Hello all,
Using Ubuntu 9.04 and R 2.8.1.
For a project I need to use the Zelig package, which in turn wants to
use the lme4 package. When trying to use Zelig and it tries to its required
packages I get the following error message.
Error in dyn.load(file, DLLpath = DLLpath, ...) :
function 'cholmod_start' not provided by package 'Matrix'
Error in loadModelDeps(model) :
This model depends on package "lme4". Please install this package and try again
However, library() lists this package:
Packages in library '/usr/lib/R/site-library':
coda Output analysis and diagnostics for MCMC
lme4 Linear mixed-effects models using S4 classes
Matrix Sparse and Dense Matrix Classes and Methods
MCMCpack Markov chain Monte Carlo (MCMC) Package
mvtnorm Multivariate Normal and t Distributions
sandwich Robust Covariance Matrix Estimators
VGAM Vector Generalized Linear and Additive Models
Zelig Everyone's Statistical Software
zoo ...
Trying to load lme4 directly with library(lme4) yields:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
function 'cholmod_start' not provided by package 'Matrix'
Error: package/namespace load failed for 'lme4'
I have looked on the web for quite a bit, but not found a solution,
what am I missing?
lme4 wants matrix version >= 0.999375-11, I have Matrix_0.999375-17,
and R >= 2.7 (I have 2.8.1). I notice that in the functions listings
for Matrix cholmod_start is not found.
(also for some odd reason, my system installs version Zelig 3.3-1 instead of
3.4-5, don't think this is a factor though)
Here are some specifics about my setup, I tried to be complete but I
am happy to provide more information if it would help.
Thanks!
Esmail
Ubuntu 9.04
Linux t61 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686
GNU/Linux
> library(lme4)
Loading required package: Matrix
Loading required package: lattice
Attaching package: 'Matrix'
The following object(s) are masked from package:stats :
xtabs
The following object(s) are masked from package:base :
colMeans,
colSums,
rcond,
rowMeans,
rowSums
Error in dyn.load(file, DLLpath = DLLpath, ...) :
function 'cholmod_start' not provided by package 'Matrix'
Error: package/namespace load failed for 'lme4'
> sessionInfo()
R version 2.8.1 (2008-12-22)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Matrix_0.999375-17 lattice_0.17-26
loaded via a namespace (and not attached):
[1] grid_2.8.1
>
Information on package 'lme4'
Description:
Package: lme4
Version: 0.999375-28
Date: 2008-12-13
Title: Linear mixed-effects models using S4 classes
Author: Douglas Bates <bates at stat.wisc.edu>, Martin Maechler
<maechler at R-project.org> and Bin Dai <dai at stat.wisc.edu>
Maintainer: Douglas Bates <bates at stat.wisc.edu>
Description: Fit linear and generalized linear mixed-effects models.
Depends: methods, R(>= 2.7.0), Matrix(>= 0.999375-11), lattice
LinkingTo: Matrix, stats
Imports: graphics, stats
Suggests: mlmRev, MEMSS
LazyLoad: yes
LazyData: yes
License: GPL (>=2)
URL: http://lme4.r-forge.r-project.org/
Packaged: Sat Dec 13 20:07:38 2008; maechler
Built: R 2.8.0; i486-pc-linux-gnu; 2008-12-15 13:16:45; unix
Information on package 'Matrix'
Description:
Package: Matrix
Version: 0.999375-17
Date: 2008-12-10
Title: Sparse and Dense Matrix Classes and Methods
Author: Douglas Bates <bates at stat.wisc.edu> and Martin
Maechler <maechler at stat.math.ethz.ch>
Maintainer: Doug and Martin <Matrix-authors at R-project.org>
Description: Classes and methods for dense and sparse matrices
and operations on them using Lapack and
SuiteSparse.
