Hi Simon, many thanks for your answer. I'll have a try with R from source and contact the maintainer. Moreover you can find the latest version of RSPerl here : http://www.omegahat.org/RSPerl/RSPerl_0.92-2.tar.gz
Regards Greg ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Greg Lefebvre, PhD Bioinformatics and Biostatistics Core Facility Federal Polytechnical School of Lausanne Webpage Download vCard On Jul 1, 2008, at 3:40 PM, Simon Urbanek wrote: > > On Jul 1, 2008, at 3:39 AM, gregory lefebvre wrote: > >> Hi all, >> >> does anybody has any experience in installing RSPerl on leopard >> (10.5.3/4) ? >> > > The way RSPerl attempts to build the code simply doesn't work in this > setup. The main problem is mismatch between what R sees and what Perl > sees. Simply pasting their compiler flags doesn't work, because R uses > 10.4u SDK whereas Perl uses 10.5 system libraries directly. The error > you get is due to that fact - libutil is only present in 10.5 and not > in 10.4, but RSPerl attempts to link it using the 10.4 setup. I > suspect that for this to work RSPerl would need to be designed more > carefully to use the separate compiler and flags for each part of the > interface. > > You can get past that error if you use R compiled specifically for > 10.5 (thus without the 10.4u SDK), but still RSPerl doesn't work for > me in that setup because of this error: >> library(RSPerl) > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared library '/Users/urbanek/Library/R/2.8/library/ > RSPerl/libs/i386/RSPerl.so': > dlopen(/Users/urbanek/Library/R/2.8/library/RSPerl/libs/i386/ > RSPerl.so, 6): Symbol not found: _boot_R > Referenced from: /Users/urbanek/Library/R/2.8/library/RSPerl/libs/ > i386/RSPerl.so > Expected in: dynamic lookup > > I didn't dig deeper, but I suspect here are even more problems with > RSPerl. You may want to contact the maintainer for help. > > Cheers, > Simon > > PS: I could only find RSPerl_0.92-1.tar.gz on the omegahat webpage, so > I'm wondering where you got 0.92-2 ... > > > >> I am using R version 2.7.1 (2008-06-23) with the command: >> sudo R CMD INSTALL -c --configure-args='--with-in-perl' >> RSPerl_0.92-2.tar.gz >> >> First the compiler stopped after returning : >> cc1: error: invalid option 'arch=nocona' >> >> Then in the /Library/Frameworks/R.framework/Resources/etc/i386/ >> Makeconf file, I removed the "-march=nocona" entries >> (https://stat.ethz.ch/pipermail/r-sig-mac/2008-January/004462.html >> ) and now here is the returned message : >> >> * 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/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 >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -c >> Converters.c -o Converters.o >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -c >> Reflectance.c -o Reflectance.o >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -c >> ForeignReference.c -o ForeignReference.o >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -c >> UserConverters.c -o UserConverters.o >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -c >> GeneralConverters.c -o GeneralConverters.o >> making libPerlConverter.dylib >> MACOSX_DEPLOYMENT_TARGET="10.3" gcc -dynamiclib -undefined >> dynamic_lookup -o libPerlConverter.dylib -install_name /Library/ >> Frameworks/R.framework/Resources/library/RSPerl/libs/ >> libPerlConverter.dylib Converters.o Reflectance.o ForeignReference.o >> UserConverters.o GeneralConverters.o -F/Library/Frameworks/ >> R.framework/.. -framework R >> if test ! -d /Library/Frameworks/R.framework/Resources/library/ >> RSPerl/libs ; then mkdir /Library/Frameworks/R.framework/Resources/ >> library/RSPerl/libs ; fi >> cp libPerlConverter.dylib /Library/Frameworks/R.framework/Resources/ >> library/RSPerl/libs >> /usr/bin/perl Makefile.PL PREFIX=/Library/Frameworks/R.framework/ >> Resources/library/RSPerl LIB=/Library/Frameworks/R.framework/ >> Resources/library/RSPerl/perl >> Warning: -L. changed to -L/tmp/R.INSTALL.D56cTa/RSPerl/src/. >> Unrecognized argument in LIBS ignored: '-F/Library/Frameworks/ >> R.framework/..' >> Unrecognized argument in LIBS ignored: '-framework' >> Unrecognized argument in LIBS ignored: 'R' >> Writing Makefile.perl for R >> make -f Makefile.perl LD=/usr/bin/gcc >> cp R.pm blib/lib/R.pm >> AutoSplitting blib/lib/R.pm (blib/lib/auto/R) >> cp RReferences.pm blib/lib/RReferences.pm >> cc -c -I. -I/Library/Frameworks/R.framework/Resources/include -I/ >> Library/Frameworks/R.framework/Resources/include/i386 -arch i386 - >> arch ppc -g -pipe -fno-common -DPERL_DARWIN -no-cpp-precomp -fno- >> strict-aliasing -Wdeclaration-after-statement -I/usr/local/include - >> O3 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" "-I/System/Library/ >> Perl/5.8.8/darwin-thread-multi-2level/CORE" -g -D_R_=1 -DUSE_R=1 - >> DWITH_R_IN_PERL=1 R.c >> Running Mkbootstrap for R () >> chmod 644 R.bs >> rm -f blib/arch/auto/R/R.bundle >> LD_RUN_PATH="/tmp/R.INSTALL.D56cTa/RSPerl/src" /usr/bin/gcc -arch >> i386 -arch ppc -bundle -undefined dynamic_lookup -L/usr/local/lib >> R.o -F/Library/Frameworks/R.framework/.. -framework R -o blib/arch/ >> auto/R/R.bundle \ >> -L/tmp/R.INSTALL.D56cTa/RSPerl/src -L/Library/Frameworks/ >> R.framework/Resources/library/RSPerl/libs -lPerlConverter \ >> >> ld: warning, duplicate dylib /usr/local/lib/libgcc_s.1.dylib >> ld: warning, duplicate dylib /usr/local/lib/libgcc_s.1.dylib >> ld: warning in /tmp/R.INSTALL.D56cTa/RSPerl/src/ >> libPerlConverter.dylib, file is not of required architecture >> ld: warning, duplicate dylib /usr/local/lib/libgcc_s.1.dylib >> ld: warning, duplicate dylib /usr/local/lib/libgcc_s.1.dylib >> chmod 755 blib/arch/auto/R/R.bundle >> cp R.bs blib/arch/auto/R/R.bs >> chmod 644 blib/arch/auto/R/R.bs >> Manifying blib/man3/R.3pm >> Manifying blib/man3/RReferences.3pm >> calling make -f Makefile.perl install >> Manifying blib/man3/R.3pm >> Manifying blib/man3/RReferences.3pm >> Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ >> perl/darwin-thread-multi-2level/auto/R/R.bs >> Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ >> perl/darwin-thread-multi-2level/auto/R/R.bundle >> Files found in blib/arch: installing files in blib/lib into >> architecture dependent library tree >> Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ >> perl/darwin-thread-multi-2level/R.pm >> Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ >> perl/darwin-thread-multi-2level/RReferences.pm >> Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ >> perl/darwin-thread-multi-2level/auto/R/autosplit.ix >> Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ >> share/man/man3/R.3pm >> Installing /Library/Frameworks/R.framework/Resources/library/RSPerl/ >> share/man/man3/RReferences.3pm >> Writing /Library/Frameworks/R.framework/Resources/library/RSPerl/ >> perl/darwin-thread-multi-2level/auto/R/.packlist >> Appending installation info to /Library/Frameworks/R.framework/ >> Resources/library/RSPerl/perl/darwin-thread-multi-2level/ >> perllocal.pod >> Finished configuration >> ** libs >> ** arch - i386 >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -c >> RPerlElements.c -o RPerlElements.o >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -c >> RPerlEval.c -o RPerlEval.o >> RPerlEval.c: In function 'RS_PerlEvalString': >> RPerlEval.c:20: warning: ISO C90 forbids mixed declarations and code >> RPerlEval.c: In function 'RS_PerlEvalString': >> RPerlEval.c:20: warning: ISO C90 forbids mixed declarations and code >> RPerlEval.c: In function 'RS_PerlGet': >> RPerlEval.c:128: warning: ISO C90 forbids mixed declarations and code >> RPerlEval.c: In function 'RS_PerlCallModified': >> RPerlEval.c:208: warning: ISO C90 forbids mixed declarations and code >> RPerlEval.c: In function 'RS_PerlGet': >> RPerlEval.c:128: warning: ISO C90 forbids mixed declarations and code >> RPerlEval.c: In function 'RS_PerlCallModified': >> RPerlEval.c:208: warning: ISO C90 forbids mixed declarations and code >> RPerlEval.c: In function 'RS_PerlCall': >> RPerlEval.c:377: warning: ISO C90 forbids mixed declarations and code >> RPerlEval.c: In function 'RS_PerlCall': >> RPerlEval.c:377: warning: ISO C90 forbids mixed declarations and code >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -c >> RPerlInit.c -o RPerlInit.o >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -c >> RPerlNew.c -o RPerlNew.o >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -c >> RPerlReference.c -o RPerlReference.o >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -c >> RPerlVars.c -o RPerlVars.o >> gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- >> version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -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 >> 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 -I/Library/Frameworks/R.framework/ >> Resources/include -I/Library/Frameworks/R.framework/Resources/ >> include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - >> DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration- >> after-statement -I/usr/local/include -I/System/Library/Perl/5.8.8/ >> 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 -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 -mmacosx-version-min=10.4 -undefined >> dynamic_lookup -single_module -multiply_defined suppress -L/usr/ >> local/lib -o RSPerl.so Converters.o ForeignReference.o >> GeneralConverters.o R.o RPerlElements.o RPerlEval.o RPerlInit.o >> RPerlNew.o RPerlReference.o RPerlVars.o Reflectance.o >> UserConverters.o Utils.o xsinit.o -arch i386 -arch ppc -L/usr/ >> local/lib /System/Library/Perl/5.8.8/darwin-thread-multi-2level/auto/ >> DynaLoader/DynaLoader.a -L/System/Library/Perl/5.8.8/darwin-thread- >> multi-2level/CORE -lperl -ldl -lm -lutil -lc -F/Library/Frameworks/ >> R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation >> ldld:: librarylibrary notnot foundfound forfor --lutillutil >> >> collect2: ld returned 1 exit status >> collect2: ld returned 1 exit status >> lipo: can't open input file: /var/tmp//cc3Fb354.out (No such file or >> directory) >> make: *** [RSPerl.so] Error 1 >> chmod: /Library/Frameworks/R.framework/Resources/library/RSPerl/libs/ >> i386/*: No such file or directory >> ERROR: compilation failed for package 'RSPerl' >> ** Removing '/Library/Frameworks/R.framework/Resources/library/ >> RSPerl' >> >> I don't have any clue for resolving this issue. >> Any idea would be really appreciated. >> In advance many thanks. >> Greg >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
