[R-sig-ME] current r-forge version fails R CMD check ... ?

Reinhold Kliegl reinhold.kliegl at gmail.com
Sat Aug 1 19:50:25 CEST 2009


Just updated to Matrix_0.999375-30. The previous problem persists and
now it also reports:
Fehler: identical(ranef(om2), ranef(om3)) is not TRUE

Reinhold

> stopifnot(identical(ranef(om2), ranef(om3)),
+          identical(deviance(om2), deviance(om3)))
Fehler: identical(ranef(om2), ranef(om3)) is not TRUE
+ if (identical(TRUE, all.equal(fixef(m2), fixef(om2))))
+    stop("offset does not change the fixed effects")
>
> cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
Time elapsed:  13.588 0.399 14.297 0 0
> sessionInfo()
R version 2.9.1 (2009-06-26)
i386-apple-darwin8.11.1

locale:
de_DE.UTF-8/en_US.UTF-8/C/C/de_DE.UTF-8/de_DE.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods
[7] base

other attached packages:
[1] lme4_0.999375-31   Matrix_0.999375-30 lattice_0.17-25


On Sat, Aug 1, 2009 at 7:37 PM, Reinhold
Kliegl<reinhold.kliegl at gmail.com> wrote:
> Ben's problem shows up with my implementation, too. Info below.
>
> Reinhold
>
>> stopifnot(identical(ranef(m0), ranef(m1)),
> +          identical(ranef(m2), ranef(m3)),
> +          inherits(tryCatch(lmer(y ~ x2|ff + x1, data = D), error =
> function(e)e),"error"))
> CHOLMOD error: xG˝ LÛR
> Fehler: identical(ranef(m0), ranef(m1)) is not TRUE
> Zusätzlich: Warnmeldung:
> In Ops.factor(ff, x1) : + nicht sinnvoll für Faktoren
> +
>> ## Check the use of offset
>> om2 <- lmer(y ~ x1 + (x2|ff), data = D, offset = x3)
>> om3 <- lmer(y ~ x1 + (x2|ff) + offset(x3), data = D)
>>
>> stopifnot(identical(ranef(om2), ranef(om3)),
> +          identical(deviance(om2), deviance(om3)))
>> if (identical(TRUE, all.equal(fixef(m2), fixef(om2))))
> +    stop("offset does not change the fixed effects")
>>
>> cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
> Time elapsed:  11.608 0.369 12.353 0 0
>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> i386-apple-darwin8.11.1
>
> locale:
> de_DE.UTF-8/en_US.UTF-8/C/C/de_DE.UTF-8/de_DE.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> [7] base
>
> other attached packages:
> [1] lme4_0.999375-31   Matrix_0.999375-29 lattice_0.17-25
>
> loaded via a namespace (and not attached):
> [1] grid_2.9.1
>>
>
>
> On Sat, Aug 1, 2009 at 6:31 PM, Ben Bolker<bolker at ufl.edu> wrote:
>>
>>  I don't mind it being public.
>>
>>  I got similar results with the CRAN lme4 (0.999375-31),
>> with Matrix ...-30.  BATCH fails on m2 != m3 (consistently);
>> source() fails on m0 != m1.
>>
>>  I'm probably doing something really really dumb, would appreciate
>> anyone else who can try this on their systems ...
>>
>>  If you don't feel like downloading or running all of lmer-1.R, the
>> following code chunk should demonstrate the problem ...
>>
>> =================
>> library(lme4)
>>
>> set.seed(1)
>> ## Wrong formula gave a seg.fault at times:
>> D <-  data.frame(y= rnorm(20,10), ff = gl(4,5),
>>                 x1=rnorm(20,3), x2=rnorm(20,7),
>>                 x3=rnorm(20,1))
>> m0 <- lmer(y ~ (x1 + x2)|ff, data = D)
>> m1 <- lmer(y ~ x1 + x2|ff  , data = D)
>> m2 <- lmer(y ~ x1 + (x2|ff), data = D)
>> m3 <- lmer(y ~ (x2|ff) + x1, data = D)
>> stopifnot(identical(ranef(m0), ranef(m1)),
