[R] Problems installing lme4 on Ubuntu

Steven McKinney smckinney at bccrc.ca
Sat Dec 20 02:43:14 CET 2008

This may just be version incompatibilities.

A similar discussion recently transpired on
r-sig-mixed-models, see e.g. 



Steven McKinney

Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney +at+ bccrc +dot+ ca

tel: 604-675-8000 x7561

Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3

-----Original Message-----
From: r-help-bounces at r-project.org on behalf of Bill Harris
Sent: Fri 12/19/2008 5:13 PM
To: r-help at r-project.org
Subject: [R] Problems installing lme4 on Ubuntu
Hash: SHA1

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 science-statistics 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/i486-pc-linux-gnu-library/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 / S-PLUS
| Packages in library '/usr/lib/R/site-library':
|   .
|   .
| latticeExtra            Extra Graphical Utilities Based on Lattice
| lme4                    Linear mixed-effects 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/site-library' contains no packages


| > library(help = arm)
| 		Information on package 'arm'
| Description:
| Package:       arm
| Version:       1.1-17
| Date:          2008-11-25
| Title:         Data Analysis Using Regression and
|                Multilevel/Hierarchical Models
| Author:        Andrew Gelman <gelman at stat.columbia.edu>, Yu-Sung 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:    Yu-Sung Su <ys463 at columbia.edu>
| Depends:       methods, R (>= 2.6.0), MASS, Matrix (>= 0.999375-10),
|                lme4 (>= 0.999375-16), 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; ; 2008-12-17 21:31:22; unix
| Index:
| GO-class                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 science-statistics.


- -- 
Bill Harris                      http://facilitatedsystems.com/weblog/
Facilitated Systems                              Everett, WA 98208 USA
http://facilitatedsystems.com/                  phone: +1 425 337-5541
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