>>>>> Andrew Piskorski
>>>>> on Fri, 1 Oct 2021 05:01:39 -0400 writes:
> 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
So this did give an error we expected (on some platforms only),
hence used try().
However, the next one "should work" (*)
and failing there, *does* fail the tests :
>> (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
On our versions of Linux (and hardware in case it should matter: Intel x64),
the above has always worked:
e.g.,
> (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 0.05947543746)
269506.3540 (3.23e+02): par = (51.75719814 -13.09155954 0.8428607699)
68969.21900 (1.03e+02): par = (76.00069849 -1.93522673 1.019085799)
633.3672239 (1.29e+00): par = (100.3761515 8.62464841 5.104490279)
151.4400266 (9.39e+00): par = (100.6344391 4.913490966 0.284920948)
53.08740235 (7.24e+00): par = (100.6830408 6.899303242 0.4637755057)
1.344478691 (5.97e-01): par = (100.0368306 9.89771414 0.5169294949)
0.9908415909 (1.55e-02): par = (100.0300625 9.9144191 0.5023516842)
0.9906046057 (1.84e-05): par = (100.0288724 9.916224018 0.5025207337)
0.9906046054 (9.94e-08): par = (100.028875 9.916228366 0.50252165)
0.9906046054 (5.06e-10): par = (100.028875 9.916228388 0.5025216549)
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
However, we had heard of "strange platforms" where it failed,
--> R's bugzilla PR#18165
and for that reason, in the R-devel version of that source file
<Rsrc>/src/library/stats/man/nls.Rd
have the code amended to not stop on error on those platforms
only:
o2 <- options(digits = 10) # more accuracy for 'trace'
## central differencing works here typically (PR#18165: not converging on
*some*):
ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smaller than above
warnOnly = (grepl("^aarch64.*linux", R.version$platform) && grepl("^NixOS",
osVersion)
))
(nlm2 <- update(nlmod, control = ctr2, trace = TRUE)); options(o2)
... now would that run w/o error on your Ubuntu-installed R ?
First guess: no
Is there anything special (system libraries, compilers, ..)
on your platform?
If not, I do wonder because indeed the
example(nls)
R code (indeed the full help page) is identical as in R 4.1.1,
and I think we can assume for sure that these examples have run
satisfactorily on most Ubuntu 18.04 LTS, no?
> ## 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)
> --
> Andrew Piskorski <a...@piskorski.com>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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