[R] RSPerl & OS X
DavidM.UK
david.merritt at bris.ac.uk
Sat May 24 18:51:44 CEST 2008
Hi,
I'm wanting to call R from Perl via the RSPerl package. However I cannot
seem to install it on my Macbook (OS X Tiger - R 2.6 - Perl 5.8.6). I try to
install the source downloaded from the sigmahat website - but it seems to
fail - when I search my system for R.pm - I can't find it? Something looks
to be going wrong with the make bits?
Cheers
David M
----
$ R CMD INSTALL --configure-args='--with-in-perl' RSPerl*
* Installing to library '/Library/Frameworks/R.framework/Resources/library'
* Installing *source* package 'RSPerl' ...
checking for perl... /usr/bin/perl
No support for any of the Perl modules from calling Perl from R.
*****************************************************
Set PERL5LIB to
/Library/Frameworks/R.framework/Versions/2.6/Resources/library/RSPerl/perl
*****************************************************
Testing: -F/Library/Frameworks/R.framework/.. -framework R
Using '/usr/bin/perl' as the perl executable
Perl modules (no):
Adding R package to list of Perl modules to enable callbacks to R from Perl
Creating the C code for dynamically loading modules with native code for
Perl: R
modules: R; linking:
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
Support R in Perl: yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating inst/scripts/RSPerl.csh
config.status: creating inst/scripts/RSPerl.bsh
config.status: creating src/RinPerlMakefile
config.status: creating src/Makefile.PL
config.status: creating cleanup
config.status: creating src/R.pm
config.status: creating R/perl5lib.R
making target all in RinPerlMakefile
RinPerlMakefile:5: /Library/Frameworks/R.framework/Resources/etc/Makeconf:
No such file or directory
make: *** No rule to make target
`/Library/Frameworks/R.framework/Resources/etc/Makeconf'. Stop.
calling make -f Makefile.perl install
make: Makefile.perl: No such file or directory
make: *** No rule to make target `Makefile.perl'. Stop.
chmod: blib/lib/R.pm: No such file or directory
Finished configuration
** libs
** arch - i386
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c Converters.c -o Converters.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c ForeignReference.c -o ForeignReference.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c GeneralConverters.c -o GeneralConverters.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c RPerlElements.c -o RPerlElements.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c RPerlEval.c -o RPerlEval.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c RPerlInit.c -o RPerlInit.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c RPerlNew.c -o RPerlNew.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c RPerlReference.c -o RPerlReference.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c RPerlVars.c -o RPerlVars.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c Reflectance.c -o Reflectance.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c UserConverters.c -o UserConverters.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c Utils.c -o Utils.o
Utils.c: In function 'characterVectorToNullTerminatedArray':
Utils.c:35: warning: assignment discards qualifiers from pointer target type
Utils.c: In function 'characterVectorToArray':
Utils.c:78: warning: assignment discards qualifiers from pointer target type
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386 -I. -g -pipe
-fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing
-I/usr/local/include
-I/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -DPERL_POLLUTE
-D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3 -fPIC
-g -O2 -march=nocona -c xsinit.c -o xsinit.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-mmacosx-version-min=10.4 -std=gnu99 -dynamiclib
-Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -undefined
dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o
RSPerl.so Converters.o ForeignReference.o GeneralConverters.o
RPerlElements.o RPerlEval.o RPerlInit.o RPerlNew.o RPerlReference.o
RPerlVars.o Reflectance.o UserConverters.o Utils.o xsinit.o
-L/usr/local/lib
/System/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/DynaLoader/DynaLoader.a
-L/System/Library/Perl/5.8.6/darwin-thread-multi-2level/CORE -lperl -ldl -lm
-lc -F/Library/Frameworks/R.framework/.. -framework R
** R
** inst
** help
>>> Building/Updating help pages for package 'RSPerl'
Formats: text html latex example
Perl text html latex example
PerlClear text html latex example
PerlDiscard text html latex example
PerlExists text html latex example
PerlExpr text html latex example
PerlFile text html latex example
PerlGetArray text html latex example
PerlGetCode text html latex example
PerlInit text html latex example
PerlInterpreter text html latex example
PerlLength text html latex example
PerlNames text html latex example
PerlNew text html latex example
PerlNewArray text html latex example
PerlPackage text html latex example
PerlReferenceDollar text html latex example
PerlReferenceObjects text html latex example
PerlReferenceSubset text html latex example
PerlSetHash text html latex example
PerlStashInfo text html latex example
PerlTerminate text html latex example
PerlType text html latex example
PerlTypes text html latex
PerlUndef text html latex example
addConverter text html latex example
foreignReference text html latex example
getNumPerlConverters text html latex example
getPerlClasses text html latex example
getPerlDynModules text html latex example
getPerlScript text html latex example
mkRef text html latex example
parseEval text html latex example
perlInitArgs text html latex example
perlModuleLoaded text html latex example
referenceHandlerGenerator text html latex example
setPerlHandler text html latex example
** building package indices ...
* DONE (RSPerl)
--
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