Re: [R] Problems installing lme4 on Ubuntu
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-boun...@r-project.org on behalf of Bill Harris Sent: Fri 12/19/2008 5:13 PM To: r-help@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 | codaOutput 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': | . | . | latticeExtraExtra Graphical Utilities Based on Lattice | lme4Linear 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 gel...@stat.columbia.edu, Yu-Sung Su |ys...@columbia.edu, Masanao Yajima |my2...@columbia.edu, Jennifer Hill |jh1...@columbia.edu, Maria Grazia Pittau |gra...@stat.columbia.edu, Jouni Kerman |jo...@kerman.com and Tian Zheng |tzh...@stat.columbia.edu | Maintainer:Yu-Sung Su ys...@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-classFunction to Recall Last Source File | balance Functions to compute the balance statistics | bayesglmBayesian generalized linear models. | bayespolr Bayesian Ordered Logistic or Probit Regression | binnedplot Binned Residual Plot | coefplotGeneric Function for Making Coefficient Plot | contr.bayes.ordered Contrast Matrices | corrplotCorrelation Plot | display Functions for Processing lm, glm, mer and polr | Output | fround Formating the Rounding of Numbers | invlogitInverse logistic function | lalonde Lalonde Dataset | matchingSingle 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
Re: [R] Problems installing lme4 on Ubuntu
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. __ R-help@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.
Re: [R] Problems installing lme4 on Ubuntu
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Steven McKinney smckin...@bccrc.ca writes: 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 Steven, That did sound promising. I ran , | sudo R CMD REMOVE -l /usr/lib/R/site-library/ lme4 ` and the files disappeared. Then I ran , | install.packages(lme4) ` - From inside R, selected a mirror in WA (USA), and let it run. I got , | trying URL 'http://cran.fhcrc.org/src/contrib/lme4_0.999375-28.tar.gz' | Content type 'application/x-gzip' length 678443 bytes (662 Kb) | opened URL | == | downloaded 662 Kb | | * Installing *source* package 'lme4' ... | ** libs | gcc -std=gnu99 -I/usr/share/R/include -I/home/bill/R/i486-pc-linux-gnu-library/2.7/Matrix/include -fpic -g -O2 -c init.c -o init.o | gcc -std=gnu99 -I/usr/share/R/include -I/home/bill/R/i486-pc-linux-gnu-library/2.7/Matrix/include -fpic -g -O2 -c lmer.c -o lmer.o | gcc -std=gnu99 -I/usr/share/R/include -I/home/bill/R/i486-pc-linux-gnu-library/2.7/Matrix/include -fpic -g -O2 -c local_stubs.c -o local_stubs.o | gcc -std=gnu99 -shared -o lme4.so init.o lmer.o local_stubs.o -llapack -lblas -lgfortran -lm -L/usr/lib/R/lib -lR | ** R | ** data | ** moving datasets to lazyload DB | ** inst | ** preparing package for lazy loading | Loading required package: Matrix | Loading required package: lattice | | Attaching package: 'Matrix' | | | The following object(s) are masked from package:stats : | |xtabs | | Creating a new generic function for coef in lme4 | Creating a new generic function for confint in lme4 | Creating a new generic function for plot in lme4 | Creating a new generic function for formula in lme4 | Creating a new generic function for anova in lme4 | Creating a new generic function for deviance in lme4 | Creating a new generic function for fitted in lme4 | Creating a new generic function for logLik in lme4 | Creating a new generic function for predict in lme4 | Creating a new generic function for residuals in lme4 | Creating a new generic function for resid in lme4 | Creating a new generic function for simulate in lme4 | Creating a new generic function for model.frame in lme4 | Creating a new generic function for model.matrix in lme4 | Creating a new generic function for terms in lme4 | Creating a new generic function for vcov in lme4 | Creating a new generic function for with in lme4 | Creating a new generic function for as.data.frame in lme4 | Creating a new generic function for xyplot in lme4 | Creating a new generic function for densityplot in lme4 | Creating a new generic function for qqmath in lme4 | ** help | Building/Updating help pages for package 'lme4' | Formats: text html latex example | BIC texthtmllatex | Dyestuff texthtmllatex example | HPDinterval texthtmllatex | Pastestexthtmllatex example | Penicillintexthtmllatex example | VarCorr-class texthtmllatex | VarCorr texthtmllatex example | VerbAgg texthtmllatex example | cake texthtmllatex example | cbpp texthtmllatex example | fixef texthtmllatex example | lmList-class texthtmllatex | lmListtexthtmllatex example | lmer texthtmllatex example | mcmcsamp texthtmllatex example | mer-class texthtmllatex example | merMCMC-class texthtmllatex example | ranef texthtmllatex example | refit texthtmllatex example | sleepstudytexthtmllatex example | ** building package indices ... | * DONE (lme4) | | The downloaded packages are in | /tmp/RtmpZmO6Lb/downloaded_packages | display() | Error: could not find function display ` The two unexpected things were the fact it seemed to load Matrix after getting lme4 -- did that mess anything up? -- and The following object(s) are masked from package:stats : xtabs statement, which seemed odd but I don't know what it means. Did I misunderstand something? Thanks, Bill - -- Bill Harris http://facilitatedsystems.com/weblog/ Facilitated Systems Everett, WA 98208 USA http://facilitatedsystems.com/ phone: +1 425 337-5541 -BEGIN PGP
Re: [R] Problems installing lme4 on Ubuntu
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dirk Eddelbuettel e...@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- __ R-help@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.
Re: [R] Problems installing lme4 on Ubuntu
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Bill Harris bill_har...@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.gou...@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- __ R-help@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.
Re: [R] Problems installing lme4 on Ubuntu
On 19 December 2008 at 19:53, Bill Harris wrote: | That did sound promising. I ran | | , | | sudo R CMD REMOVE -l /usr/lib/R/site-library/ lme4 | ` | | and the files disappeared. Still not a good idea. See /etc/R/Renviron -- the directory /usr/lib/R/site-library is used by your Ubuntu R/CRAN packages. As you installed them via apt-get / aptitude / ... you should uninstall them via the package management system. R and Ubuntu and somewhat unaware of their respective package systems. So your Ubuntu system now thinks it has files below /usr/lib/R/site-library/lme4/ when it really doesn't anymore. This can lead to inconsistent bahviour. You could just re-install the Ubuntu version, and then remove it, or you could leave it as it is. As a general rule, files below /usr/local or /opt or /home are yours, everything else is done via the package management system. | Then I ran | | , | | install.packages(lme4) | ` | | - From inside R, selected a mirror in WA (USA), and let it run. I got You can also hardwire a mirror via ~/.Rprofile and a line like options(repos=c(CRAN=http://cran.us.r-project.org;)) which selects the same Fred Hutch. mirror too. | , | | trying URL 'http://cran.fhcrc.org/src/contrib/lme4_0.999375-28.tar.gz' | | Content type 'application/x-gzip' length 678443 bytes (662 Kb) | | opened URL | | == | | downloaded 662 Kb | | | | * Installing *source* package 'lme4' ... | | ** libs [...] That's what I suggested in my last email too. | | display() | | Error: could not find function display | ` | | The two unexpected things were the fact it seemed to load Matrix after | getting lme4 -- did that mess anything up? -- and The following Normal -- that is what the Depends: the DESCRIPTION file for lme4 imples. | object(s) are masked from package:stats : xtabs statement, which seemed | odd but I don't know what it means. Normal warning telling you that the xtabs function are masked. Not to worry. Hope this helps, Dirk -- Three out of two people have difficulties with fractions. __ R-help@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.
