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Andrew Piskorski

2021-Oct-01 09:01 UTC

[Rd] R 4.1.x make check fails, stats-Ex.R, step factor reduced below minFactor

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)

-- 
Andrew Piskorski <atp at piskorski.com>

Sebastian Meyer

2021-Oct-01 10:03 UTC

head link

[Rd] R 4.1.x make check fails, stats-Ex.R, step factor reduced below minFactor

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)
>

Martin Maechler

2021-Oct-01 13:45 UTC

head link

[Rd] R 4.1.x make check fails, stats-Ex.R, step factor reduced below minFactor

>>>>> 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 <atp at piskorski.com>

    > ______________________________________________
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    > https://stat.ethz.ch/mailman/listinfo/r-devel

R devel - Oct 2021 - R 4.1.x make check fails, stats-Ex.R, step factor reduced below minFactor

[Rd] R 4.1.x make check fails, stats-Ex.R, step factor reduced below minFactor

[Rd] R 4.1.x make check fails, stats-Ex.R, step factor reduced below minFactor

[Rd] R 4.1.x make check fails, stats-Ex.R, step factor reduced below minFactor