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 <[email protected]>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 >>>>>>>> [email protected] >>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > -- > Brian D. Ripley, [email protected] > 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]] _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
