
> package as well.


Works for me as well!

2017-02-07 23:10 GMT+01:00 Gábor Csárdi <csardi.gabor at gmail.com>:

> On Tue, Feb 7, 2017 at 8:16 PM, Henrik Bengtsson <
> henrik.bengtsson at gmail.com> wrote:
> [...]
>
>>
>> So, to me it's not clear how this could make a difference in Patrick
>> case.   By disabling this, i.e. Sys.setenv(R_TESTS=""), I don't see
>> how it affects running parallel+foreach+doParallel.  Maybe because one
>> of those packages are relying on fancy quotes in some protocol,
>> passing command-line arguments or ... something.  I would be curious
>> to see what file.path(R.home("share"), "R", "tests-startup.R")
>> contains on the system where the problem occurs.
>>
>
> I investigated a bit, and the problem (or at least one problem) is that
> the R subprocess will try
> to source() startup.Rs from the working directory, and that file might not
> be there.
> For testthat, the tests run in tests/testthat, and it is typically not
> there.
>
> For other regular tests, RUnit, etc. AFAIK the tests run in tests/ and
> startup.Rs is
> there. Unless the tests change the working directory, in which case it is
> not.
> So another workaround is to put an empty startup.Rs file there.
>
> Maybe there are other problems as well, but just putting an empty
> startup.Rs file at the appropriate
> location fixed all cases I tried.
>
> The parallel case above in this thread is a bit unusual I think, because
> usually there
> is no freeze, the R subprocess just aborts, and this typically causes a
> testthat (or other) test
> failure.
>
> Nevertheless, putting an empty startup.Rs file in tests/testthat fixes the
> testParallel
> package as well.
>
> G
>
>
>>
>> >
>> > A lot of packages have to work around this:
>> > https://github.com/search?q=user%3Acran+R_TESTS&type=Code
>>
>> I wonder if those are mostly there because of cut'n'paste behavior.
>>
>> >
>> > Most of these use testthat, but not all of them.
>>
>> My interest in this issue is because I haven't yet experienced this
>> myself and I run lots and lots of package tests in future that
>> utilizes the parallel package.  In doFuture I do similar tests, which
>> is on top of the foreach package.   I don't use testthat and I also
>> don't use doParallel in my testing.
>>
>> /Henrik
>>
>> >
>> > 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
>> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> >
>> >
>>
>
>

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