RICHET Yann
2023-Jan-11 17:35 UTC
[Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack
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... Yann -----Message d'origine----- De?: Duncan Murdoch <murdoch.duncan at gmail.com> Envoy??: mercredi 11 janvier 2023 00:36 ??: Sebastian Meyer <seb.meyer at fau.de>; Ivan Krylov <krylov.r00t at gmail.com>; RICHET Yann <yann.richet at irsn.fr> Cc?: Pascal Hav? <pascal at haveneer.com>; R-devel at 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 at 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
Duncan Murdoch
2023-Jan-11 18:09 UTC
[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 at gmail.com> > Envoy??: mercredi 11 janvier 2023 00:36 > ??: Sebastian Meyer <seb.meyer at fau.de>; Ivan Krylov <krylov.r00t at gmail.com>; RICHET Yann <yann.richet at irsn.fr> > Cc?: Pascal Hav? <pascal at haveneer.com>; R-devel at 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 at 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
Dirk Eddelbuettel
2023-Jan-11 18:34 UTC
[Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack
On 11 January 2023 at 17:35, 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... BTW your package failed its tests for me in a reverse-depends run when I had `ccache` as usual in the definition of CC, CXX, FC, CXX14, ... That usually works with other packages using CMake. Maybe something you could look into. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org