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
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)
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. >
>>>>> "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. >>