current r-forge version fails R CMD check ... ?
Thanks, Reinhold, I'm glad I'm not completely nuts. With Doug Bates (quite reasonably) occupied with other things, it strikes me it might be a little hard to dig deep enough into the guts to see what's going on ... I will see how far I can get, but this is the kind of problem where **if** we understood what was going on and it looked hard to fix, it would seem reasonable to replace the "must be identical" criterion with "abs(difference)<1e-7" or some such in the tests ... Ben
Reinhold Kliegl wrote:
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? L?R Fehler: identical(ranef(m0), ranef(m1)) is not TRUE Zus?tzlich: Warnmeldung: In Ops.factor(ff, x1) : + nicht sinnvoll f?r 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: =*?1????@???T??o????
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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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