I'm running 10.6 from clean install, with the supplied Xcode, and R 2.9.2. I am unable to build a package (specifically the phylobase package [1]) which built fine under 10.5.8. Even more confusingly it seems to build fine for others using 10.6. The end of the install log (appended below) contains the these potentially informative errors:
ld: warning: in ncl/ncl/.libs/libncl.a, file is not of required architecture ld: warning: duplicate dylib /usr/local/lib/libgcc_s.1.dylib The latter error I get with any source package, but doesn't seem to prevent them from being installed. The package also makes use of the Rcpp interface to use an included library (NCL). It is this included library that seems to not build correctly, which could very well be related to the old version of Rcpp, or the makefiles responsible for building it. I've tried all manner of tweaking, upgrading, and list searching, but the (probably obvious) solution still eludes me. Any pointers in the right direction are greatly appreciated. Peter [1] https://r-forge.r-project.org/projects/phylobase/ ========================= > sessionInfo() R version 2.9.2 (2009-08-24) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base ========================= birch$ which gfortran /usr/local/bin/gfortran birch$ gfortran --version GNU Fortran (GCC) 4.2.3 Copyright (C) 2007 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING ============================ * Installing to library ‘/Library/Frameworks/R.framework/Resources/library’ * Installing *source* package ‘phylobase’ ... 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 g++ -arch i386 accepts -g... yes checking how to run the C++ preprocessor... g++ -arch i386 -E Building libRcpp.a in RcppSrc... g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c Rcpp.cpp -o Rcpp.o ar crs libRcpp.a Rcpp.o g++ --version i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5646) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Building libncl.a in ncl... checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... config/install-sh -c -d checking for gawk... awk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for a BSD-compatible install... /usr/bin/install -c checking for g++... g++ 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 g++ accepts -g... yes checking for style of include used by make... 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(cached) ranlib checking for strip... strip checking if gcc static flag works... yes checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fno-common checking if gcc PIC flag -fno-common works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin10.0.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes configure: creating libtool appending configuration tag "CXX" to libtool checking for ld used by g++... /usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld checking if the linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no checking whether the g++ linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common checking if g++ PIC flag -fno-common works... yes checking if g++ supports -c -o file.o... yes checking whether the g++ linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin10.0.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes appending configuration tag "F77" to libtool checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gfortran option to produce PIC... -fno-common checking if gfortran PIC flag -fno-common works... yes checking if gfortran supports -c -o file.o... yes checking whether the gfortran linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin10.0.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for ANSI C header files... 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(cached) yes configure: creating ./config.status config.status: creating Makefile config.status: creating ncl/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands make all-recursive Making all in ncl /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsassumptionsblock.lo -MD -MP -MF .deps/nxsassumptionsblock.Tpo -c -o nxsassumptionsblock.lo nxsassumptionsblock.cpp mkdir .libs g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsassumptionsblock.lo -MD -MP -MF .deps/nxsassumptionsblock.Tpo -c nxsassumptionsblock.cpp -fno-common -DPIC -o .libs/nxsassumptionsblock.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsassumptionsblock.lo -MD -MP -MF .deps/nxsassumptionsblock.Tpo -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1 mv -f .deps/nxsassumptionsblock.Tpo .deps/nxsassumptionsblock.