[R-SIG-Mac] installing R-2.8 from source - segmentation faults at make check

[Michael Braun]

I need to re-install R on my Mac Pro running OS X 10.5.5.  Because I  
work with large datasets, I need a 64-bit installation, and since  
there is no 64-bit binary available for Leopard yet (or is there?), I  
am compiling from source.  I am having some difficulty with this, and  
I am hoping that someone on this list can help.

The configure flags I am using are:

./configure SHELL='/bin/bash' \
r_arch=x86_64 \
CC="gcc-4.2 -arch x86_64 -g -p -std=gnu99" \
CXX="g++-4.2 -arch x86_64 -g -p" \
OBJC="gcc-4.2 -arch x86_64 -g -p" \
F77="gfortran-4.2 -arch x86_64 -g -p" \
FC="gfortran-4.2 -arch x86_64 -g -p" \
R_PAPERSIZE='letter' \
--with-system-zlib \
--enable-R-framework --enable-BLAS-shlib --with-tcltk --with-aqua \
--enable-R-profiling \
--with-blas='-framework vecLib' --with-lapack\

Configure and make run without errors, but when I run "make check," I  
get:

BRAUNM2: ~/Downloads/R-install/rd64 $ make check
make[4]: `Makedeps' is up to date.
running code in 'base-Ex.R' ...\c
/bin/bash: line 1: 69863 Segmentation fault      ../../bin/R --vanilla  
< base-Ex.R > base-Ex.Rout 2>&1
make[4]: *** [base-Ex.Rout] Error 1
make[3]: *** [test-Examples-Base] Error 2
make[2]: *** [test-Examples] Error 2
make[1]: *** [test-all-basics] Error 1
make: *** [check] Error 2

If I were then to launch R from the command line, I get the following  
errors:

Error in capabilities("aqua") :
   0 arguments passed to .Internal(capabilities) which requires 1
Error : .onLoad failed in 'loadNamespace' for 'grDevices'
Error: package/namespace load failed for 'grDevices'
Error in capabilities("aqua") :
   0 arguments passed to .Internal(capabilities) which requires 1
Error : .onLoad failed in 'loadNamespace' for 'grDevices'
Error in capabilities("aqua") :
   0 arguments passed to .Internal(capabilities) which requires 1
In addition: Warning message:
package grDevices in options("defaultPackages") was not found
Error : .onLoad failed in 'loadNamespace' for 'grDevices'
Error in capabilities("aqua") :
   0 arguments passed to .Internal(capabilities) which requires 1
In addition: Warning message:
package graphics in options("defaultPackages") was not found
Error : .onLoad failed in 'loadNamespace' for 'grDevices'
During startup - Warning message:
package stats in options("defaultPackages") was not found

Also, I cannot seem to be able to download and install any new packages.

I then tried a 32-bit build with the same flags as above, except  
replacing x86_64 with i386.  With the 32-bit, build,  make check"  
fails when it gets to:

running code in '../../R-release-branch/tests/lapack.R' ...\c
/bin/bash: line 1:  3900 Segmentation fault      LC_ALL=C SRCDIR=../../ 
R-release-branch/tests R_DEFAULT_PACKAGES= ../bin/R --vanilla < ../../ 
R-release-branch/tests/lapack.R > lapack.Rout 2>&1
make[3]: *** [lapack.Rout] Error 1
make[2]: *** [test-Specific] Error 2
make[1]: *** [test-all-basics] Error 1
make: *** [check] Error 2

However, I do not get errors when launching the 32-bit build, and I am  
able to install packages.

I should note that the only reason I am compiling from source is that,  
as far as I can tell, there are no 64-bit binaries available for  
Leopard yet.  If someone could point me to such binaries, that might  
solve my problem.

So, I'm not sure what's going on, and I'd appreciate any help you can  
provide.

Thanks,

Michael Braun
braunm at mit.edu