[R-sig-Debian] lme4 installation

[Douglas Bates]

On Wed, Aug 29, 2012 at 2:45 PM, Michael Rutter <mar36 at psu.edu> wrote:
>
>
> 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’

Searching for cholmod_l_start instead of cholmod_start is a sign of
version skew between lme4 and Matrix.

As Michael points out, using the r-cran packages for Debian or Ubuntu
should provide consistent package versions
>>> 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
>
>
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