[R-sig-Debian] lme4 installation

[Michael Rutter]

On 08/29/2012 03:31 PM, Scott Raynaud wrote:
> Being rather inept at all things Linux, I paid a consultant
> to fix some things on my computer,  Unforntately, good
> help is hard to find.  Here's where I am:
>
> ...
> Loading required package: Matrix
> Loading required package: lattice
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>    function 'cholmod_l_start' not provided by package 'Matrix'
> Error: package/namespace load failed for ‘lme4’
> Error: package/namespace load failed for ‘lme4’
>
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8           LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8
>   [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8
> [11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Matrix_1.0-6   lattice_0.20-6 MASS_7.3-19    rkward_0.5.6
>
> loaded via a namespace (and not attached):
> [1] grid_2.15.1   nlme_3.1-104  stats4_2.15.1 tools_2.15.1
>> installed.packages()[c("lme4","nlme","Matrix"),c(2,3,12)]
>         LibPath                   Version       Built
> lme4   "/usr/lib/R/site-library" "0.999375-40" "2.13.1"
> nlme   "/usr/lib/R/library"      "3.1-104"     "2.15.0"
> Matrix "/usr/lib/R/library"      "1.0-6"       "2.15.0"
>
>
>> install.packages("lme4")
> Installing package(s) into ‘/home/vm-cook/R/x86_64-pc-linux-gnu-library/2.15’
> (as ‘lib’ is unspecified)
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> Warning: unable to access index for repository http://cran.cnr.Berkeley.edu/src/contrib
> Warning: unable to access index for repository http://rkward.sf.net/R/src/contrib
> Warning messages:
> 1: In open.connection(con, "r") :
>    unable to connect to 'cran.r-project.org' on port 80.
> 2: package ‘lme4’ is not available (for R version 2.15.1)
>>
>
>
> You can see that there's a problem with program loading lme4.  A litlle
> sluething around revelaed that it's the wrong version. When I attmept to
> install I get the warnings above.
>
> Also tried the apt-get command at the console to no avail:
>
> vm-cook at GRNTv01:~$ sudo apt-get install lme4
> [sudo] password for vm-cook:
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> E: Unable to locate package lme4
> vm-cook at GRNTv01:~$
>
>
> What next?

Scott,

All the R packages from CRAN in the repository have an "r-cran-" prefix. 
  So the correct command would be:

sudo apt-get install r-cran-lme4

Not sure if you are using Debian or Ubuntu, so you mileage may vary with 
the above command.  If you are using Ubuntu, you could install the 
cran2deb4ubuntu PPA which has the latest lme4.  (http://tiny.cc/c2d4u).

Michael


-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
4205 College Drive
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter
mar36 at psu.edu