Re: [R-pkg-devel] details of CRAN's r-devel-linux-x86_64-debian-clang

[Jan Gorecki]

Thanks to Kurt Hornik for confirming that following should be sufficient.
export _R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_=false
export _R_S3_METHOD_LOOKUP_REPORT_SEARCH_PATH_USES_=true

I did more tests and found out that for the issue to manifest I had to
install xts, rather than just zoo (which registers generic method),
because a particular unit test required xts to be present.
Now I am able to reproduce the problem.

On Sun, Oct 25, 2020 at 12:17 PM Jan Gorecki  wrote:
>
> Thanks Hugh,
> I must have dropped it when pasting to email. I checked again and it
> doesn't make any difference. So my question is still valid then.
>
> On Sun, Oct 25, 2020 at 11:14 AM Hugh Parsonage
>  wrote:
> >
> > _R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_
> >
> > not
> >
> >  R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_
> >
> > (i.e. you seem to have dropped the initial underscore)?
> >
> > On Sun, 25 Oct 2020 at 20:01, Jan Gorecki  wrote:
> > >
> > > Dear community,
> > >
> > > I am getting an error on CRAN on r-devel-linux-x86_64-debian-clang 
> > > machine only:
> > >
> > >   S3 method lookup found 'as.x.y' on search path
> > >
> > > I know how to fix the error. I am interested to know how to reproduce
> > > this error locally. I tried combination of
> > > R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_
> > > and
> > > _R_S3_METHOD_LOOKUP_REPORT_SEARCH_PATH_USES_
> > > but didn't manage to reproduce the error.
> > >
> > > What is the proper way to set up checks to detect these kinds of issues?
> > >
> > > Moreover, I kindly request to provide "details" for other CRAN
> > > machines in flavors page:
> > > https://cran.r-project.org/web/checks/check_flavors.html
> > > "Details" are currently provided only for 3 machines there. Having
> > > "details" for r-devel-linux-x86_64-debian-clang would probably answer
> > > my question without involving readers of this mailing list.
> > >
> > > Best Regards,
> > > Jan Gorecki
> > >
> > > __
> > > R-package-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel

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[R-pkg-devel] Run-times of examples in vignettes

[Helmut Schütz]

Dear all,

is there somewhere an official statement about the maximum run-times of 
examples in vignettes?


Currently I got for our seven vignettes on my six-years old machine 7.9 
minutes. One of them (containing a lot of simulation code) take 7.1 
minutes. Hence, in the submission we asked for --no-vignettes (on 
Windows only). Interestingly on some flavours and operating systems this 
was also observed, whereas on others not. What I don't understand: Some 
zip-files (e.g. Windows r-oldrel) which state in the result-Flag 
--no-vignettes contain not only the *.Rmd (what I would expect) but also 
the *.R and *.html.
Since a while we submit the time-critical vignette pre-compiled, which 
should bring the total execution time below one minute. Is that fine for 
all flavours & OSs?


Helmut

--
Ing. Helmut Schütz
BEBAC – Consultancy Services for
Bioequivalence and Bioavailability Studies
Neubaugasse 36/11
1070 Vienna, Austria
E helmut.schu...@bebac.at
W https://bebac.at/
F https://forum.bebac.at/

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Re: [R-pkg-devel] Run-times of examples in vignettes

[Dirk Eddelbuettel]

On 27 October 2020 at 12:21, Helmut Schütz wrote:
| is there somewhere an official statement about the maximum run-times of 
| examples in vignettes?

Seven minutes is excessive. I have (long) gone by the rule of "about one
minute" each for tests and examples. Rcpp is slightly above [1], especially
on Windows. I also tone down tests when on CRAN (using a scheme devised
almost a decade ago and described a few times here and in other places) where
to the package, having an extra fourth digit in the microrelease such as the
.4 currently in 1.0.5.4 signals 'full tests' whereas a three-digit release
number (such as 1.0.5 on CRAN signals reduced tests).  Works for me and on
all CI instances, requires no user input and no magic environment variable.

Now, we have some (partial) empirics on this as my reverse depends checks for 
Rcpp time
the runs (and the success/failure) in a small SQLite db (all on GH) [2]. I
also explicitly skip some packages taking too much time. I should probably
automate looking at the times and updating the list of skipped packages
automatically...