>>          identical(ranef(m2), ranef(m3)),
>>          inherits(tryCatch(lmer(y ~ x2|ff + x1, data = D), error =
>> function(e)e),
>>                   "error"))
>>
>> ## Check the use of offset
>> om2 <- lmer(y ~ x1 + (x2|ff), data = D, offset = x3)
>> om3 <- lmer(y ~ x1 + (x2|ff) + offset(x3), data = D)
>>
>> stopifnot(identical(ranef(om2), ranef(om3)),
>>          identical(deviance(om2), deviance(om3)))
>> if (identical(TRUE, all.equal(fixef(m2), fixef(om2))))
>>    stop("offset does not change the fixed effects")
>>
>> cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
>>
>>
>> Martin Maechler wrote:
>>> Hi Ben,
>>> as you took this "private", I'd like at least Doug Bates
>>> to be in the CC ..
>>> Personally I would prefer to have this continue in the R-SIG-ME list
>>> rather than privately...  I'll be pretty offline from now till Monday
>>> in any case
>>>
>>> On Fri, Jul 31, 2009 at 20:17, Ben Bolker<bolker at ufl.edu> wrote:
>>>> Martin Maechler wrote:
>>>>>>>>>> "BB" == Ben Bolker <bolker at ufl.edu>
>>>>>>>>>>     on Thu, 30 Jul 2009 17:30:17 -0400 writes:
>>>>>     BB> When I use the latest r-forge version of lme4
>>>>>     BB> (  0.999375-32 ) it seems to fail R CMD check on a tiny
>>>>>     BB> numerical mismatch of two objects that are supposed
>>>>>     BB> (??) to be identical (I also
>>>>>     BB> get a mangled CHOLMOD error message, but I suspect that
>>>>>     BB> comes from somewhere within Matrix ...)
>>>>>
>>>>> yes, and those should be gone with the version of Matrix
>>>>> (0.999375-30) of two days ago.
>>>>>
>>>>>     BB> can anyone confirm?
>>>>>
>>>>> No.  To the contrary.
>>>>> I have had a slightly updated version of tests/lmer-1.Rout.save
>>>>> ready to be committed for a while, but that's only trivial
>>>>> changes.
>>>>>
>>>>> and below, from your sessionInfo(), it looks like you are using
>>>>> a current version of R and packages ...
>>>>> hmm ...
>>>>>
>>>>> Regards,
>>>>> Martin
>>>>>
>>>>>
>>>>>     BB> can anyone confirm? any ideas for a fix?
>>>>>
>>>>>
>>>>>     BB> The offending mismatch between ranef(m2) and ranef(m3)
>>>>>     BB> is very small ...
>>>>>
>>>>> well; it's interesting that the offending mismatch in the error
>>>>> message below is between  m0 and m1,  ...
>>>>  hmmm indeed.  Maybe I was already hacking things.  I have
>>>> (1) updated Matrix, (2) installed lme4 directly from r-forge.
>>>> sessionInfo() says
>>>>
>>>>  lme4_0.999375-32   Matrix_0.999375-30
>>>>
>>>> in ../tests, I do
>>>>
>>>> R --vanilla
>>>> library(lme4)
>>>> source("lmer-1.R",echo=TRUE)
>>>>
>>>> or
>>>>
>>>> R CMD BATCH --vanilla lmer-1.R
>>>>
>>>>  oddly, the second (BATCH) always fails on m0/m1; the
>>>> first (source) fails at different comparisons (sometimes m0/m1;
>>>> sometimes m2/m3; sometimes om2/om3 in the next section ... ???
>>>
>>> I just can't understand how that *can* happen.
>>> It would mean that the algorithms used were slightly "random",  or
>>> e.g. using slightly different precision depending on memory
>>> allocation, or ??,
>>> ???
>>>
>>> As I said i the first e-mail: The slightly different formula should
>>> produce absolutely identical matrices and vectors which define the
>>> loglikelihood (or RE-LogLik.) and then the minimization really should
