[R-sig-ME] Something broken in lme4 after update?

Nick Isaac njbisaac at googlemail.com
Thu Nov 27 15:11:55 CET 2008

>> The issue is a bit more subtle than that.  You need to reinstall the
>> lme4 package after changing the version of the Matrix package.
>> There is a change in the internal code in the Matrix package between
>> -16 and -17.  The -16 version requires two versions of every function
>> in the CHOLMOD, AMD and COLAMD libraries whereas the -17 version is
>> back to only one version.  However, lme4 must be reinstalled (in
>> particular, the C code must be recompiled) after a change in the
>> Matrix package.

On 28 Oct 2008, at 10:12, ONKELINX, Thierry wrote:
> Dear Douglas,
> Reinstalling lme4 from R-forge after removing it from the harddisk
> worked.
> Thank you,
> Thierry

I have come up against the same issue as Thierry, but Prof Bates'  
solution does not work for me. The problem seems to be at:

Matrix_stubs.c:494: error: conflicting types for ‘M_R_cholmod_error’
cholmod.h:798: error: previous declaration of ‘M_R_cholmod_error’ was  

I have tried removing both lme4 and Matrix in a different order and  
by various means (deleting the folder in library vs remove.packages 
()). Most recently, I removed both lme4 and Matrix, emptied the trash  
then reinstalled Matrix from r-forge before quitting R and restarting  
my machine. On restarting R I tried:

 > install.packages("lme4",type="source",repos="http://r-forge.r- 

A full transcript of the session is attached.

The attached is a full session history from the most recent attempt.  
I would be grateful for any suggestions.
Best wishes, Nick

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 > sessionInfo()
R version 2.8.0 (2008-10-20)


attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Matrix_0.999375-17 lattice_0.17-15

loaded via a namespace (and not attached):
[1] grid_2.8.0  tools_2.8.0

 > install.packages("lme4",type="source",repos="http://r-forge.r- 


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