Re: [R-pkg-devel] R CMD Check: Tests running infinite
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 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.
Ah... that makes sence, because R CMD check passes/sets
R_TESTS=startup.Rs specifying only a relative pathname. From runone()
part of src/library/tools/R/testing.R:
if (WINDOWS) {
Sys.setenv(LANGUAGE="C")
Sys.setenv(R_TESTS="startup.Rs")
} else
cmd <- paste("LANGUAGE=C", "R_TESTS=startup.Rs", cmd)
Maybe a more robust version would be to use something like:
if (WINDOWS) {
Sys.setenv(LANGUAGE="C")
Sys.setenv(R_TESTS=normalizePath("startup.Rs"))
} else
cmd <- paste("LANGUAGE=C", paste0("R_TESTS=",
normalizePath("startup.Rs")), cmd)
On the other hand, if it should be assumed that the test is run in the
same directory as startup.Rs, then testthat, and other test frameworks
that don't run under tests/, could copy startup.Rs as:
local({
fn <- Sys.getenv("R_TESTS")
if (nzchar(fn) && file_test("-f", pn <- file.path("..", fn)))
file.copy(pn, fn)
})
@Patrick,
>> By disabling this, i.e. Sys.setenv(R_TESTS="")
>
> Note that the fix from Gabor is Sys.unsetenv("R_TESTS"). What´s the
> difference between both?
My bad; Sys.unsetenv("R_TESTS") is the *correct* way to unset an env
variable. My approach sets it to an empty string, which also happens
to work because the test to source the file or not is based on
nzchar(Sys.setenv("R_TESTS")) == TRUE.
/Henrik
>
> 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
>> > 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
>> >> 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
>> >> > :
>> >> >>
>> >> >> 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
>> >> >> :
>> >> >>>
>> >> >>> 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
>> >>
Re: [R-pkg-devel] R CMD Check: Tests running infinite
>
> 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'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
>> > 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
>> >> 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.schr...@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
>> >> >> :
>> >> >>>
>> >> >>> 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" > >
>> >> >>> 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
>> >> :
>> >>
>> >> > Check whether the parallel cluster is closed. Can it be that the
>> >> > cluster
>> >> > is still open and the check
Re: [R-pkg-devel] R CMD Check: Tests running infinite
>
> 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
options(useFancyQuotes = FALSE)
By disabling this, i.e. Sys.setenv(R_TESTS="")
Note that the fix from Gabor is Sys.unsetenv("R_TESTS"). What´s the
difference between both?
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.
So if you use `foreach` and `parallel`, the major difference points to
`doParallel`. If I get my tests running by avoiding `doParallel`, we would
have some kind of evidence.
Any source on how to quickly substitute my `doParallel` code using
`parallel`? I know its just a few lines, but thats how it always starts..;)
2017-02-07 21:16 GMT+01:00 Henrik Bengtsson :
> 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, and
> > then R_TESTS confuses this process. (I am not sure how exactly.)
>
> I wasn't aware of R_TESTS. Looking at the R source code, if set, will
> cause the base package to source that file _before_ and .Rprofile
> scripts; it basically calls source(Sys.getenv("R_TESTS")).
>
> Next, R CMD check runs each of the test script using
> R_TESTS=startup.Rs, where startup.Rs:
>
> file.copy(file.path(R.home("share"), "R", "tests-startup.R"),
> "startup.Rs")
> if (use_gct) cat("gctorture(TRUE)" , file = "startup.Rs", append =
> TRUE)
>
> Looking at the tests-startup.R file that comes with my R 3.3.2 on
> Ubuntu 16.04, it seems pretty harmless:
>
> ## A custom startup file for tests
> ## Run as if a system Rprofile, so no packages, no assignments
> options(useFancyQuotes = FALSE)
>
> 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.
>
> >
> > 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
> > 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
> >> 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 >:
> >> >>
> >> >> 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
> >> >> :
> >> >>>
> >> >>> 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"
> >> >>> wrote:
> >>
> >> Dear Uwe,
> >>
> >> thanks for the hint. My cluster is closed after the `foreach`call
> >> using
> >> `stopCluster()`.
