[R] Problems installing lme4 on Ubuntu

[Bill Harris]

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"Steven McKinney" <smckinney at 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                               text    html    latex
|   Dyestuff                          text    html    latex   example
|   HPDinterval                       text    html    latex
|   Pastes                            text    html    latex   example
|   Penicillin                        text    html    latex   example
|   VarCorr-class                     text    html    latex
|   VarCorr                           text    html    latex   example
|   VerbAgg                           text    html    latex   example
|   cake                              text    html    latex   example
|   cbpp                              text    html    latex   example
|   fixef                             text    html    latex   example
|   lmList-class                      text    html    latex
|   lmList                            text    html    latex   example
|   lmer                              text    html    latex   example
|   mcmcsamp                          text    html    latex   example
|   mer-class                         text    html    latex   example
|   merMCMC-class                     text    html    latex   example
|   ranef                             text    html    latex   example
|   refit                             text    html    latex   example
|   sleepstudy                        text    html    latex   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
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