Compiling packages on Snow Leopard for 64bit
Erich,
On Sep 13, 2009, at 12:02 PM, Erich Neuwirth wrote:
Here is is another one. I am trying to compile rscproxy for R64. So I downloaded the sources, and I tried sudo R --arch=x86_64 CMD INSTALL rscproxy_1.3-1.tar.gz I get things like gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/ Resources/include -I/Library/Frameworks/R.framework/Resources/ include/i386 -I../inst/include -I/usr/local/include -fPIC -g -O2 -c bdx_SEXP.c -o bdx_SEXP.o and ** arch - ppc gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/ Resources/include -I/Library/Frameworks/R.framework/Resources/ include/ppc -I../inst/include -I/usr/local/include -fPIC -g -O2 - c bdx_SEXP.c -o bdx_SEXP.o but nothing about x86_64 What am I doing wrong this time?
For packages that don't have configure or Makefile regular R CMD INSTALL will build all architectures so you don't need --arch. However, if you see i386 and ppc but don't see x86_64 then it looks as if you have 32-bit R from CRAN ... (yet if --arch x86_64 works it should be the 64-bit R - so I'm a bit confused). Are you sure you are using the correct R version? You should see: Fino:~$ ls /Library/Frameworks/R.framework/Resources/bin/exec i386 ppc ppc64 x86_64 In fact on Snow Leopard you want to run rm -rf /Library/Frameworks/R.framework/Resources/bin/exec/ppc* because Rosetta is not installed by default and ppc64 libraries are missing, so on SL you should see Fino:~$ ls /Library/Frameworks/R.framework/Resources/bin/exec i386 x86_64 Cheers, Simon
On Sep 13, 2009, at 4:05 PM, Simon Urbanek wrote:
Erich, On Sep 13, 2009, at 4:52 AM, Erich Neuwirth wrote:
Thanks for the hints. It turns out that the part I originally missed was
install.packages("JGR",type="mac.binary")
which I had never used before. Now, getting more adventurous, I am trying to build the gmp package in R64.
install.packages("gmp",type="mac.binary")
....
library(gmp)
Error: package 'gmp' is not installed for 'arch=x86_64'
You can use type="mac.binary" only for packages that have no native library inside (gmp does).
So I am trying to build the package I downloaded gmp from gmplig.org and it compiled and passed all the tests. The output alsi indicated that it compiled a 64bit version. Now for the R build: Mini:devel neuwirth$ sudo R CMD INSTALL gmp_0.4-10.tar.gz * Installing to library ?/Library/Frameworks/R.framework/Resources/ library? * Installing *source* package ?gmp? ... creating cache ./config.cache checking for __gmpz_ui_sub in -lgmp... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs ** arch - i386 g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c apply.cc -o apply.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c biginteger.cc -o biginteger.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigintegerR.cc -o bigintegerR.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigmod.cc -o bigmod.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigrational.cc -o bigrational.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigrationalR.cc -o bigrationalR.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigvec.cc -o bigvec.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigvec_q.cc -o bigvec_q.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c extract_matrix.cc -o extract_matrix.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c factor.cc -o factor.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c matrix.cc -o matrix.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c matrixq.cc -o matrixq.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c solve.cc -o solve.o g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names - undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o gmp.so apply.o biginteger.o bigintegerR.o bigmod.o bigrational.o bigrationalR.o bigvec.o bigvec_q.o extract_matrix.o factor.o matrix.o matrixq.o solve.o -L/usr/local/ lib/ -lgmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,- framework -Wl,CoreFoundation ld: warning: in /usr/local/lib/libgmp.dylib, file is not of required architecture ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices
Building/Updating help pages for package 'gmp'
