Esmail
2010-Jan-10 16:50 UTC
[R] lme4 and function 'cholmod_start' not provided by package 'Matrix' / Ubuntu
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
....
Dieter Menne
2010-Jan-10 17:12 UTC
[R] lme4 and function 'cholmod_start' not provided by package 'Matrix' / Ubuntu
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.