[Phylobase-devl] failed mac build

[Steve Kembel]

Scratch that, was using the rev 104 tarball from the project home  
page, the nightly build tarball installs fine (with a non-fatal  
warning about In method for function "[": expanding the signature to  
include omitted arguments in definition: j = "missing",
drop = "missing").

Steve

On Mar 31, 2008, at 2:09 PM, Steve Kembel wrote:
> 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 2.5.1 (I'm out of date but not *that* bad!), but I upgraded to 2.6.2  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'
>
> <config.log>
> _______________________________________________
> Phylobase-devl mailing list
> Phylobase-devl at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl

______________________________________________
Dr. Steven Kembel - skembel at berkeley.edu
http://www.phylodiversity.net/skembel/