Dirk

[1] https://cloud.r-project.org/web/checks/check_results_Rcpp.html

[2] This is from an machine that is loaded by the reverse depends running six
tests in parallel over four cores. This would be quicker on a nicer machine
but ... this what we have, and what we very much appreciate having access
to. It is also 'total time' for 'R CMD check'.


sqlite> select package, runtime/60 as timeInMins from results order by 
timeInMins desc limit 10;
package timeInMins  
--  
cbq 54.2629543542862
rstanarm51.9673245469729
OpenMx  44.4183359424273
survHE  40.4267136971156
pcFactorSt  36.404546391964 
metaBMA 35.6222194115321
trialr  35.2238613526026
emIRT   34.6994982639949
bmgarch 34.3939555843671
bsem33.4894991954168
sqlite>

So the first four or five clearly are candidates for skipping.


-- 
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[R-pkg-devel] How to set an environment variable during package installation?

[Akshit Achara]

Hi everyone,

I have created an R package which depends on a third party library. I need
to set an environment variable whose value will be the argument provided by
the user during the package installation. Is there any way I can set the
environment variable using autotools?

Thanks,
Akshit Achara

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Re: [R-pkg-devel] Run-times of examples in vignettes

[Helmut Schütz]

Hi Dirk,

Dirk Eddelbuettel wrote on 2020-10-27 13:32:

| is there somewhere an official statement about the maximum run-times of
| examples in vignettes?

Seven minutes is excessive.


Sure. The one vignette contains simulation code which needs 1E5 to 1E6 
sims to get a stable result. Fewer sims are simply not meaningful.
Since we use a pre-complied vignette now the execution time is 
essentially zero.

The others take 45 seconds in total.
If we would pre-compile the second slowest as well, we would be down for 
the remaining four at 12 seconds.



I have (long) gone by the rule of "about one minute" each for tests and 
examples.


OK. Do you know of any reference for this "rule"?

Helmut

--
Ing. Helmut Schütz
BEBAC – Consultancy Services for
Bioequivalence and Bioavailability Studies
Neubaugasse 36/11
1070 Vienna, Austria
E helmut.schu...@bebac.at
W https://bebac.at/
F https://forum.bebac.at/

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Re: [R-pkg-devel] Run-times of examples in vignettes

[Ben Bolker]

  My general solution is to run time-consuming computations in advance 
and store the results in (e.g.) inst/vignette_data, whence they can be 
retrieved via system.file("vignette_data", "output.rda", 
package="my_pkg"). (I might also include the R script required to 
generate the file so that I could automatically re-make those outputs as 
required ...)



On 10/27/20 8:53 AM, Helmut Schütz wrote:

Hi Dirk,

Dirk Eddelbuettel wrote on 2020-10-27 13:32:

| is there somewhere an official statement about the maximum run-times of
| examples in vignettes?

Seven minutes is excessive.


Sure. The one vignette contains simulation code which needs 1E5 to 1E6 
sims to get a stable result. Fewer sims are simply not meaningful.
Since we use a pre-complied vignette now the execution time is 
essentially zero.

The others take 45 seconds in total.
If we would pre-compile the second slowest as well, we would be down for 
the remaining four at 12 seconds.


I have (long) gone by the rule of "about one minute" each for tests 
and examples.


OK. Do you know of any reference for this "rule"?

Helmut



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Re: [R-pkg-devel] Run-times of examples in vignettes

[Thierry Onkelinx]

My solution is similar to Ben's solution. Except that the code for creating
the data is in the vignette. The chunk only runs when the data is not
available. The trick is to pass code to the eval argument instead of a
fixed TRUE or FALSE. See
https://github.com/ropensci/git2rdata/blob/bad8a4cf42049faa72a04b202c5a4dfc233b4046/vignettes/efficiency.Rmd#L293
for an example.

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///




Op di 27 okt. 2020 om 16:29 schreef Ben Bolker :

>
>My general solution is to run time-consuming computations in advance
> and store the results in (e.g.) inst/vignette_data, whence they can be
> retrieved via system.file("vignette_data", "output.rda",
> package="my_pkg"). (I might also include the R script required to
> generate the file so that I could automatically re-make those outputs as
> required ...)
>
>
> On 10/27/20 8:53 AM, Helmut Schütz wrote:
> > Hi Dirk,
> >
> > Dirk Eddelbuettel wrote on 2020-10-27 13:32:
> >> | is there somewhere an official statement about the maximum run-times
> of
> >> | examples in vignettes?
> >>
> >> Seven minutes is excessive.
> >
> > Sure. The one vignette contains simulation code which needs 1E5 to 1E6
> > sims to get a stable result. Fewer sims are simply not meaningful.
> > Since we use a pre-complied vignette now the execution time is
> > essentially zero.
> > The others take 45 seconds in total.
> > If we would pre-compile the second slowest as well, we would be down for
> > the remaining four at 12 seconds.
> >
> >> I have (long) gone by the rule of "about one minute" each for tests
> >> and examples.
> >
> > OK. Do you know of any reference for this "rule"?
> >
> > Helmut
> >
>
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>

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