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joris.dewolf at cropdesign.com

2007-Jan-14 18:15 UTC

[R] changes in the structure of mer objects?

Dear all,

I try to run the example of lmer and get the following error message.
> library(lme4)
> example(lmer)lmer> (fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy))
[[1]]
Error in get(x, envir, mode, inherits) : variable "as.dpoMatrix" was
not
found

This error message is similar to what I get with other models. It looks
like the mer class has a slightly different structure. Anybody an idea how
to solve this?


I am using R 2.4.1 under linux and the latest releases of lme4 and Matrix

lme4_0.9975-10
Matrix_0.9975-8
> version               _
platform       x86_64-unknown-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          4.1
year           2006
month          12
day            18
svn rev        40228
language       R
version.string R version 2.4.1 (2006-12-18)

Thanks

Joris De Wolf
Phone: +32 9 2429155, E-Mail: joris.dewolf at cropdesign.com
Postal Address: CropDesign N.V. Technologiepark 3, 9052 Gent Belgium

Martin Maechler

2007-Jan-15 13:00 UTC

head link

[R] changes in the structure of mer objects?

Hi Joris,

I suspect you somehow load an older version lme4 or Matrix than
you think you are loading.
Or then you have an lmer() function or a class definition 
{from a saved workspace ????}
in your work space.

example(lmer) *must* run correctly for the 'lme4' package to get
onto CRAN at all,
hence it must be unique to your setup.

Maybe as a first step,
run R as "R --vanilla" ?

Regards,
Martin Maechler, ETH Zurich
>>>>> "joris" == joris dewolf <joris.dewolf at
cropdesign.com>
>>>>>     on Sun, 14 Jan 2007 19:15:43 +0100 writes:
    joris> Dear all,

    joris> I try to run the example of lmer and get the following error
message.

    >> library(lme4)
    >> example(lmer)
    lmer> (fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy))
    joris> [[1]]
    joris> Error in get(x, envir, mode, inherits) : variable
"as.dpoMatrix" was not
    joris> found

    joris> This error message is similar to what I get with
    joris> other models. It looks like the mer class has a
    joris> slightly different structure. Anybody an idea how to
    joris> solve this?


    joris> I am using R 2.4.1 under linux and the latest releases of lme4 and
Matrix

    joris> lme4_0.9975-10
    joris> Matrix_0.9975-8

    >> version
    joris> _
    joris> platform       x86_64-unknown-linux-gnu
    joris> arch           x86_64
    joris> os             linux-gnu
    joris> system         x86_64, linux-gnu
    joris> status
    joris> major          2
    joris> minor          4.1
    joris> year           2006
    joris> month          12
    joris> day            18
    joris> svn rev        40228
    joris> language       R
    joris> version.string R version 2.4.1 (2006-12-18)

Doran, Harold

2007-Jan-15 14:18 UTC

head link

[R] changes in the structure of mer objects?

help(package='lme4') will tell you 
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of 
> joris.dewolf at cropdesign.com
> Sent: Monday, January 15, 2007 8:37 AM
> To: Martin Maechler
> Cc: Bates at wisc.edu; r-help at stat.math.ethz.ch; 
> r-help-bounces at stat.math.ethz.ch
> Subject: Re: [R] changes in the structure of mer objects?
> 
> Thanks Martin,
> 
> R --vanilla did the trick.
> By the way, is there a way to check which version of a lme4 
> or Matrix I am using in a certain instance of R?
> 
> We are running multiple versions of R on the same server 
> until we are sure all our operational code is behaving well 
> under a new version of R or of a package.
> Now I start doubting if we ever have been testing what we 
> were intendng to test...
> 
> Joris
> 
> 
> r-help-bounces at stat.math.ethz.ch wrote on 15/01/2007 14:00:12:
> 
> > Hi Joris,
> >
> > I suspect you somehow load an older version lme4 or Matrix than you 
> > think you are loading.
> > Or then you have an lmer() function or a class definition {from a 
> > saved workspace ????} in your work space.
> >
> > example(lmer) *must* run correctly for the 'lme4' package 
> to get onto 
> > CRAN at all, hence it must be unique to your setup.
> >
> > Maybe as a first step,
> > run R as "R --vanilla" ?
> >
> > Regards,
> > Martin Maechler, ETH Zurich
> >
> > >>>>> "joris" == joris dewolf
<joris.dewolf at cropdesign.com>
> > >>>>>     on Sun, 14 Jan 2007 19:15:43 +0100 writes:
> >
> >     joris> Dear all,
> >
> >     joris> I try to run the example of lmer and get the following 
> > error message.
> >
> >     >> library(lme4)
> >     >> example(lmer)
> >     lmer> (fm1 <- lmer(Reaction ~ Days + (Days | Subject), 
> sleepstudy))
> >     joris> [[1]]
> >     joris> Error in get(x, envir, mode, inherits) : variable
"as.
> > dpoMatrix" was not
> >     joris> found
> >
> >     joris> This error message is similar to what I get with
> >     joris> other models. It looks like the mer class has a
> >     joris> slightly different structure. Anybody an idea how to
> >     joris> solve this?
> >
> >
> >     joris> I am using R 2.4.1 under linux and the latest releases
of
> > lme4 and Matrix
> >
> >     joris> lme4_0.9975-10
> >     joris> Matrix_0.9975-8
> >
> >     >> version
> >     joris> _
> >     joris> platform       x86_64-unknown-linux-gnu
> >     joris> arch           x86_64
> >     joris> os             linux-gnu
> >     joris> system         x86_64, linux-gnu
> >     joris> status
> >     joris> major          2
> >     joris> minor          4.1
> >     joris> year           2006
> >     joris> month          12
> >     joris> day            18
> >     joris> svn rev        40228
> >     joris> language       R
> >     joris> version.string R version 2.4.1 (2006-12-18)
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Martin Maechler

2007-Jan-15 14:28 UTC

head link

[R] changes in the structure of mer objects?