Depends: R (>= 2.6.0), stats, methods, utils, lattice
Imports: graphics, lattice, grid, stats
Enhances: graph, SparseM
SystemRequirements: GNU make
LazyLoad: yes
LazyData: no
LazyDataNote: no longer available, since we use data/*.R *and*
our classes
....
all.equal-methods Matrix Methods for Function all.equal()
atomicVector-class Virtual Class "atomicVector" of Atomic Vectors
band Extract bands of a matrix
bdiag Construct a Block Diagonal Matrix
cBind Versions of 'cbind' and 'rbind' recursively
built on cbind2/rbind2
chol Choleski Decomposition - 'Matrix' S4 Generic
colSums Form Row and Column Sums and Means
compMatrix-class Class "compMatrix" of Composite (Factorizable)
Matrices
....
lme4 and function 'cholmod_start' not provided by package 'Matrix' / Ubuntu
5 messages · Dieter Menne, Douglas Bates, Esmail
Esmail Bonakdarian-4 wrote:
Using Ubuntu 9.04 and R 2.8.1. For a project I need to use the Zelig package, which in turn wants to use the lme4 package. When trying to use Zelig and it tries to its required packages I get the following error message. Error in dyn.load(file, DLLpath = DLLpath, ...) : function 'cholmod_start' not provided by package 'Matrix' Error in loadModelDeps(model) : This model depends on package "lme4". Please install this package and try again
Looks like a version mismatch. It's probably easiest if you update to R 2.10.1 and try again; you will have to reinstall all your packages, because of the change help format in 2.9.x Dieter
View this message in context: http://n4.nabble.com/lme4-and-function-cholmod-start-not-provided-by-package-Matrix-Ubuntu-tp1010729p1010740.html Sent from the R help mailing list archive at Nabble.com.
As Dieter points out, this is likely a mismatch between the versions of the lme4 and the Matrix packages, which are very closely linked together. It appears that the version of the lme4 package is too old for the version of the Matrix package, which is hard to catch in the dependencies (lme4 depends on Matrix but not the other way around). As Dieter suggests, it would be best to install the most recent version of R which can then pull in the most recent versions of the lme4 and Matrix packages. On Sun, Jan 10, 2010 at 11:12 AM, Dieter Menne
<dieter.menne at menne-biomed.de> wrote:
Esmail Bonakdarian-4 wrote:
Using Ubuntu 9.04 and R 2.8.1. For a project I need to use the Zelig package, which in turn wants to use the lme4 package. When trying to use Zelig and it tries to its required packages I get the following error message. Error in dyn.load(file, DLLpath = DLLpath, ...) : ? ?function 'cholmod_start' not provided by package 'Matrix' Error in loadModelDeps(model) : ? ?This model depends on package "lme4". Please install this package and try again
Looks like a version mismatch. It's probably easiest if you update to R 2.10.1 and try again; you will have to reinstall all your packages, because of the change help format in 2.9.x Dieter -- View this message in context: http://n4.nabble.com/lme4-and-function-cholmod-start-not-provided-by-package-Matrix-Ubuntu-tp1010729p1010740.html Sent from the R help mailing list archive at Nabble.com.
______________________________________________ R-help at r-project.org 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.
On 10-Jan-10 12:12, Dieter Menne wrote:
Esmail Bonakdarian-4 wrote:
Using Ubuntu 9.04 and R 2.8.1.
For a project I need to use the Zelig package, which in turn wants to
use the lme4 package. When trying to use Zelig and it tries to its
required
packages I get the following error message.
Error in dyn.load(file, DLLpath = DLLpath, ...) :
function 'cholmod_start' not provided by package 'Matrix'
Error in loadModelDeps(model) :
This model depends on package "lme4". Please install this package and
try again
Looks like a version mismatch. It's probably easiest if you update to R 2.10.1 and try again; you will have to reinstall all your packages, because of the change help format in 2.9.x Dieter
Ok, I'll give this a try (probably not a bad idea to be more up-to-date. Hopefully that will make the problem go away. Thanks, Esmail
On 10-Jan-10 12:40, Douglas Bates wrote:
As Dieter points out, this is likely a mismatch between the versions of the lme4 and the Matrix packages, which are very closely linked together. It appears that the version of the lme4 package is too old for the version of the Matrix package, which is hard to catch in the dependencies (lme4 depends on Matrix but not the other way around). As Dieter suggests, it would be best to install the most recent version of R which can then pull in the most recent versions of the lme4 and Matrix packages.
Hi, Yes, you were both right on the money. I took your suggestion and upgraded R to 2.10.1 and I had to install lme4 and zelig from source to get the current packages. Thanks again! Esmail