[R-SIG-Mac] JGR on Mac OS X 10.6 (Snow Leopard)
Simon Urbanek
simon.urbanek at r-project.org
Sun Sep 13 16:05:41 CEST 2009
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")
>
>
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