gfortran question
Anand,
On Nov 9, 2007, at 12:04 PM, Anand C. Patel wrote:
Does this mean that the Quartz/Aqua support has been backported into 2.6?
No, it's simply disabled. Technically speaking the 64-bit Quartz is a big and new change (it's a complete re-write of the Quartz device, hence aka Quartz II), so for QC reasons it cannot go to R 2.6.x. Also it's untested with the old GUI (there is a new Leopard GUI in the works that uses a different approach), so I don't feel comfortable putting it in the release. However, it's trivial to back-port if you desire so since the code didn't change, but then you may as well just pick R-devel.
I have a working copy of R 2.6 compiled for both i386 and x86_64 (as advised) that is working nicely with bioconductor packages. The 64-bit version does allow me to run the large maSigPro analysis without malloc errors, which is great!
No. R-devel compiles just fine and it did so for quite a while. (FWIW: R-2.6-branch compiles now, too.)
2) working configure commmands (in other words, should I still just be typing in what's listed for building 64-bit R on Simon's web-site? with changing "8.8.1" to "9.0.0")
The configure "command" supplied with R works just fine.
Does this mean we can use just ../R-patched/configure? I would assume we'd still need to generate both i386 and x86_64 versions using subdirectories and specific configure calls i.e.: ../R-patched/configure CC='gcc -arch x86_64' CXX='g++ -arch x86_64' \ F77='gfortran -arch x86_64' FC='gfortran -arch x86_64' 'CFLAGS=-g -O3 -I/readline/include -L/readline/lib' 'OBJCFLAGS=-g -O3 -I/readline/ include -L/readline/lib' 'LDFLAGS=-L/usr/local/lib' 'FFLAGS=-g -O3 -I/readline/include -L/readline/lib ' 'CXXFLAGS=-g -O3 -I/readline/ include -L/readline/lib' 'FCFLAGS=-g -O3 -I/readline/include -L/readline/ lib' \ r_arch=x86_64 \ --with-blas='-framework vecLib' --with-lapack \ --with-system-zlib --build=x86_64-apple-darwin9.0.0 \ --with-tcl-config=/usr/local/lib/tclConfig.sh --with-tk-config=/usr/local/lib/tkConfig.sh \ --without-aqua Is this not the case?
It is, but you're using the same configure script ;). My current Leopard flags are as simple as setting r_arch and adding - arch x86_64 to the compilers. BTW: there will be at least an unofficial Leopard nightly build soon (I'm just shuffling my machines to have one for the Tiger builds and one for the Leopard builds). Cheers, Simon