Rplinkseq fails to compile: framework not found

[Daniel Weeks]

When trying to install the Rplinkseq package into R on a Mac OS X 10.8.5 machine with R 3.0.1, it dies with this error message:

llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o Rplinkseq.so allele.o annot.o bcf.o bed.o bgzf.o crandom.o dcdflib.o defs.o em.o eval.o filemap.o fisher.o genotype.o glm.o globals.o gstore.o helper.o inddb.o individual.o indmap.o iterate.o locdb.o mask.o matrix.o meta.o netdb.o output.o permute.o phmap.o pp.o pp.pb.o refdb.o reffuncs.o regions.o rint.o segments.o seqdb.o sqlite3.o sqlwrap.o statistics.o svar.o token.o vardb.o varfunc.o variant.o variant.pb.o varmeta.o vcf.o vcfiterate.o vcfz.o vgroup.o zfstream.o -lprotobuf -ldl -lpthread -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

ld: framework not found R

collect2: ld returned 1 exit status make: *** [Rplinkseq.so] Error 1 ERROR: compilation failed for package ‘Rplinkseq’ * removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rplinkseq’

Any ideas how to fix this?

Looks to me like /Library/Frameworks/R.framework/ contains the R framework as expected, so I don't understand why this framework is not being found.

R version 3.0.1 (2013-05-16) -- "Good Sport" Mac OS X 10.8.5 Rplinkseq: pulled from Bitbucket; corrected by adding the missing protdb.h file. (Also got the framework error with Rplinkseq-0.08.tar.gz too)

[Daniel Weeks]

This failure to compile was the result of a corrupt file in the R.framework folder. Re-installing R resolved this error.

[Daniel Weeks]

The "ld: framework not found R" error message was due to a corrupted symbolic link in my installation of R. Reinstallation of R resolved this problem.