[R-SIG-Mac] lme4 fails to load in R GUI 2.8.0

Martin Maechler mmaechler at gmail.com
Tue Dec 16 22:35:16 CET 2008 

Yes, this new lme4 package should solve your problem.
However, you could have removed lme4 and re-installed it even with the
previous version  (as Prof. Ripley suggested I think).

Martin

On Tue, Dec 16, 2008 at 22:30, Christopher Desjardins
<cddesjardins at gmail.com> wrote:
> 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 at 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 at stat.math.ethz.ch
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
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>>>
>>
>> --
>> Brian D. Ripley,                  ripley at 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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> "There are a host of pirates, but they don't identify themselves with
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