[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.
https://stat.ethz.ch/pipermail/r-sig-mixed-models/2008q4/001526.html
HTH
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney +at+ bccrc +dot+ ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
-----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
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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 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
`----
and
,----
| > 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.
Thanks,
Bill
- --
Bill Harris http://facilitatedsystems.com/weblog/
Facilitated Systems Everett, WA 98208 USA
http://facilitatedsystems.com/ phone: +1 425 337-5541
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