Thanks Doug and Malcolm.
I noticed that on Ubuntu when I after loading nlme I experience the same
error message. This seemed to be causing the conflict and ranef() error (for
me at least).
Chris

On Tue, Oct 19, 2010 at 11:56 AM, Malcolm Fairbrother <
m.fairbrother@bristol.ac.uk> wrote:

> Dear Chris,
>
> I've had problems similar to this before, and it's often due to having nlme
> loaded along with lme4. I use a Mac. I see from your sessionInfo() that you
> had nlme loaded on Mac, but not Ubuntu. I'd trying detaching:
>
> > ranef(fm1)
> Error in UseMethod("ranef") :
>  no applicable method for 'ranef' applied to an object of class "mer"
> > detach(package:nlme)
> > ranef(fm1)
> $Subject
>    (Intercept)        Days
> 308   2.2571870   9.1992523
> 309 -40.3984020  -8.6211497
>
> etc.
>
> Hope that works.
>
> - Malcolm
>
>
> Dr Malcolm Fairbrother
> Lecturer
> School of Geographical Sciences
> University of Bristol
>
>
> > Message: 4
> > Date: Tue, 19 Oct 2010 11:31:18 -0500
> > From: Christopher Desjardins <desja004@umn.edu>
> > To: r-sig-mixed-models@r-project.org
> > Subject: [R-sig-ME] ranef() on Mac OS X
> > Message-ID:
> >       <AANLkTin=ksZK=5eC30fHiaY9OH-Y3ExaU=5yktc0DB9O@mail.gmail.com>
> > Content-Type: text/plain
> >
> > I am unable to use the ranef() function on a lmer function on a Mac. I
> get
> > the following error:
> >
> >> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> >> ranef(fm1)
> > Error in UseMethod("ranef") :
> >  no applicable method for 'ranef' applied to an object of class "mer"
> >> sessionInfo()
> > R version 2.11.1 (2010-05-31)
> > i386-apple-darwin9.8.0
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] plyr_1.2.1         nlme_3.1-96        lme4_0.999375-34
> > Matrix_0.999375-39 lattice_0.18-8     foreign_0.8-40
> >
> > loaded via a namespace (and not attached):
> > [1] grid_2.11.1   stats4_2.11.1 tools_2.11.1
> >
> > This works as expected on Ubuntu 10.10 64 bit (see below). I built the
> lme4
> > package from source on the Mac and I know that lme4 has had some issues
> on
> > Mac for a while (i.e. it hasn't been available as a binary for some
> time). I
> > just wanted to post this here to see if this was either a new bug,
> something
> > already documented, or something that I've overlooked. Googling 'ranef
> lme4
> > Mac' brought me to this thread
> > https://stat.ethz.ch/pipermail/r-sig-mixed-models/2010q3/004091.html ...
> but
> > the author was able to use the ranef() function.
> >
> > Thanks,
> > Chris
> >
> >
> > #################
> > ### From Linux ###
> > #################
> >> fm1 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy)
> >> ranef(fm1)
> > $Subject
> >    (Intercept)
> > 308   40.787403
> > 309  -77.856603
> > 310  -63.114282
> > 330    4.406841
> > 331   10.217114
> > 332    8.221982
> > 333   16.501988
> > 334   -2.997253
> > 335  -45.286227
> > 337   72.189222
> > 349  -21.198168
> > 350   14.112641
> > 351   -7.862933
> > 352   36.381719
> > 369    7.037018
> > 370   -6.363279
> > 371   -3.294571
> > 372   18.117387
> >> sessionInfo()
> > R version 2.11.1 (2010-05-31)
> > x86_64-pc-linux-gnu
> >
> > locale:
> > [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
> > [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
> > [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
> > [7] LC_PAPER=en_US.utf8       LC_NAME=C
> > [9] LC_ADDRESS=C              LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] lme4_0.999375-35   Matrix_0.999375-40 lattice_0.18-8
> >
> > loaded via a namespace (and not attached):
> > [1] grid_2.11.1   nlme_3.1-96   stats4_2.11.1 tcltk_2.11.1  tools_2.11.1
> >
> >
> >
> >
> > --
> > Christopher David Desjardins
> > Ph.D. student, Quantitative Methods in Education
> > M.S. student, Statistics
> > University of Minnesota
> >
> >       [[alternative HTML version deleted]]
> >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Tue, 19 Oct 2010 11:44:58 -0500
> > From: Douglas Bates <bates@stat.wisc.edu>
> > To: Christopher Desjardins <desja004@umn.edu>
> > Cc: r-sig-mixed-models@r-project.org
> > Subject: Re: [R-sig-ME] ranef() on Mac OS X
> > Message-ID:
> >       <AANLkTimOmPM0cdw6zLFjrSRrF_M_GgT9d3Q4RYM0F8WA@mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Notice that you have different versions of the lme4 package on Ubuntu
