[R-SIG-Mac] JGR on Mac OS X 10.6 (Snow Leopard)
Erich Neuwirth
erich.neuwirth at univie.ac.at
Sun Sep 13 16:29:23 CEST 2009
Thanks, with all your help I finally managed!
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")
>>
>>
>
>
More information about the R-SIG-Mac
mailing list