>>> be 100% reproducible on a given R+Platform+Installed-Packages setup.
>>>
>>> I assume you have tried the same with the CRAN-version of lme4 ...
>>> which has exactly the same tests/lmer-1.R  ?
>>> ....
>>> the phenomenon looks so illogical,  I even start to wonder if it's a
>>> bug in your computer (hardware-low-level software combination)?
>>> Maybe you could ask again on R-SIg-ME if others could reproduce?
>>>
>>>>> BTW: Have you noticed that we (Doug Bates and I, when at the
>>>>> useR/DSC meetings) have moved the former 'allcoef' branch into a
>>>>> ``regular R-forge package''  called  'lme4a'
>>>>  yes.
>>>>> But yes, that definitely does not pass 'CMD check at the moment'.
>>>>>
>>>>>     >> getwd()
>>>>>     BB> [1] "/home/ben/lib/R/pkgs/lme4/pkg/lme4/tests"
>>>>>
>>>>>     >> source("lmer-1.R",echo=TRUE)
>>>>>
>>>>>     BB> ...
>>>>>     >> D <-  data.frame(y= rnorm(20,10), ff = gl(4,5),
>>>>>     BB> x1=rnorm(20,3), x2=rnorm(20,7),
>>>>>     BB> x3=rnorm(20,1))
>>>>>     >> m0 <- lmer(y ~ (x1 + x2)|ff, data = D)
>>>>>     >> m1 <- lmer(y ~ x1 + x2|ff  , data = D)
>>>>>
>>>>> We had added these checks exactly *because* we wanted to be sure
>>>>> that a slightly different use of formulas would lead to the
>>>>> identical 'X', 'Z', .... matrices, and L(theta)
>>>>> parametrizations,
>>>>> so I wonder how your version of lme4 could give different
>>>>> results here....
>>>>>
>>>>>     >> m2 <- lmer(y ~ x1 + (x2|ff), data = D)
>>>>>     >> m3 <- lmer(y ~ (x2|ff) + x1, data = D)
>>>>>     >> stopifnot(identical(ranef(m0), ranef(m1)),
>>>>>     BB> +           identical(ranef(m2), ranef(m3)),
>>>>>     BB> +           inherits(tryCatch(lmer(y ~ x2|ff + x1, data = D) ....
>>>>>     BB> [TRUNCATED]
>>>>>     BB> CHOLMOD error: =*ᶈ1ñ¿@ÀTôoá¶
>>>>>     BB> Error: identical(ranef(m0), ranef(m1)) is not TRUE
>>>>>     BB> In addition: Warning message:
>>>>>     BB> In Ops.factor(ff, x1) : + not meaningful for factors
>>>>>
>>>>> Note that the cholmod error and warning is from the
>>>>>    lmer(y ~ x2|ff + x1, data = D)
>>>>> part {which is wrapped in  tryCatch(...)}.
>>>>>
>>>>> Also, if I execute
>>>>>
>>>>> ##----------------------------------------------------
>>>>> D <-  data.frame(y= rnorm(20,10), ff = gl(4,5),
>>>>>                  x1=rnorm(20,3), x2=rnorm(20,7),
>>>>>                  x3=rnorm(20,1))
>>>>> m0 <- lmer(y ~ (x1 + x2)|ff, data = D)
>>>>> m1 <- lmer(y ~ x1 + x2|ff  , data = D)
>>>>> m2 <- lmer(y ~ x1 + (x2|ff), data = D)
>>>>> m3 <- lmer(y ~ (x2|ff) + x1, data = D)
>>>>> stopifnot(identical(ranef(m0), ranef(m1)),
>>>>>           identical(ranef(m2), ranef(m3)))
>>>>> cat("Ok\n")
>>>>> ##----------------------------------------------------
>>>>>
>>>>> many times, I never see a problem.
>>>>>
>>>>> Are you sure you are not using your already-hacked version of
>>>>> lme4 ???
>>>>>
>>>>> Martin Maechler, ETH Zurich
>>>>>
>>>>  I'm not 100.0000% sure, but I don't see how I could be ...
>>>>
>>>>  Ben
>>>>
>>>>
>>
>>
>> --
>> Ben Bolker
>> Associate professor, Biology Dep't, Univ. of Florida
>> bolker at ufl.edu / www.zoology.ufl.edu/bolker
>> GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>
>




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