[R-sig-ME] current r-forge version fails R CMD check ... ?
Reinhold Kliegl
reinhold.kliegl at gmail.com
Sat Aug 1 19:37:14 CEST 2009
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
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
More information about the R-sig-mixed-models
mailing list