[R] Problems installing lme4 on Ubuntu
Bill Harris
bill_harris at facilitatedsystems.com
Sat Dec 20 02:13:59 CET 2008
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While I'm not an R expert, I have used R on Windows XP. Now I've moved
to Ubuntu (Intrepid), and I'm trying to configure R to work with the
Gelman and Hill _Data Analysis Using Regression and
Multilevel/Hierarchical Models_. So far, it's not working.
I start by following the instructions for installing arm and BRugs at
<http://www.stat.columbia.edu/~gelman/bugsR/>. At first, it kept
failing, but I kept installing more Ubuntu packages. Finally, I
installed the sciencestatistics package, and things seemed to work: I
got the required packages to show up as loaded when I run library().
When I run library(arm) (FWIW, I'm using ESS in Emacs), I get
,
 > library(arm)
 Loading required package: MASS
 Loading required package: Matrix
 Loading required package: lattice

 Attaching package: 'Matrix'


 The following object(s) are masked from package:stats :

 xtabs

 Loading required package: lme4
 Error in dyn.load(file, DLLpath = DLLpath, ...) :
 function 'cholmod_start' not provided by package 'Matrix'
 Error: package 'lme4' could not be loaded
`
even though
,
 > library()
 Packages in library '/home/bill/R/i486pclinuxgnulibrary/2.7':

 arm Data Analysis Using Regression and
 Multilevel/Hierarchical Models
 coda Output analysis and diagnostics for MCMC
 Matrix Sparse and Dense Matrix Classes and Methods
 R2WinBUGS Running WinBUGS and OpenBUGS from R / SPLUS

 Packages in library '/usr/lib/R/sitelibrary':
 .
 .
 latticeExtra Extra Graphical Utilities Based on Lattice
 lme4 Linear mixedeffects models using S4 classes
 lmtest Testing Linear Regression Models
 .
 .

 Packages in library '/usr/lib/R/library':

 .
 .
 .

 Warning message:
 In library() : library ‘/usr/local/lib/R/sitelibrary’ contains no packages
`
and
,
 > library(help = arm)

 Information on package 'arm'

 Description:

 Package: arm
 Version: 1.117
 Date: 20081125
 Title: Data Analysis Using Regression and
 Multilevel/Hierarchical Models
 Author: Andrew Gelman <gelman at stat.columbia.edu>, YuSung Su
 <ys463 at columbia.edu>, Masanao Yajima
 <my2167 at columbia.edu>, Jennifer Hill
 <jh1030 at columbia.edu>, Maria Grazia Pittau
 <grazia at stat.columbia.edu>, Jouni Kerman
 <jouni at kerman.com> and Tian Zheng
 <tzheng at stat.columbia.edu>
 Maintainer: YuSung Su <ys463 at columbia.edu>
 Depends: methods, R (>= 2.6.0), MASS, Matrix (>= 0.99937510),
 lme4 (>= 0.99937516), R2WinBUGS
 Suggests: car, foreign
 Description: R functions for processing lm, glm, mer and polr
 outputs.
 URL: http://www.stat.columbia.edu/~gelman/software/
 License: GPL (>= 2)
 Packaged: Tue Nov 25 15:26:57 2008; SUYS
 Built: R 2.7.1; ; 20081217 21:31:22; unix

 Index:

 GOclass Function to Recall Last Source File
 balance Functions to compute the balance statistics
 bayesglm Bayesian generalized linear models.
 bayespolr Bayesian Ordered Logistic or Probit Regression
 binnedplot Binned Residual Plot
 coefplot Generic Function for Making Coefficient Plot
 contr.bayes.ordered Contrast Matrices
 corrplot Correlation Plot
 display Functions for Processing lm, glm, mer and polr
 Output
 fround Formating the Rounding of Numbers
 invlogit Inverse logistic function
 lalonde Lalonde Dataset
 matching Single Nearest Neighborhood Matching
 model.matrix.bayes Construct Design Matrices
 multicomp.plot Multiple Comparison Plot
 rescale Function for Standardizing by Centering and
 Dividing by 2 sd's
 residual.plot residual plot for the observed values
 se.coef Extract Standard Errors of Model Coefficients
 sigma.hat Extract Residual Errors
 sim Functions to Get Posterior Distributions
 standardize Function for Standardizing Regression
 Predictors by Centering and Dividing by 2 sd's
 traceplot Trace plot of bugs object
 triangleplot Triangle Plot
`
To demonstrate that things aren't well,
,
 > display()
 Error: could not find function "display"
`
Any suggestions on next steps? The best I found in searching was that I
needed to load certain packages in Ubuntu, and I hoped I had done that
when I finally loaded sciencestatistics.
Thanks,
Bill
 
Bill Harris http://facilitatedsystems.com/weblog/
Facilitated Systems Everett, WA 98208 USA
http://facilitatedsystems.com/ phone: +1 425 3375541
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