lme4 package install failing on Ubuntu 12.04

Question

EDIT :

Many thanks to user20650, whose answer solved this problem. But if anyone knows why the .Rprofile file affects lme4 install on Ubuntu 12.04, please advise because I'd really like to know.

Original post :

I'm attempting to install the doBy package and am having some issues. It depends on lme4, which for some reason is not compiling from any source I've tried so far. I've been to a few links on SO including this one and haven't had any success.

Here are snippets of the errors I'm getting on install. I tried it three different ways, as noted below. Anyone know if something's up with lme4?

Attempt 1:

> install.packages('doBy')
# ...
# ERROR: compilation failed for package ‘lme4’
# * removing ‘/home/richard/R/x86_64-pc-linux-gnu-library/3.1/lme4’
# Warning in install.packages :
#   installation of package ‘lme4’ had non-zero exit status
# 
# Successfully loaded .Rprofile at Wed May 21 13:33:34 2014 
# ERROR: dependency ‘lme4’ is not available for package ‘doBy’
# * removing ‘/home/richard/R/x86_64-pc-linux-gnu-library/3.1/doBy’
# Warning in install.packages :
#   installation of package ‘doBy’ had non-zero exit status

Attempt 2:

> install.packages("lme4",repos = "http://r-forge.r-project.org")
# Installing package into ‘/home/richard/R/x86_64-pc-linux-gnu-library/3.1’
# (as ‘lib’ is unspecified)
# Warning in install.packages :
#   package ‘lme4’ is not available (for R version 3.1.0)

Attempt 3:

> install_github(repo = 'lme4/lme4', username = 'stevencarlislewalker')

enter image description here

Running Ubuntu 12.04 LTS

> version
# _                           
# platform       x86_64-pc-linux-gnu         
# arch           x86_64                      
# os             linux-gnu                   
# system         x86_64, linux-gnu           
# status                                     
# major          3                           
# minor          1.0                         
# year           2014                        
# month          04                          
# day            10                          
# svn rev        65387                       
# language       R                           
# version.string R version 3.1.0 (2014-04-10)
# nickname       Spring Dance

Maybe sudo apt-get install r-cran-lme4 can help? Else you could try to backtrack to older source versions using the CRAN Archive... — Dirk Eddelbuettel
@DirkEddelbuettel, well that got me a bit closer. Now it's in my list, but I get Error: package ‘lme4’ was built before R 3.0.0: please re-install it — Rich Scriven
(1) I'm not sure why lme4 wouldn't be available for 3.1 (package checks and CRAN page both look fine). (2) I'm not really surprised that lme4 isn't building on R-forge, but try repos="http://lme4.r-forge.r-project.org/repos" (3) sudo apt-get install texinfo — Ben Bolker

user20650 user20650 · Accepted Answer · 2014-05-22T12:36:15

This (possibly) may not be an answer to Richard's Q. but does replicate a problem i had installing lme4 on ubuntu 12,04 on Rv3.1. It would be good if others could reproduce this.

So following on from my comment - noticing that Richard had a .Rprofile, defining .First and .Last in my .Rprofile caused packages not to install.

Exmaple

First uninstall lme4

remove.packages("lme4")

Define .Rprofile file

## .First() run at the start of every R session.
.First <- function() {
cat("\nSuccessfully loaded your .Rprofile at", date(), "\n")
}

## .Last() run at the end of the session
.Last <- function() {
cat("\nGoodbye at ", date(), "\n")
}

Open R

Try an install lme4 - no success & similar error to Richard's above

install.packages("lme4")

...
* removing ‘/home/admin1/R/i686-pc-linux-gnu-library/3.1/lme4’
Warning in install.packages :
  installation of package ‘lme4’ had non-zero exit status

So rename (or remove) .Rprofile file in terminal

mv .Rprofile temp.Rprofile

Open R again and try to install lme4

install.packages("lme4")

...
* installing vignettes
** testing if installed package can be loaded
* DONE (lme4)

 library(lme4)
# Loading required package: Matrix
# Loading required package: Rcpp

lme4 package install failing on Ubuntu 12.04

4 Answers