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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