> >>
> >> Before, I´ll do th
Re: [R-pkg-devel] R CMD Check: Tests running infinite
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 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
> > 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
> >> 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 >:
> >> >>
> >> >> 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
> >> >> :
> >> >>>
> >> >>> 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"
> >> >>> 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
> >> :
> >>
> >> > 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:*
>
Re: [R-pkg-devel] R CMD Check: Tests running infinite
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 packages. So it is definitely real. I also think that the workaround is fine. (Please FIXME if not.) When Sys.unsetenv() is evaluated, it has already had its effect. G. [...] [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R CMD Check: Tests running infinite
>> 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 you) >> 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. The motivation for unsetting in in devtools is to avoid problems when you run R CMD check from inside another R CMD check. I think it affects some behaviour deep inside R, not just fancy quoting. Hadley -- http://hadley.nz __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R CMD Check: Tests running infinite
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, and
> then R_TESTS confuses this process. (I am not sure how exactly.)
I wasn't aware of R_TESTS. Looking at the R source code, if set, will
cause the base package to source that file _before_ and .Rprofile
scripts; it basically calls source(Sys.getenv("R_TESTS")).
Next, R CMD check runs each of the test script using
R_TESTS=startup.Rs, where startup.Rs:
file.copy(file.path(R.home("share"), "R", "tests-startup.R"), "startup.Rs")
if (use_gct) cat("gctorture(TRUE)" , file = "startup.Rs", append = TRUE)
Looking at the tests-startup.R file that comes with my R 3.3.2 on
Ubuntu 16.04, it seems pretty harmless:
## A custom startup file for tests
## Run as if a system Rprofile, so no packages, no assignments
options(useFancyQuotes = FALSE)
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.
>
> 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
> 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
>> 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 :
>> >>
>> >> 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$par.units, outfile = out.progress)
>> >> registerDoParallel(cl)
>> >>
>> >> foreach()
>> >>
>> >> parallel::stopCluster(cl)
>> >> doParallel::registerDoSEQ()
>> >> doParallel::stopImplicitCluster()
>> >>
>> >> 2017-02-05 15:04 GMT+01:00 Henrik Bengtsson
>> >> :
>> >>>
>> >>> Use
>> >>>
>> >>> registerDoParallel(cl)
>> >>>
>> >>> The number of parallel workers is already contained in the 'cl'
>> >>> object,
>> >>> so don't specify 'cores'! (If you do that, I suspect you create yet
>> >>> another
>> >>> cluster (a multicore one) which is used but never closed)
>> >>>
>> >>> registerDoParallel() should ideally give an error in your case. Author
>> >>> BCC:ed.
>> >>>
>> >>> Henrik
>> >>>
>> >>> On Feb 5, 2017 03:56, "Patrick Schratz"
>> >>> wrote:
>>
>> Dear Uwe,
>>
>> thanks for the hint. My cluster is closed after the `foreach`call
>> using
>> `stopCluster()`.
>>
>> Before, I´ll do the following to init the cluster:
>>
>> *cl <- makeCluster(par.args$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
>> :
>>
>> > 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
>> >> *
>> >>
Re: [R-pkg-devel] R CMD Check: Tests running infinite
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 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 > 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 : > >> > >> 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 >: > >>> > >>> 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" > >>> 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 >: > > > 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@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > >> > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > >> > > > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R CMD Check: Tests running infinite
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/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 but tests are >> still running infinite.. >> >> cl <- makeCluster(par.args$par.units, outfile = out.progress) >> registerDoParallel(cl) >> >> foreach() >> >> parallel::stopCluster(cl) >> doParallel::registerDoSEQ() >> doParallel::stopImplicitCluster() >> >> 2017-02-05 15:04 GMT+01:00 Henrik Bengtsson : >>> >>> Use >>> >>> registerDoParallel(cl) >>> >>> The number of parallel workers is already contained in the 'cl' object, >>> so don't specify 'cores'! (If you do that, I suspect you create yet another >>> cluster (a multicore one) which is used but never closed) >>> >>> registerDoParallel() should ideally give an error in your case. Author >>> BCC:ed. >>> >>> Henrik >>> >>> On Feb 5, 2017 03:56, "Patrick Schratz" >>> wrote: Dear Uwe, thanks for the hint. My cluster is closed after the `foreach`call using `stopCluster()`. Before, I´ll do the following to init the cluster: *cl <- makeCluster(par.args$par.units, outfile = out.progress)* *registerDoParallel(cl, cores = par.args$par.units)* *foreach()* *stopCluster(cl)* Do you know of any other package which is using foreach in combination with tests and is hosted on Github? So I could compare settings. Best, Patrick 2017-02-02 0:01 GMT+01:00 Uwe Ligges : > Check whether the parallel cluster is closed. Can it be that the > cluster > is still open and the check process waits for them to complete? > > Best, > Uwe Ligges > > > > On 31.01.2017 13:45, Patrick Schratz wrote: > >> Hello, >> >> when running R CMD check / devtools::check, section "running >> tests..." is >> not finishing (40 min+). >> >> *Checking tests only works:* >> >> *==> Sourcing R files in 'tests' directory* >> >> *testthat results >> * >> *OK: 7 SKIPPED: 0 FAILED: 0* >> >> *Tests complete* >> >> >> As well as running tests line-by-line. >> >> How can I debug my tests to discover the problem during R CMD check? >> >> *Tests are using parallelization (foreach + doParallel)* >> >> Best, Patrick >> >> [[alternative HTML version deleted]] >> >> __ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> >> [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel >> >> > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R CMD Check: Tests running infinite
@gaborcsardi solved it :) See here: https://github.com/hadley/testthat/issues/567#issuecomment-277536577 2017-02-05 16:07 GMT+01:00 Patrick Schratz : > Thanks for the hint, Hendrik! > However, this change did not make a difference :/ > > I tried to use all cluster closing functions I came across but tests are > still running infinite.. > > *cl <- makeCluster(par.args$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 : > >> 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" >> 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 : >>> >>> > 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@r-project.org mailing list >>> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >>> >> >>> >> >>> >>> [[alternative HTML version deleted]] >>> >>> __ >>> R-package-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel >>> >> > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R CMD Check: Tests running infinite
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$par.units, outfile = out.progress)* *registerDoParallel(cl)* *foreach()* *parallel::stopCluster(cl)* *doParallel::registerDoSEQ()* *doParallel::stopImplicitCluster()* 2017-02-05 15:04 GMT+01:00 Henrik Bengtsson : > Use > > registerDoParallel(cl) > > The number of parallel workers is already contained in the 'cl' object, so > don't specify 'cores'! (If you do that, I suspect you create yet another > cluster (a multicore one) which is used but never closed) > > registerDoParallel() should ideally give an error in your case. Author > BCC:ed. > > Henrik > > On Feb 5, 2017 03:56, "Patrick Schratz" wrote: > >> Dear Uwe, >> >> thanks for the hint. My cluster is closed after the `foreach`call using >> `stopCluster()`. >> >> Before, I´ll do the following to init the cluster: >> >> *cl <- makeCluster(par.args$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 : >> >> > 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@r-project.org mailing list >> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> __ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R CMD Check: Tests running infinite
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" 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$par.units)* > > *foreach()* > > *stopCluster(cl)* > > Do you know of any other package which is using foreach in combination with > tests and is hosted on Github? So I could compare settings. > > Best, Patrick > > 2017-02-02 0:01 GMT+01:00 Uwe Ligges : > > > Check whether the parallel cluster is closed. Can it be that the cluster > > is still open and the check process waits for them to complete? > > > > Best, > > Uwe Ligges > > > > > > > > On 31.01.2017 13:45, Patrick Schratz wrote: > > > >> Hello, > >> > >> when running R CMD check / devtools::check, section "running tests..." > is > >> not finishing (40 min+). > >> > >> *Checking tests only works:* > >> > >> *==> Sourcing R files in 'tests' directory* > >> > >> *testthat results > >> * > >> *OK: 7 SKIPPED: 0 FAILED: 0* > >> > >> *Tests complete* > >> > >> > >> As well as running tests line-by-line. > >> > >> How can I debug my tests to discover the problem during R CMD check? > >> > >> *Tests are using parallelization (foreach + doParallel)* > >> > >> Best, Patrick > >> > >> [[alternative HTML version deleted]] > >> > >> __ > >> R-package-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > >> > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R CMD Check: Tests running infinite
Dear Uwe, thanks for the hint. My cluster is closed after the `foreach`call using `stopCluster()`. Before, I´ll do the following to init the cluster: *cl <- makeCluster(par.args$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 : > 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@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> >> [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R CMD Check: Tests running infinite
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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] R CMD Check: Tests running infinite
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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