> > and on the Mac.  For some reason the lme4 package is failing a test on
> > Mac OS X only and we haven't been able to diagnose why the -35 version
> > fails there.  Also, we haven't been able to reproduce this on other
> > operating systems and we can't decide why it should fail on Mac OS X
> > unless it is an obscure memory issue.  As neither Martin nor I use Mac
> > OS X we aren't able to debug the issue.  Other folks have looked at it
> > but all they can say is that it is failing, no idea why.  We even
> > tried to bypass the test on the Mac but that doesn't seem to have
> > worked either.
> >
> > I'm open to suggestions from the list on what can be done about lme4
> > and Mac OS X.  If you look at the test results for the package on
> > CRAN, e.g.
> >
> > http://cran.us.r-project.org/web/checks/check_results_lme4.html
> >
> > you will see that Mac OS X is the only system on which there is a
> > problem and the test on which it fails doesn't make sense for it to
> > fail.  The only difference between the two models being compared is
> > that they were generated from slightly different formulas but the
> > models are identical once the formula is parsed.
> >
> > On Tue, Oct 19, 2010 at 11:31 AM, Christopher Desjardins
> > <desja004@umn.edu> wrote:
> >> I am unable to use the ranef() function on a lmer function on a Mac. I
> get
> >> the following error:
> >>
> >>> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> >>> ranef(fm1)
> >> Error in UseMethod("ranef") :
> >> ?no applicable method for 'ranef' applied to an object of class "mer"
> >>> sessionInfo()
> >> R version 2.11.1 (2010-05-31)
> >> i386-apple-darwin9.8.0
> >>
> >> locale:
> >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> >>
> >> attached base packages:
> >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
> >>
> >> other attached packages:
> >> [1] plyr_1.2.1 ? ? ? ? nlme_3.1-96 ? ? ? ?lme4_0.999375-34
> >> Matrix_0.999375-39 lattice_0.18-8 ? ? foreign_0.8-40
> >>
> >> loaded via a namespace (and not attached):
> >> [1] grid_2.11.1 ? stats4_2.11.1 tools_2.11.1
> >>
> >> This works as expected on Ubuntu 10.10 64 bit (see below). I built the
> lme4
> >> package from source on the Mac and I know that lme4 has had some issues
> on
> >> Mac for a while (i.e. it hasn't been available as a binary for some
> time). I
> >> just wanted to post this here to see if this was either a new bug,
> something
> >> already documented, or something that I've overlooked. Googling 'ranef
> lme4
> >> Mac' brought me to this thread
> >> https://stat.ethz.ch/pipermail/r-sig-mixed-models/2010q3/004091.html... but
> >> the author was able to use the ranef() function.
> >>
> >> Thanks,
> >> Chris
> >>
> >>
> >> #################
> >> ### From Linux ###
> >> #################
> >>> fm1 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy)
> >>> ranef(fm1)
> >> $Subject
> >> ? ?(Intercept)
> >> 308 ? 40.787403
> >> 309 ?-77.856603
> >> 310 ?-63.114282
> >> 330 ? ?4.406841
> >> 331 ? 10.217114
> >> 332 ? ?8.221982
> >> 333 ? 16.501988
> >> 334 ? -2.997253
> >> 335 ?-45.286227
> >> 337 ? 72.189222
> >> 349 ?-21.198168
> >> 350 ? 14.112641
> >> 351 ? -7.862933
> >> 352 ? 36.381719
> >> 369 ? ?7.037018
> >> 370 ? -6.363279
> >> 371 ? -3.294571
> >> 372 ? 18.117387
> >>> sessionInfo()
> >> R version 2.11.1 (2010-05-31)
> >> x86_64-pc-linux-gnu
> >>
> >> locale:
> >> ?[1] LC_CTYPE=en_US.utf8 ? ? ? LC_NUMERIC=C
> >> ?[3] LC_TIME=en_US.utf8 ? ? ? ?LC_COLLATE=en_US.utf8
> >> ?[5] LC_MONETARY=C ? ? ? ? ? ? LC_MESSAGES=en_US.utf8
> >> ?[7] LC_PAPER=en_US.utf8 ? ? ? LC_NAME=C
> >> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C
> >> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
> >>
> >> other attached packages:
> >> [1] lme4_0.999375-35 ? Matrix_0.999375-40 lattice_0.18-8
> >>
> >> loaded via a namespace (and not attached):
> >> [1] grid_2.11.1 ? nlme_3.1-96 ? stats4_2.11.1 tcltk_2.11.1 ?tools_2.11.1
> >>
> >>
> >>
> >>
> >> --
> >> Christopher David Desjardins
> >> Ph.D. student, Quantitative Methods in Education
> >> M.S. student, Statistics
> >> University of Minnesota
>
>


-- 
Christopher David Desjardins
Ph.D. student, Quantitative Methods in Education
M.S. student, Statistics
University of Minnesota

	[[alternative HTML version deleted]]


