[Phylobase-devl] failed mac build

Steve Kembel skembel at berkeley.edu
Mon Mar 31 23:09:06 CEST 2008


Thanks Ben... that worked. Actually that was a typo, meant to say R  
2.5.1 (I'm out of date but not *that* bad!), but I upgraded to 2.6.2  
and now I can install via the install.packages("phylobase", repos="http://r-forge.r-project.org 
") command within R, but at the command line using the latest source  
tarball with R CMD INSTALL phylobase I get the following errors. I  
know this is the error that Thibaut was having before, what was the  
resolution?:

[...]
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/usr/share/R/include -I/usr/share/R/include     -IRcppSrc -Incl/ 
ncl -fpic  -g -O2 -c NCLInterface.cpp -o NCLInterface.o
g++ -I/usr/share/R/include -I/usr/share/R/include     -IRcppSrc -Incl/ 
ncl -fpic  -g -O2 -c ReadWithNCL.cpp -o ReadWithNCL.o
g++ -shared  -o phylobase.so NCLInterface.o ReadWithNCL.o -LRcppSrc - 
lRcpp -Lncl/ncl/.libs -lncl  -L/usr/lib64/R/lib -lR
/usr/bin/ld: ncl/ncl/.libs/libncl.a(nxsassumptionsblock.o): relocation  
R_X86_64_32 against `a local symbol' can not be used when making a  
shared object; recompile with -fPIC
ncl/ncl/.libs/libncl.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [phylobase.so] Error 1
chmod: cannot access `/usr/local/lib/R/site-library/phylobase/libs/*':  
No such file or directory
ERROR: compilation failed for package 'phylobase'
** Removing '/usr/local/lib/R/site-library/phylobase'

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