Re: [R] RSPerl & OS X

From: Duncan Temple Lang <duncan_at_wald.ucdavis.edu>
Date: Sun, 25 May 2008 08:31:36 +1200

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DavidM.UK wrote:
| 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

That will need the architecture-specific directory, e.g. etc/i386/Makeconf or etc/ppc/Makeconf

There is an updated version at
~ http://www.omegahat.org/RSPerl/RSPerl_0.92-2.tar.gz

that will hopefully bypass that issue. (It is a rapid fix that may have other issues.)

As for finding R.pm, use the appropriate shell script in <R-library>/RSPerl/scripts/ to set the relevant environment variables to find the Perl code, etc.

Thanks for letting me know
~ D.

| `/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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