On Mac, I also don't get the error, but I think this is a different issue. If I remember correctly, the error is known to occur on some platforms, but not all, which is the reason for the ## IGNORE_RDIFF_BEGIN ... END.
However _when_ it occurs, R should just print the error and continue. If it doesn't, something is up. One possible reason is that something has been playing with options(error=), e.g. in a start-up file. -pd > On 1 Oct 2021, at 12:03 , Sebastian Meyer <seb.me...@fau.de> wrote: > > For what it's worth, make check runs OK for me with sessionInfo() > > R version 4.1.1 Patched (2021-09-30 r80997) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 18.04.6 LTS > > Matrix products: default > BLAS: /home/smeyer/R/base/release/build/lib/libRblas.so > LAPACK: /home/smeyer/R/base/release/build/lib/libRlapack.so > > The output of these examples is: > >>> try(nlm1 <- update(nlmod, control = list(tol = 1e-7))) # where central >>> diff. work here: >> Warning in nls(formula = y ~ Const + A * exp(B * x), algorithm = "default", >> : >> No starting values specified for some parameters. >> Initializing ‘Const’, ‘A’, ‘B’ to '1.'. >> Consider specifying 'start' or using a selfStart model >> Error in nls(formula = y ~ Const + A * exp(B * x), algorithm = "default", : >> step factor 0.000488281 reduced below 'minFactor' of 0.000976562 >>> (nlm2 <- update(nlmod, control = list(tol = 8e-8, nDcentral=TRUE), >>> trace=TRUE)) >> Warning in nls(formula = y ~ Const + A * exp(B * x), algorithm = "default", >> : >> No starting values specified for some parameters. >> Initializing ‘Const’, ‘A’, ‘B’ to '1.'. >> Consider specifying 'start' or using a selfStart model >> 1017460.306 (4.15e+02): par = (1 1 1) >> 758164.7503 (2.34e+02): par = (13.42031396 1.961485 0.05947543745) >> 269506.3537 (3.23e+02): par = (51.75719817 -13.09155958 0.8428607712) >> 68969.21891 (1.03e+02): par = (76.0006985 -1.93522675 1.0190858) >> 633.3672224 (1.29e+00): par = (100.3761515 8.624648408 5.104490252) >> 151.4400170 (9.39e+00): par = (100.6344391 4.913490999 0.2849209664) >> 53.08739445 (7.24e+00): par = (100.6830407 6.899303393 0.4637755095) >> 1.344478582 (5.97e-01): par = (100.0368306 9.897714144 0.5169294926) >> 0.9908415908 (1.55e-02): par = (100.0300625 9.9144191 0.5023516843) >> 0.9906046057 (1.84e-05): par = (100.0288724 9.916224018 0.5025207336) >> 0.9906046054 (9.94e-08): par = (100.028875 9.916228366 0.50252165) >> 0.9906046054 (5.00e-08): par = (100.028875 9.916228377 0.5025216525) >> Nonlinear regression model >> model: y ~ Const + A * exp(B * x) >> data: parent.frame() >> Const A B 100.0288750 9.9162284 0.5025217 >> residual sum-of-squares: 0.9906046 > > Running with example(nls) in an interactive session gives the extra output > >> Number of iterations to convergence: 11 Achieved convergence tolerance: >> 4.996813e-08 > > (when the "show.nls.convergence" option is not set to FALSE. It is set to > FALSE in SSasymp.Rd but not reset at the end.) > > Best regards, > > Sebastian > > > Am 01.10.21 um 11:01 schrieb Andrew Piskorski: >> I recently built R 4.1.1 (Patched) from source, as I have many older >> versions over the years. This version, on Ubuntu 18.04.4 LTS: >> R 4.1.1 (Patched), 2021-09-21, svn.rev 80946, x86_64-pc-linux-gnu >> Surprisingly, "make check" fails, which I don't recall seeing before. >> The error is in from stats-Ex.R, which unfortunately terminates all >> further testing! This particular error, "step factor ... reduced >> below 'minFactor'" does not seem very serious, but I can't figure out >> why it's happening. >> I installed with "make install install-tests" as usual, which seemed >> to work fine. Running the same tests after install, I'm able to get >> more coverage by using errorsAreFatal=FALSE. However, it seems the >> rest of the 'stats' tests after the bad one still do not run. >> I'm confused about the intent of this particular test. The comment >> above it seems to says that it's SUPPOSED to throw this error, yet >> getting the error still terminates further testing, which seems >> strange. What's supposed to happen here? >> Any ideas on why this error