-----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-----
Problems installing lme4 on Ubuntu
4 messages · Bill Harris, Dirk Eddelbuettel
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.
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dirk Eddelbuettel <edd at debian.org> writes:
First off, see the R FAQ and the Ubuntu README on CRAN: http://cran.r-project.org/bin/linux/ubuntu/
Dirk, Thanks; that looks promising!
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.
I tried that, but using the mirrors at fhcrc and wustl both gave me errors when I tried to install: ,---- | WARNING: The following packages cannot be authenticated! | ess r-base-core r-cran-lattice r-cran-mgcv r-cran-vr r-base r-recommended | r-cran-rodbc r-base-html | Install these packages without verification [y/N]? `---- Is that to be expected? I aborted the process, but, if you say that's normal, I'll try again.
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 :)
Thanks. I'll sign up shortly. I had used Debian some years ago in a colinux setting, and it's truly fun to compute again now that I'm on Ubuntu.
The following object(s) are masked from package:stats :
xtabs
Ah. So, whatever that means, it must be okay. :-) 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) iEYEARECAAYFAklMb5UACgkQ3J3HaQTDvd8ZTwCcCiP4gSaEI2eN87kmviY6qVX2 BngAn0hn56BS1fnP445VIifxguUOT4xV =FP2i -----END PGP SIGNATURE-----
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Bill Harris <bill_harris at facilitatedsystems.com> writes:
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.
I tried that, but using the mirrors at fhcrc and wustl both gave me errors when I tried to install: ,---- | WARNING: The following packages cannot be authenticated! | ess r-base-core r-cran-lattice r-cran-mgcv r-cran-vr r-base r-recommended | r-cran-rodbc r-base-html | Install these packages without verification [y/N]? `---- Is that to be expected? I aborted the process, but, if you say that's normal, I'll try again.
I should have said I tried the process shown on that page under SECURE APT: ,---- | $ gpg --keyserver subkeys.pgp.net --recv-key E2A11821 | gpg: requesting key E2A11821 from hkp server subkeys.pgp.net | gpg: key E2A11821: "Vincent Goulet <vincent.goulet at act.ulaval.ca>" not changed | gpg: Total number processed: 1 | gpg: unchanged: 1 | $ gpg -a --export E2A11821 | sudo apt-key add - | OK `---- 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) iEYEARECAAYFAklMccoACgkQ3J3HaQTDvd9CygCeLw7BSsZPghGgEoToz3zKD+D/ QA8AnjsCLqrf7cyXX11B1aBzg3FpWREJ =qlMf -----END PGP SIGNATURE-----