[R-sig-ME] installing lme4.0 on OS X 10.9

[Hugo.Mildenberger at web.de]

Roger,

the file lme4/src/Makevars contains the line

     PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"`

so reinstalling Rcpp might help? libgfortran.so comes with gcc if fortran support 
was configured. I believe Rcpp or some other packages had been compiled by a 
rather old version of gcc.  You may run the Rscript command manually to
see if the Rcpp libraries are part of the problem.

Best

Hugo


On Sun, 9 Feb 2014 22:41:46 +0000
"Levy, Roger" <rlevy at ucsd.edu> wrote:

> Thanks so much, Tobias.  Unfortunately, setting up a Makevars file like you suggested simply leaves me with the same errors in R as I get in the command line:
> 
> > install.packages("lme4.0", repos="http://r-forge.r-project.org",type="source")
> …
> <snip>
> …
> clang -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o lme4.so init.o lmer.o local_stubs.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
> …
> ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
> ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
> ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
> ld: library not found for -lgfortran
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> 
> 
> Any further thoughts or suggestions on this, anyone?
> 
> Best
> 
> Roger
> 
> On Feb 7, 2014, at 12:06 PM, Tobias Heed <tobias.heed.uhh at gmail.com> wrote:
> 
> > Dear Roger,
> > 
> > if I remember correctly, this solved the problem for me:
> > on the top level of your user account, create a folder .R (if it’s not there yet);
> > in there, create a new text file named Makevars;
> > into this file, paste the following:
> > 
> > CC=clang
> > CXX=clang++ -arch x86_64 -ftemplate-depth-256 -stdlib=libstdc++
> > CXXFLAGS= -O3 -pedantic
> > 
> > hope it helps
> > Best,
> > Tobias
> > 
> > 
> > From: Levy, Roger rlevy at ucsd.edu
> > Reply: Levy, Roger rlevy at ucsd.edu
> > Date: February 7,2014 at 20:59:11
> > To: r-sig-mixed-models at r-project.org r-sig-mixed-models at r-project.org
> > Subject:  [R-sig-ME] installing lme4.0 on OS X 10.9 
> >> Hi all, 
> >> 
> >> My Mac laptop died and I am now reinstalling all my packages from scratch. Previously I was using lme4_0.999999-2 and I figure that with a fresh install, I might as well install lme4.0 instead. But I am having trouble compiling it: 
> >> 
> >> > install.packages("lme4.0", repos="http://r-forge.r-project.org",type="source") 
> >> trying URL 'http://r-forge.r-project.org/src/contrib/lme4.0_0.999999-4.tar.gz' 
> >> Content type 'application/x-gzip' length 772384 bytes (754 Kb) 
> >> opened URL 
> >> ================================================== 
> >> downloaded 754 Kb 
> >> 
> >> * installing *source* package ‘lme4.0’ ... 
> >> ** libs 
> >> llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Matrix/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include" -fPIC -mtune=core2 -g -O2 -c init.c -o init.o 
> >> /bin/sh: llvm-gcc-4.2: command not found 
> >> 
> >> 
> >> This happens even after I install Xcode and also llvm-gcc42 on MacPorts; 
> >> 
> >> Does anyone have any suggestions? FWIW: 
> >> 
> >> > sessionInfo() 
> >> R version 3.0.2 (2013-09-25) 
> >> Platform: x86_64-apple-darwin10.8.0 (64-bit) 
> >> 
> >> locale: 
> >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 
> >> 
> >> attached base packages: 
> >> [1] stats graphics grDevices utils datasets methods base 
> >> 
> >> loaded via a namespace (and not attached): 
> >> [1] tools_3.0.2 
> >> 
> >> 
> >> I’ve also tried installing from the command line; this bottoms out in a different error: 
> >> 
> >> $ R CMD build lme4.0 
> >> … 
> >> <snip> 
> >> … 
> >> ld: warning: directory not found for option ‘-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64’ 
> >> ld: warning: directory not found for option ‘-L/usr/local/lib/x86_64’ 
> >> ld: warning: directory not found for option ‘-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3’ 
> >> ld: library not found for -lgfortran 
> >> clang: error: linker command failed with exit code 1 (use -v to see invocation) 
> >> make: *** [lme4.so] Error 1 
> >> 
> >> 
> >> More generally, I’m having trouble figuring out what I should install in order to be able to compile lme4.0 from source. 
> >> 
> >> Best & many thanks in advance for any guidance, 
> >> 
> >> Roger Levy 
> >> 
> >> _______________________________________________ 
> >> R-sig-mixed-models at r-project.org mailing list 
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> 
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