-----BEGIN PGP SIGNED MESSAGE----- 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 `---- 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) iEYEARECAAYFAklMRtwACgkQ3J3HaQTDvd+iTwCeNEl4fdSwndRWjg2akgRZ0uZI 4JEAn39tP8td6c+tWNMWRb4yivNPyVHx =Y+Yn -----END PGP SIGNATURE-----
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 -----BEGIN PGP SIGNED MESSAGE----- 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 `---- 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) iEYEARECAAYFAklMRtwACgkQ3J3HaQTDvd+iTwCeNEl4fdSwndRWjg2akgRZ0uZI 4JEAn39tP8td6c+tWNMWRb4yivNPyVHx =Y+Yn -----END PGP SIGNATURE----- ______________________________________________ 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 19 December 2008 at 17:13, Bill Harris wrote: | 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(). First off, see the R FAQ and the Ubuntu README on CRAN: http://cran.r-project.org/bin/linux/ubuntu/ This shows you how you can get current R binaries with just one apt-get command. With that, you then get to decide if you want the prebuild r-cran-* packages (as e.g. r-cran-lme4) or whether you want to built them yourself in R via install.packages(). In which case r-base-dev will be helpful to install needed packages. Either way, I have no problems with lme4 etc. or arm, see below. Also note that there is a Debian/Ubuntu specific mailing list r-sig-debian where you may want to subscribe. You are likely to find more focussed help for Ubuntu there, and we'd be glad to walk you through individual steps. Welcome to Debian and Ubuntu :) Regards, Dirk>From my Debian system running the beta release of R 2.8.1:> 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 The following object(s) are masked from package:base : colMeans, colSums, rcond, rowMeans, rowSums Loading required package: lme4 Loading required package: R2WinBUGS Loading required package: coda Attaching package: 'coda' The following object(s) are masked from package:lme4 : HPDinterval arm (Version 1.1-17, built: 2008-11-25) Working directory is /home/edd options( digits = 2 ) Loading required package: car Loading required package: foreign Attaching package: 'arm' The following object(s) are masked from package:coda : traceplot>-- Three out of two people have difficulties with fractions.