[R] RSPerl & OS X

From: DavidM.UK <david.merritt_at_bris.ac.uk>
Date: Sat, 24 May 2008 09:51:44 -0700 (PDT)

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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