It looks like there is a new lme4 package (-28) that was released on the
13th.  When this gets built I'd be happy to test it on R 2.8.0 as the
current version is at -27.

Thanks!
Chris

On Sat, Dec 13, 2008 at 10:09 AM, Prof Brian Ripley
<ripley@stats.ox.ac.uk>wrote:

> On Sat, 13 Dec 2008, Christopher David Desjardins wrote:
>
>  It was suggested to update my lme4 package to the lastest version at CRAN.
>> After installing it I get the following 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'
>>
>> Searching on the internet it seems someone had the same error
>>
>
> with an unreleased R-forge version, I believe, but it is basic good
> practice to give a URL for such comments.
>
>  and downgrade their Matrix from *-17 to *-16 except that I can't find a
>> binary for 2.8 for Matrix anywhere.
>>
>
> This is a known problem (as of a couple of days ago when -17 was released).
>  The binary of lme4 needs to be rebuilt -- I have already suggested that a
> new version be released urgently so that this happens automatically.  AFAIK
> Simon is in Japan for another week, so most likely this will not happen
> unless the Matrix/lme4 authors do help out.
>
> [More verbosely, the new version of Matrix has changed the C-level
> entrypoint names and requires that lme4 be re-compiled against the new
> version of Matrix.  This was not announced, and apparently unknown to the
> Matrix authors.]
>
> The only option I can offer is to install lme4 from the sources.  Because
> the CRAN R build has special features (static Fortran, particular BLAS
> struture, special location for libgcc_s ...), even if I or someone else
> builds lme4 for you it is unlikely to work on your machine.  (Again, I've
> asked for this to be documented so others can produce distributable binary
> packages.)
>
> To everyone else using binary packages I suggest not updating Matrix until
> you see an lme update offered.
>
> (Copying Uwe Ligges because the same thing will happen on Windows: and
> bumping the lme4 number will be needed to ensure that update.packages() gets
> the new version.)
>
>
>
>> Thanks,
>> Chris
>>
>>
>>
>>
>> On Nov 19, 2008, at 2:28 PM, Simon Urbanek wrote:
>>
>>
>>> On Nov 19, 2008, at 15:07 , Christopher David Desjardins wrote:
>>>
>>>  Thanks.  What I am still a bit confused about is why it loads in
>>>> Aquamacs and from Terminal but not from R.app GUI.  This still seems like a
>>>> bit of a mystery to me.
>>>>
>>>>
>>> Because you have set different library paths in each. Check .libPaths()
>>> as I was suggesting in the first e-mail.
>>>
>>> Cheers
>>> S
>>>
>>>
>>>
>>>> On Nov 19, 2008, at 8:34 AM, Simon Urbanek wrote:
>>>>
>>>>
>>>>> On Nov 18, 2008, at 22:30 , Christopher David Desjardins wrote:
>>>>>
>>>>>  Am I correct in thinking then that's it this old version of lme4 that
>>>>>> I have installed?  This version is from 14 October 2007 but I need this
>>>>>> specific version for a course I'm taking.
>>>>>>
>>>>>
>>>>> Yes, it appears so. You cannot use such an old version (binary) with
>>>>> the current R. For the course it should not matter which version you are
>>>>> using.
>>>>> If you feel brave, you can try to compile the old version from sources
>>>>> in the new R (download the source .tar.gz file and use R CMD INSTALL to
>>>>> install it). It may not work because old versions are not designed to work
>>>>> in new R versions, but you can try your luck if you really can't live with
>>>>> the new version.
>>>>>
>>>>> Cheers,
>>>>> S
>>>>>
>>>>>
>>>>>
>>>>>> On Nov 18, 2008, at 8:23 PM, Simon Urbanek wrote:
>>>>>>
>>>>>>  You are picking up a very ancient binary for R 2.5.0 (as you can see
>>>>>>> from the error). Check your .libPath() for old package binaries and
>>>>>>> remove/reinstall them.
>>>>>>>
>>>>>>> Cheers,
>>>>>>> S
>>>>>>>
>>>>>>> On Nov 18, 2008, at 8:37 PM, Christopher David Desjardins wrote:
>>>>>>>
>>>>>>>  When I try to load lme4 on R (2.8.0) in the R GUI for Mac OS X, I
>>>>>>>> get the following warnings and errors ...
>>>>>>>>
>>>>>>>>  library(lme4)
>>>>>>>>>
>>>>>>>> Loading required package: Matrix
>>>>>>>> Loading required package: lattice
>>>>>>>>
>>>>>>>> Attaching package: 'Matrix'
>>>>>>>>
>>>>>>>>
>>>>>>>>        The following object(s) are masked from package:stats :
>>>>>>>>
>>>>>>>>         xtabs
>>>>>>>>
>>>>>>>>
>>>>>>>>        The following object(s) are masked from package:base :
>>>>>>>>
>>>>>>>>         colMeans,
>>>>>>>>         colSums,
>>>>>>>>         rcond,
>>>>>>>>         rowMeans,
>>>>>>>>         rowSums
>>>>>>>>
>>>>>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>>>>>> unable to load shared library
>>>>>>>> '/Library/Frameworks/R.framework/Resources/library/lme4/libs/i386/lme4.so':
>>>>>>>> dlopen(/Library/Frameworks/R.framework/Resources/library/lme4/libs/i386/lme4.so,
>>>>>>>> 6): Library not loaded:
>>>>>>>> /Library/Frameworks/R.framework/Versions/2.5/Resources/lib/libRlapack.dylib
>>>>>>>> Referenced from:
>>>>>>>> /Library/Frameworks/R.framework/Resources/library/lme4/libs/i386/lme4.so
>>>>>>>> Reason: image not found
>>>>>>>> In addition: Warning messages:
>>>>>>>> 1: In namespaceImportFrom(self, asNamespace(ns)) :
>>>>>>>> replacing previous import: cov2cor
>>>>>>>> 2: In namespaceImportFrom(self, asNamespace(ns)) :
>>>>>>>> replacing previous import: update
>>>>>>>> 3: In namespaceImportFrom(self, asNamespace(ns)) :
>>>>>>>> replacing previous import: xtabs
>>>>>>>> Error: package/namespace load failed for 'lme4'
>>>>>>>>
>>>>>>>> However, I can properly load lme4 from Aquamacs via ESS and from
>>>>>>>> Terminal.  I get the same warnings just not the dyn.load() error.
>>>>>>>>
>>>>>>>> Does anyone know what I need to do?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Chris
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> R-SIG-Mac mailing list
>>>>>>>> R-SIG-Mac@stat.math.ethz.ch
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>
>> _______________________________________________
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>>
>
> --
> Brian D. Ripley,                  ripley@stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/<http://www.stats.ox.ac.uk/%7Eripley/>
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>



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