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
installing R-2.8 from source - segmentation faults at make check
3 messages · Michael Braun, Steve Lianoglou, Simon Urbanek
Hi Michael,
On Nov 24, 2008, at 12:03 PM, Michael Braun wrote:
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.
Check out this page here: http://r.research.att.com/ Primarily that blue box about 1/2-way down the page, that says: Leopard builds can be installed as follows - paste in Terminal (for R 2.8.x): curl -s http://r.research.att.com/R-2.8-branch-leopard- universal.tar.gz | sudo tar fvxz - -C / That should do the trick and save you the hassle of compiling yourself. ;-) -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos
On Nov 24, 2008, at 12:33 , Steve Lianoglou wrote:
Hi Michael, On Nov 24, 2008, at 12:03 PM, Michael Braun wrote:
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.
Check out this page here: http://r.research.att.com/ Primarily that blue box about 1/2-way down the page, that says: Leopard builds can be installed as follows - paste in Terminal (for R 2.8.x): curl -s http://r.research.att.com/R-2.8-branch-leopard-universal.tar.gz | sudo tar fvxz - -C / That should do the trick and save you the hassle of compiling yourself. ;-)
Thanks, Steve. Just to add - this location of 64-bit builds is explicitly mentioned on the CRAN webpage: "Information, tools and most recent daily builds of the R GUI, R- patched and R-devel can be found at http://R.research.att.com/. Please visit that page especially during beta stages to help us test the Mac OS X binaries before final release! The page also contains links to experimental builds as such 64-bit R for OS X." Cheers, S