On Tue, Feb 7, 2017 at 2:10 PM, Gábor Csárdi wrote:
> On Tue, Feb 7, 2017 at 8:16 PM, Henrik Bengtsson
> 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 pa
>
> 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 :
> On Tue, Feb 7, 2017 at 8:16 PM, Henrik Bengtsson <
> henrik.bengts...@gmail.com> wrote:
> [...]
>
>>
>> So, to me it
>
> I would be curious
> to see what file.path(R.home("share"), "R", "tests-startup.R")
> contains on the system where the problem occurs.
Contents of mine on macOS are the same as on your Ubuntu:
## A custom startup file for tests
## Run as if a system Rprofile, so no packages, no assignments
o
On Tue, Feb 7, 2017 at 8:16 PM, Henrik Bengtsson 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
On Tue, Feb 7, 2017 at 8:16 PM, Henrik Bengtsson wrote:
[...]
> I wonder if those are mostly there because of cut'n'paste behavior.
>
I don't know. What I know is that I have seen it in about 5 of my packages,
and I have also helped about 5 people that were stumbled upon it with their
own packag
>> 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.
It's not something I've ever advocated; I didn't realise there were so
many people unsetting it. (devtools does it for
On Mon, Feb 6, 2017 at 12:41 AM, Gábor Csárdi wrote:
> 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,
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 exa
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
wrote:
> @gaborcsardi solved it :) See here:
> https://github.com/hadle
@gaborcsardi solved it :) See here:
https://github.com/hadley/testthat/issues/567#issuecomment-277536577
2017-02-05 16:07 GMT+01:00 Patrick Schratz :
> Thanks for the hint, Hendrik!
> However, this change did not make a difference :/
>
> I tried to use all cluster closing functions I came across
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$par.units, outfile = out.progress)*
*registerDoParallel(cl)*
*foreach()*
*parallel::stop
Use
registerDoParallel(cl)
The number of parallel workers is already contained in the 'cl'
object, so don't
specify 'cores'! (If you do that, I suspect you create yet another cluster
(a multicore one) which is used but never closed)
registerDoParallel() should ideally give an error in your ca
Dear Uwe,
thanks for the hint. My cluster is closed after the `foreach`call using
`stopCluster()`.
Before, I´ll do the following to init the cluster:
*cl <- makeCluster(par.args$par.units, outfile = out.progress)*
*registerDoParallel(cl, cores = par.args$par.units)*
*foreach()*
*stopCluster(cl
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 finishin
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