>>>>> "HaroldD" == Doran, Harold <HDoran at
air.org>
>>>>>     on Mon, 15 Jan 2007 09:18:12 -0500 writes:
    HaroldD> help(package='lme4') will tell you 

yes, or with more input but less output

   packageDescription("lme4")$Version

Further note

	sessionInfo()

which gives you all versions of all attached packages and more
and which is really *the* thing to be used in such
problem-report e-mails.

Martin

    >> -----Original Message-----
    >> From: r-help-bounces at stat.math.ethz.ch 
    >> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of 
    >> joris.dewolf at cropdesign.com
    >> Sent: Monday, January 15, 2007 8:37 AM
    >> To: Martin Maechler
    >> Cc: Bates at wisc.edu; r-help at stat.math.ethz.ch; 
    >> r-help-bounces at stat.math.ethz.ch
    >> Subject: Re: [R] changes in the structure of mer objects?
    >> 
    >> Thanks Martin,
    >> 
    >> R --vanilla did the trick.
    >> By the way, is there a way to check which version of a lme4 
    >> or Matrix I am using in a certain instance of R?
    >> 
    >> We are running multiple versions of R on the same server 
    >> until we are sure all our operational code is behaving well 
    >> under a new version of R or of a package.
    >> Now I start doubting if we ever have been testing what we 
    >> were intendng to test...
    >> 
    >> Joris
    >> 
    >> 
    >> r-help-bounces at stat.math.ethz.ch wrote on 15/01/2007 14:00:12:
    >> 
    >> > Hi Joris,
    >> >
    >> > I suspect you somehow load an older version lme4 or Matrix
than you
    >> > think you are loading.
    >> > Or then you have an lmer() function or a class definition
{from a
    >> > saved workspace ????} in your work space.
    >> >
    >> > example(lmer) *must* run correctly for the 'lme4'
package
    >> to get onto 
    >> > CRAN at all, hence it must be unique to your setup.
    >> >
    >> > Maybe as a first step,
    >> > run R as "R --vanilla" ?
    >> >
    >> > Regards,
    >> > Martin Maechler, ETH Zurich
    >> >
    >> > >>>>> "joris" == joris dewolf
<joris.dewolf at cropdesign.com>
    >> > >>>>>     on Sun, 14 Jan 2007 19:15:43 +0100
writes:
    >> >
    >> >     joris> Dear all,
    >> >
    >> >     joris> I try to run the example of lmer and get the
following
    >> > error message.
    >> >
    >> >     >> library(lme4)
    >> >     >> example(lmer)
    >> >     lmer> (fm1 <- lmer(Reaction ~ Days + (Days |
Subject),
    >> sleepstudy))
    >> >     joris> [[1]]
    >> >     joris> Error in get(x, envir, mode, inherits) :
variable "as.
    >> > dpoMatrix" was not
    >> >     joris> found
    >> >
    >> >     joris> This error message is similar to what I get with
    >> >     joris> other models. It looks like the mer class has a
    >> >     joris> slightly different structure. Anybody an idea
how to
    >> >     joris> solve this?
    >> >
    >> >
    >> >     joris> I am using R 2.4.1 under linux and the latest
releases of
    >> > lme4 and Matrix
    >> >
    >> >     joris> lme4_0.9975-10
    >> >     joris> Matrix_0.9975-8
    >> >
    >> >     >> version
    >> >     joris> _
    >> >     joris> platform       x86_64-unknown-linux-gnu
    >> >     joris> arch           x86_64
    >> >     joris> os             linux-gnu
    >> >     joris> system         x86_64, linux-gnu
    >> >     joris> status
    >> >     joris> major          2
    >> >     joris> minor          4.1
    >> >     joris> year           2006
    >> >     joris> month          12
    >> >     joris> day            18
    >> >     joris> svn rev        40228
    >> >     joris> language       R
    >> >     joris> version.string R version 2.4.1 (2006-12-18)
    >> >
    >> > ______________________________________________
    >> > R-help at stat.math.ethz.ch mailing list
    >> > https://stat.ethz.ch/mailman/listinfo/r-help
    >> > PLEASE do read the posting guide
    >> http://www.R-project.org/posting-guide.html
    >> > and provide commented, minimal, self-contained, reproducible
code.
    >> 
    >> ______________________________________________
    >> R-help at stat.math.ethz.ch mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-help
    >> PLEASE do read the posting guide 
    >> http://www.R-project.org/posting-guide.html
    >> and provide commented, minimal, self-contained, reproducible code.
    >>

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