Error installing Kernlab from Source on MacOS X (lazy loading failed)

Question

I have been trying to install the R package, Kernlab from source, but I have been running into problems. At first, I had some error related to gfortran, so I downloaded the GNU fortran compiler from http://r.research.att.com/tools/

Then when I type the following command: R CMD INSTALL kernlab_0.9-12.tar.gz

I get the following error:

installing to /Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab/libs/x86_64
** R
** data
** inst
** preparing package for lazy loading
Error in .walkClassGraph(ClassDef, "contains", where, attr(ext, "conflicts")) : 
  the "superClass" list for class "list", includes an undefined class "input"
Error in .walkClassGraph(ClassDef, "contains", where, attr(ext, "conflicts")) : 
  the "superClass" list for class "numeric", includes an undefined class "output"
Error : evaluation nested too deeply: infinite recursion / options(expressions=)?
Error in setClassUnion("listI", c("list", "numeric", "vector", "integer",  : 
  unable to create union class:  could not set members "list", "numeric"
Error : unable to load R code in package 'kernlab'
ERROR: lazy loading failed for package ‘kernlab’
* removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab’

Does anyone know how to solve this error? PS. For the GNU fortran compiler I downloaded, it says that is for Xcode version up to 3.2.5; and I have Xcode version 3.2.6. Is this the source of my error, or am I looking in the wrong direction?

Answer 1

It must be something with your system. On my Linux box, kernlab_0.9-12 installs fine:

edd@max:/tmp$ R CMD INSTALL kernlab_0.9-12.tar.gz 
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘kernlab’ ...
** libs
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c brweight.cpp -o brweight.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c ctable.cpp -o ctable.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c cweight.cpp -o cweight.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dbreakpt.c -o dbreakpt.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dcauchy.c -o dcauchy.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dgpnrm.c -o dgpnrm.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dgpstep.c -o dgpstep.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dprecond.c -o dprecond.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dprsrch.c -o dprsrch.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dspcg.c -o dspcg.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtron.c -o dtron.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtrpcg.c -o dtrpcg.o
dtrpcg.c: In function ‘dtrpcg’:
dtrpcg.c:157: warning: value computed is not used
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtrqsol.c -o dtrqsol.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c esa.cpp -o esa.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c expdecayweight.cpp -o expdecayweight.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c inductionsort.cpp -o inductionsort.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c kspectrumweight.cpp -o kspectrumweight.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c lcp.cpp -o lcp.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c misc.c -o misc.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c msufsort.cpp -o msufsort.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c solvebqp.c -o solvebqp.o
gcc-4.4 -I/usr/share/R/include      -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c stringk.c -o stringk.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c stringkernel.cpp -o stringkernel.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c svm.cpp -o svm.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c wkasailcp.cpp -o wkasailcp.o
g++-4.4 -I/usr/share/R/include      -fpic  -O3 -pipe -c wmsufsort.cpp -o wmsufsort.o
g++ -shared -o kernlab.so brweight.o ctable.o cweight.o dbreakpt.o dcauchy.o dgpnrm.o dgpstep.o dprecond.o dprsrch.o dspcg.o dtron.o dtrpcg.o dtrqsol.o esa.o expdecayweight.o inductionsort.o kspectrumweight.o lcp.o misc.o msufsort.o solvebqp.o stringk.o stringkernel.o svm.o wkasailcp.o wmsufsort.o -llapack -lblas -lgfortran -lm -L/usr/lib64/R/lib -lR
installing to /usr/local/lib/R/site-library/kernlab/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "terms" in "kernlab"
Creating a new generic function for "fitted" in "kernlab"
Creating a new generic function for "coef" in "kernlab"
Creating a new generic function for "predict" in "kernlab"
Creating a new generic function for "plot" in "kernlab"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (kernlab)
edd@max:/tmp$ 

Moreover, it has nothing to do with gfortran as the package seems to contain only C and C++ files.

Answer 2

I doubt that a minor version shift in Xcode is the source of your problem (with the unstated version of fortran ... and the unstated version of R), but why not just install the Mac binary?

http://cran.r-project.org/bin/macosx/leopard/contrib/r-release/kernlab_0.9-12.tgz