might be occurring, and how I should debug >> it? What's the right way for me to disable this one failing test, so >> the ones after it can run? >> Thanks for your help! >> ## "make check" output: >> make[1]: Entering directory >> '/home/nobackup/co/R/R-4-1-branch/Build-x86_64/tests' >> make[2]: Entering directory >> '/home/nobackup/co/R/R-4-1-branch/Build-x86_64/tests' >> make[3]: Entering directory >> '/home/nobackup/co/R/R-4-1-branch/Build-x86_64/tests/Examples' >> Testing examples for package 'base' >> Testing examples for package 'tools' >> comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK >> Testing examples for package 'utils' >> Testing examples for package 'grDevices' >> comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK >> Testing examples for package 'graphics' >> comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK >> Testing examples for package 'stats' >> Error: testing 'stats' failed >> Execution halted >> Makefile:37: recipe for target 'test-Examples-Base' failed >> make[3]: *** [test-Examples-Base] Error 1 >> make[3]: Leaving directory >> '/home/nobackup/co/R/R-4-1-branch/Build-x86_64/tests/Examples' >> ../../tests/Makefile.common:198: recipe for target 'test-Examples' failed >> make[2]: *** [test-Examples] Error 2 >> make[2]: Leaving directory >> '/home/nobackup/co/R/R-4-1-branch/Build-x86_64/tests' >> ../../tests/Makefile.common:184: recipe for target 'test-all-basics' failed >> make[1]: *** [test-all-basics] Error 1 >> make[1]: Leaving directory >> '/home/nobackup/co/R/R-4-1-branch/Build-x86_64/tests' >> Makefile:305: recipe for target 'check-all' failed >> make: *** [check-all] Error 2 >> ## From file: tests/Examples/stats-Ex.Rout.fail >>> ## Here, requiring close convergence, you need to use more accurate >>> numerical >>> ## differentiation; this gives Error: "step factor .. reduced below >>> 'minFactor' .." >>> options(digits = 10) # more accuracy for 'trace' >>> ## IGNORE_RDIFF_BEGIN >>> try(nlm1 <- update(nlmod, control = list(tol = 1e-7))) # where central >>> diff. work here: >> Warning in nls(formula = y ~ Const + A * exp(B * x), algorithm = "default", >> : >> No starting values specified for some parameters. >> Initializing 'Const', 'A', 'B' to '1.'. >> Consider specifying 'start' or using a selfStart model >>> (nlm2 <- update(nlmod, control = list(tol = 8e-8, nDcentral=TRUE), >>> trace=TRUE)) >> Warning in nls(formula = y ~ Const + A * exp(B * x), algorithm = "default", >> : >> No starting values specified for some parameters. >> Initializing 'Const', 'A', 'B' to '1.'. >> Consider specifying 'start' or using a selfStart model >> 1017460.306 (4.15e+02): par = (1 1 1) >> 758164.7503 (2.34e+02): par = (13.42031396 1.961485 0.05947543745) >> 269506.3538 (3.23e+02): par = (51.75719816 -13.09155957 0.8428607709) >> 68969.21893 (1.03e+02): par = (76.0006985 -1.935226745 1.0190858) >> 633.3672230 (1.29e+00): par = (100.3761515 8.624648402 5.104490259) >> 151.4400218 (9.39e+00): par = (100.6344391 4.913490985 0.2849209569) >> 53.08739850 (7.24e+00): par = (100.6830407 6.899303317 0.4637755074) >> 1.344478640 (5.97e-01): par = (100.0368306 9.897714142 0.5169294939) >> 0.9908415909 (1.55e-02): par = (100.0300625 9.9144191 0.5023516843) >> 0.9906046057 (1.84e-05): par = (100.0288724 9.916224018 0.5025207336) >> 0.9906046054 (9.95e-08): par = (100.028875 9.916228366 0.50252165) >> 0.9906046054 (9.93e-08): par = (100.028875 9.916228366 0.50252165) >> Error in nls(formula = y ~ Const + A * exp(B * x), algorithm = "default", : >> step factor 0.000488281 reduced below 'minFactor' of 0.000976562 >> Calls: update -> update.default -> eval -> eval -> nls >> Execution halted >> ## After install, start R with --vanilla and run tests like this: >> ## >> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Testing-a-Unix_002dalike-Installation >> Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en") >> pdf("tests.pdf") >> tools::testInstalledPackages(scope="base", errorsAreFatal=FALSE) >> > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd....@cbs.dk Priv: pda...@gmail.com ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
