[R-SIG-Mac] lme4 fails to load in R GUI 2.8.0
Prof Brian Ripley
ripley at stats.ox.ac.uk
Wed Dec 17 00:35:37 CET 2008
Unfortunately it looks like the automated build of -28 failed, since
other updates of the same time period are now on CRAN. I noticed that -27
failed on the CRAN daily check page
http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/lme4-00check.html
and I am seeing the same error with the CRAN binary of 2.8.0 and the CRAN
build of Matrix when I try R CMD check on the lme4...-28 sources.
If you build from the sources you should get a usable version, even if it
fails one of the tests.
On Tue, 16 Dec 2008, Martin Maechler wrote:
> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>> _______________________________________________
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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
>>>
>>
>>
>>
>> --
>> "There are a host of pirates, but they don't identify themselves with
>> eye-patches and hook hands so it isn't immediately obvious that they are
>> pirates."
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
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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