Formats: text html latex example Oakley text html latex example add.biginteger text html latex example apply text html latex example biginteger text html latex example biginteger.rand text html latex example bigrational text html latex example comp.biginteger text html latex example comp.bigq text html latex example cumsum text html latex example extract text html latex example extract.bigq text html latex example extreme text html latex example factor text html latex example fibonacci text html latex example gcd text html latex example gcdex text html latex example isprime text html latex example Note: removing empty section \examples in file 'matrix.Rd' matrix text html latex modulus text html latex example nextprime text html latex example operators_bigq text html latex example powm text html latex example sizeinbase text html latex example solve text html latex example ** building package indices ... Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Library/Frameworks/R.framework/ Resources/library/gmp/libs/i386/gmp.so': dlopen(/Library/Frameworks/R.framework/Resources/library/gmp/libs/ i386/gmp.so, 6): Symbol not found: ___gmpq_add Referenced from: /Library/Frameworks/R.framework/Resources/library/ gmp/libs/i386/gmp.so Expected in: flat namespace in /Library/Frameworks/R.framework/Resources/library/gmp/libs/i386/ gmp.so Warning in eval(expr, envir, enclos) : Data for RFC 2409 Oakley groups requires package 'gmp' Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Library/Frameworks/R.framework/ Resources/library/gmp/libs/i386/gmp.so': dlopen(/Library/Frameworks/R.framework/Resources/library/gmp/libs/ i386/gmp.so, 6): Symbol not found: ___gmpq_add Referenced from: /Library/Frameworks/R.framework/Resources/library/ gmp/libs/i386/gmp.so Expected in: flat namespace in /Library/Frameworks/R.framework/Resources/library/gmp/libs/i386/ gmp.so Warning in eval(expr, envir, enclos) : Data for RFC 2409 Oakley groups requires package 'gmp' * DONE (gmp) Mini:devel neuwirth$ trying to do 'library(gmp)' in R64 then produces
library(gmp)
Error: package 'gmp' is not installed for 'arch=x86_64' again, therefore I tried Mini:devel neuwirth$ R_ARCH=x86_64 sudo R CMD INSTALL --libs-only gmp_0.4-10.tar.gz
It is either R_ARCH=/x86_64 ... (note the slash!) or R --arch=x86_64
and this produced the following output * Installing to library ?/Library/Frameworks/R.framework/Resources/ library? * Installing *source* package ?gmp? ... creating cache ./config.cache checking for __gmpz_ui_sub in -lgmp... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs ** arch - i386
^--- it's still building 32-bit as you can see here
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c apply.cc -o apply.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c biginteger.cc -o biginteger.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigintegerR.cc -o bigintegerR.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigmod.cc -o bigmod.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigrational.cc -o bigrational.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigrationalR.cc -o bigrationalR.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigvec.cc -o bigvec.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c bigvec_q.cc -o bigvec_q.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c extract_matrix.cc -o extract_matrix.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c factor.cc -o factor.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c matrix.cc -o matrix.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c matrixq.cc -o matrixq.o g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - I/usr/local/include/ -I/usr/local/include -fPIC -g -O2 -c solve.cc -o solve.o g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names - undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o gmp.so apply.o biginteger.o bigintegerR.o bigmod.o bigrational.o bigrationalR.o bigvec.o bigvec_q.o extract_matrix.o factor.o matrix.o matrixq.o solve.o -L/usr/local/ lib/ -lgmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,- framework -Wl,CoreFoundation ld: warning: in /usr/local/lib/libgmp.dylib, file is not of required architecture
Since you apparently have only 64-bit libgmp, don't use --libs-only since the 32-bit version of the package fails anyway. Cheers, Simon
* DONE (gmp) Mini:devel neuwirth$ What am I doing wrong here. My guess is that I am still getting some switches wrong. On Sep 13, 2009, at 1:59 AM, Simon Urbanek wrote:
To answer all those recent posts on both mailing lists regarding
JGR on OS X 10.6 (Snow Leopard):
2) install necessary packages as follows:
install.packages(c("rJava","JavaGD","iplots"))
install.packages("JGR",type="mac.binary")