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

[Daniel Ezra Johnson]

Hello,

Sorry if the solution to this was already posted...

I'm getting this error:

> library(lme4)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  function 'cholmod_start' not provided by package 'Matrix'
Error: package/namespace load failed for 'lme4'

trying to install lme4 version 0.999375-27 on top of Matrix
0.999375-17 (both from CRAN, not using R-Forge).

This is with R for Mac OS X 2.8.0.

Any suggestions would be appreciated.

Thanks,
Daniel

On Thu, Nov 27, 2008 at 3:39 PM, Douglas Bates <bates at stat.wisc.edu> wrote:
> Is anyone else encountering this problem?  It looks like Mac OS X and
> apparently a problem with the Matrix package declarations.  It is a
> trivial-enough problem, a declaration of an argument as "const char*"
> in one case and "char*" in another but I don't know which installed
> version of the Matrix package this occurs in.
>
> On Thu, Nov 27, 2008 at 8:11 AM, Nick Isaac <njbisaac at googlemail.com> wrote:
>>
>>>> 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 here
>>
>> 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-project.org")
>>
>> 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
>>
>>
>>
>>
>>
>>
>>
>>> sessionInfo()
>> R version 2.8.0 (2008-10-20)
>> i386-apple-darwin8.11.1
>>
>> locale:
>> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>>
>> 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-project.org")
>>
>>>
>>
>>
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>