[Bioc-devel] Bioc 2.2 versus x86_64-only R 2.7 on OS X
Hi Anand, I hope some Mac expert will be able to help you. Have you tried the R-SIG-Mac mailing list? Because in the end, the problem you found is not strictly a Bioconductor question but more generally about compiling R packages (that have a configure script) for the x86_64 arch on Mac OS X. Anyway, here are my 2 cents (continued below).
Anand C. Patel wrote:
OK. In the process of running maSigPro on 30 arrays in an affyBatch (output from combineAffyBatch), my previously happy R 2.6 threw malloc errors -- starting with an inability to allocate a vector of 1.3 gb. This happened on multiple occasions, and happened regardless of whether or not other data was cleared, OS X memory was free and available, etc. The last time it happened OS X had 3.4 gb of free physical memory . . .
You should be able to alloc a vector of 1.3GB. Have you reported this to R-devel or R-SIG-Mac? For example, have you tried this: x <- raw(2000000000) in a fresh R session? This works for me with a 32-bit R-2.6.0 on an Intel Mac Mini with only 2GB of RAM.
So, I figured I'd compile a 64-bit version of R 2.7 for OS X 10.5. After some issues, that is now working. The last easily available 64-bit R for OS X is 2.5, and I wanted to use the newer packages from 2.6 (at least). R 2.6 won't compile in 64-bit mode with Quartz, but R 2.7 will. It is compiled specifically for x86_64, as I don't personally need it to run on all 4 possible architectures. I did this by declaring multiple flags at ./configure time: ./configure CC='gcc -arch x86_64' CXX='g++ -arch x86_64' \ F77='gfortran -arch x86_64' FC='gfortran -arch x86_64' 'CFLAGS=-g -O3 -m64 -I/readline/include -L/readline/lib' 'OBJCFLAGS=-g -O3 -m64 -I/readline/include -L/readline/lib' 'LDFLAGS=-L/usr/local/lib' 'FFLAGS=-g -O3 -m64 -I/readline/include -L/readline/lib ' 'CXXFLAGS=-g -O3 -m64 -I/readline/include -L/readline/lib' 'FCFLAGS=-g -O3 -m64 -I/readline/include -L/readline/lib' \ --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
I hope this syntax 'CFLAGS=...', 'OBJCFLAGS=...', etc... instead of CFLAGS='...', OBJCFLAGS='...', etc... is correct (should be OK but...) Also, the step-by-step guide on http://r.research.att.com/exp/ doesn't use any of those args so I hope you know what you are doing.
However, when I try to install bioc 2.2 packages, there is a significant problem. Most packages compile from source just fine. However, some of the core packages fail to compile because the packages themselves declare PKG_CFLAGS and this creates a conflict with the flags above. affy, affyio, and preprocessCore all do their own variation of the following:
It seems that only packages with a configure script are affected, is that right?
(excerpt taken from affyio, but the other two do the same thing) configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -arch x86_64 -std=gnu99 -I/R-devel/include -I/R-devel/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/sw/include -I/usr/local/include -arch ppc -arch ppc64 -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -fPIC -g -O3 -m64 -I/readline/include -L/readline/lib -c fread_functions.c -o fread_functions.o lipo: /var/tmp//ccdPcoay.out and /var/tmp//ccz02Cr2.out have the same architectures (x86_64) and can't be in the same fat output file
Have you tried to not use 'CFLAGS=-g -O3 -m64 -I/readline/include -L/readline/lib' when you compile R. What does it do? Note that if I use R-25-br-quad.tar.gz from http://r.research.att.com/exp/, then affyio compiles with no problem: creating ./config.status creating src/Makevars ** libs ** arch - x86_64 gcc -arch x86_64 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -fPIC -g -O2 -c read_abatch.c -o read_abatch.o gcc -arch x86_64 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -fPIC -g -O2 -c read_bpmap.c -o read_bpmap.o (of course this is not the same affyio as yours, because I'm using R-2.5, so I get affyio 1.4.1 when I do biocLite("affyio", type="source")) As for trying with a 64-bit R-2.7, I didn't have much luck when I tried to compile R: Error: C stack usage is too close to the limit :-( Cheers, H.
I fixed this by extracting the packages, and individually changing the PKGS_CFLAGS line in the Makevars.in files in all 3 packages from: PKG_CFLAGS = @CFLAGS@ to PKG_CFLAGS = -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 I am overly aware that this is an ugly kludge. However, again using affyio as an example: configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -arch x86_64 -std=gnu99 -I/R-devel/include -I/R-devel/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/sw/include -I/usr/local/include -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -fPIC -g -O3 -m64 -I/readline/include -L/readline/lib -c fread_functions.c -o fread_functions.o and it successfully builds and installs. A glance at the problem and the instructions for Mac R building from R.research.att.com suggests that the root of the problem is that the architecture specification seems to need to happen at the level of the CC flag rather than the CFLAGS flag. When I tried to compile placing the architecture specification (-arch x86_64) in the CFLAGS (and other compiler flags) the R compile fails. Up front it looks like the downside of setting the packages up to automatically recognize OS X and compile to all 4 possible architectures. Is there an easier/better way to do this? Thanks, Anand C. Patel, MD Washington University School of Medicine acpatel at usa.net
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