[Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack

[RICHET Yann]

Well, I tried to move the tests outside testthat.R logic, because I expect that CRAN output will not give me the reporter results... and as I re-submitted the package, I wanted to ensure readable result. But maybe I am wrong about that... ?


-----Message d'origine-----
De : Duncan Murdoch <murdoch.duncan using gmail.com> 
Envoyé : mercredi 11 janvier 2023 19:09
À : RICHET Yann <yann.richet using irsn.fr>; Sebastian Meyer <seb.meyer using fau.de>; Ivan Krylov <krylov.r00t using gmail.com>
Cc : Pascal Havé <pascal using haveneer.com>; R-devel using r-project.org
Objet : Re: [Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack

On 11/01/2023 12:35 p.m., RICHET Yann wrote:
> Thank you all, for these advices.
> 
> So I try to fix OMP_THREADS, cleanup tests, and display explicitly what test is running by moving in tests/ instead of tests/testthat/...
> Next step should be to investigate blocking test using a reporter (maybe "list").
> For now, waiting for CRAN results...

I think Sebastian or my suggestion is easier than redoing all of your tests.  They are each one line changes.

Duncan Murdoch

> 
> Yann
> 
> -----Message d'origine-----
> De : Duncan Murdoch <murdoch.duncan using gmail.com> Envoyé : mercredi 11 
> janvier 2023 00:36 À : Sebastian Meyer <seb.meyer using fau.de>; Ivan Krylov 
> <krylov.r00t using gmail.com>; RICHET Yann <yann.richet using irsn.fr> Cc : Pascal 
> Havé <pascal using haveneer.com>; R-devel using r-project.org Objet : Re: [Rd] 
> rhub vs. CRAN fedora-*-devel, using armadillo & slapack
> 
> On 10/01/2023 4:07 p.m., Sebastian Meyer wrote:
>> Am 10.01.23 um 21:28 schrieb Duncan Murdoch:
>>> On 10/01/2023 2:05 p.m., Ivan Krylov wrote:
>>>> On Tue, 10 Jan 2023 16:27:53 +0000
>>>> RICHET Yann <yann.richet using irsn.fr> wrote:
>>>>
>>>>> In facts, 10 threads are asked by armadillo for some LinAlg, which 
>>>>> backs to two threads as warned.
>>>>
>>>> I think you're right about your tests de-facto using two threads, 
>>>> but it might be a good idea to _default_ to up to two threads in 
>>>> tests and examples. This is especially valuable for third-party 
>>>> developers who have to mass-test packages (one of which could be
>>>> rlibkriging) in parallel.
>>>>
>>>>> - is there any reason that could explain that fedora-*-devel is so 
>>>>> slow for this package or compilation of Rcpp/testthat ?
>>>>
>>>> Compilation time is definitely not the reason. Something in tests/* 
>>>> actually runs for 30 minutes by itself.
>>>>
>>>>> - is there any chance that I can get a deeper log of what happened ?
>>>>
>>>> If you split your tests into separate files under tests/*.R instead 
>>>> of using a single tests/testthat.R calling the rest of the tests, R 
>>>> will be able to show you the individual test file that hung and 
>>>> maybe the line where it happened. (Also, you'll get per-file
>>>> timing.) But that is potentially a huge investment: you may have to 
>>>> rewrite the tests to work outside the testthat harness, and you'd 
>>>> also have to prepare another CRAN submission just to have those 
>>>> tests run. It's also against CRAN policy to knowingly submit a package with unfixed ERRORs.
>>>>
>>>> (Currently, R can only tell you that the tests hung in the
>>>> test_check('rlibkriging') call in the tests/testthat.R, which isn't 
>>>> precise enough.)
>>>
>>> You can specify a different "reporter" in the test_check() call, and 
>>> it will print more useful information.  I don't think there's a 
>>> perfect one, but
>>>
>>>      test_check('rlibkriging', reporter = "progress")
>>>
>>> should at least show you the tests that finished running before the 
>>> timeout.
>>
>> I had similar problems with testthat and timeouts when mass-checking 
>> packages on patched R versions. My notes say
>>
>>> ## testthat's 'LocationReporter' does cat() after each expectation 
>>> ## so we can see results even if timeout is reached 
>>> options(testthat.default_check_reporter = c("Location", "Check"))
>>
>> The help("LocationReporter") says: "This reporter simply prints the 
>> location of every expectation and error. This is useful if you're 
>> trying to figure out the source of a segfault, or you want to figure 
>> out which code triggers a C/C++ breakpoint"
>>
>> HTH!
> 
> Yes, that looks like it would pin down the location of the problem.
> Here's some sample output from it:
> 
>     Running ‘testthat.R’ [41s/42s]
> Running the tests in ‘tests/testthat.R’ failed.
> Last 13 lines of output:
>     Start test: can use constructed calls in verify_output() (#945)
>       'test-verify-output.R:55' [success]
>     End test: can use constructed calls in verify_output() (#945)
> 
>     Start test: verify_output() doesn't use cli unicode by default
>       'test-verify-output.R:65' [success]
>       'test-verify-output.R:73' [success]
>     End test: verify_output() doesn't use cli unicode by default
> 
>     Start test: verify_output() handles carriage return
>       'test-verify-output.R:82' [success]
>     End test: verify_output() handles carriage return
> 
>     Error: Test failures
>     Execution halted
> 
> One other thing:  you enabled this by using
> 
>     options(testthat.default_check_reporter = c("Location", "Check"))
> 
> before running the tests; the package writer could do the same thing 
> by using
> 
>     test_check('rlibkriging', reporter = c("Location", "Check"))
> 
> Duncan Murdoch