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

Answer 1

 sudo apt-get install r-base-dev

solved the problem for me

Answer 2

This was a bug, should be fixed by this commit in the development version (on Github) and in release 1.1-7 when it comes out (soon?)

Answer 3

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

Answer 4

Based on your comments and expanded questions:

• You are shooting yourself in the foot by installing R 3.1.0 onto Ubuntu 12.04.

• You now run an R that is out of sync with packages like r-cran-lme4 in the distro.

• The good news is that you can ask the distribution for information about the so-called Build-Depends it knows, and rebuild lme4 under R 3.1.0

• Or can benefit from Michael's other work over at launchpad and use his other repo which is what eg the r-travis code does: sudo add-apt-repository -y "ppa:marutter/rrutter" followed by and sudo add-apt-repository -y "ppa:marutter/c2d4u"

That last step will give you loads of pre-built packages. In the long run you are of course better off being to able to build packages from source yourself...