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ 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/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsreader.lo -MD -MP -MF .deps/nxsreader.Tpo -c -o nxsreader.lo nxsreader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsreader.lo -MD -MP -MF .deps/nxsreader.Tpo -c nxsreader.cpp -fno-common -DPIC -o .libs/nxsreader.o nxsreader.cpp: In member function 'char* NxsReader::NCLCopyrightNotice()': nxsreader.cpp:398: warning: deprecated conversion from string constant to 'char*' nxsreader.cpp: In member function 'char* NxsReader::NCLHomePageURL()': nxsreader.cpp:406: warning: deprecated conversion from string constant to 'char*' nxsreader.cpp: In member function 'char* NxsReader::NCLNameAndVersion()': nxsreader.cpp:415: warning: deprecated conversion from string constant to 'char*' g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsreader.lo -MD -MP -MF .deps/nxsreader.Tpo -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1 mv -f .deps/nxsreader.Tpo .deps/nxsreader.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxssetreader.lo -MD -MP -MF .deps/nxssetreader.Tpo -c -o nxssetreader.lo nxssetreader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxssetreader.lo -MD -MP -MF .deps/nxssetreader.Tpo -c nxssetreader.cpp -fno-common -DPIC -o .libs/nxssetreader.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxssetreader.lo -MD -MP -MF .deps/nxssetreader.Tpo -c nxssetreader.cpp -o nxssetreader.o >/dev/null 2>&1 mv -f .deps/nxssetreader.Tpo .deps/nxssetreader.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsstring.lo -MD -MP -MF .deps/nxsstring.Tpo -c -o nxsstring.lo nxsstring.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsstring.lo -MD -MP -MF .deps/nxsstring.Tpo -c nxsstring.cpp -fno-common -DPIC -o .libs/nxsstring.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsstring.lo -MD -MP -MF .deps/nxsstring.Tpo -c 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-I.. -O3 -ffast-math -fPIC -MT nxsunalignedblock.lo -MD -MP -MF .deps/nxsunalignedblock.Tpo -c nxsunalignedblock.cpp -fno-common -DPIC -o .libs/nxsunalignedblock.o nxsunalignedblock.cpp: In member function 'virtual void NxsUnalignedBlock::Report(std::ostream&)': nxsunalignedblock.cpp:1283: warning: deprecated conversion from string constant to 'char*' g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsunalignedblock.lo -MD -MP -MF .deps/nxsunalignedblock.Tpo -c nxsunalignedblock.cpp -o nxsunalignedblock.o >/dev/null 2>&1 mv -f .deps/nxsunalignedblock.Tpo .deps/nxsunalignedblock.Plo /bin/sh ../libtool --tag=CXX --mode=link g++ -O3 -ffast-math -fPIC -release 2.0.04 -o libncl.la -rpath /usr/local/lib/ncl nxsassumptionsblock.lo nxsblock.lo nxscharactersblock.lo nxsdatablock.lo nxsdiscretedatum.lo nxsdiscretematrix.lo nxsdistancedatum.lo nxsdistancesblock.lo nxsexception.lo nxsreader.lo nxssetreader.lo nxsstring.lo nxstaxablock.lo nxstoken.lo nxstreesblock.lo nxsunalignedblock.lo g++ -dynamiclib -single_module ${wl}-flat_namespace ${wl}-undefined ${wl}suppress -o .libs/libncl-2.0.04 .libs/nxsassumptionsblock.o .libs/nxsblock.o .libs/nxscharactersblock.o .libs/nxsdatablock.o .libs/nxsdiscretedatum.o .libs/nxsdiscretematrix.o .libs/nxsdistancedatum.o .libs/nxsdistancesblock.o .libs/nxsexception.o .libs/nxsreader.o .libs/nxssetreader.o .libs/nxsstring.o .libs/nxstaxablock.o .libs/nxstoken.o .libs/nxstreesblock.o .libs/nxsunalignedblock.o -install_name /usr/local/lib/ncl/libncl-2.0.04 (cd .libs && rm -f libncl && ln -s libncl-2.0.04 libncl) ar cru .libs/libncl.a nxsassumptionsblock.o nxsblock.o nxscharactersblock.o nxsdatablock.o nxsdiscretedatum.o nxsdiscretematrix.o nxsdistancedatum.o nxsdistancesblock.o nxsexception.o nxsreader.o nxssetreader.o nxsstring.o nxstaxablock.o nxstoken.o nxstreesblock.o nxsunalignedblock.o ranlib .libs/libncl.a creating libncl.la (cd .libs && rm -f libncl.la && ln -s ../libncl.la libncl.la) configure: creating ./config.status config.status: creating src/Makevars ** libs ** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -IRcppSrc -Incl/ncl -fPIC -g -O2 -c NCLInterface.cpp -o NCLInterface.o g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -IRcppSrc -Incl/ncl -fPIC -g -O2 -c ReadWithNCL.cpp -o ReadWithNCL.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c descendants.c -o descendants.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c reorderBinary.c -o reorderBinary.o gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c reorderRobust.c -o reorderRobust.o g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o phylobase.so NCLInterface.o ReadWithNCL.o descendants.o reorderBinary.o reorderRobust.o -LRcppSrc -lRcpp -Lncl/ncl/.libs -lncl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: in ncl/ncl/.libs/libncl.a, file is not of required architecture ld: warning: duplicate dylib /usr/local/lib/libgcc_s.1.dylib ** R ** data ** inst ** preparing package for lazy loading Creating a new generic function for "summary" in "phylobase" Creating a new generic function for "plot" in "phylobase" ** help *** installing help indices >>> Building/Updating help pages for package 'phylobase' Formats: text html latex example addData text html latex example as-methods text html latex example check.phylo4 text html latex extract.tree text html latex example formatData text html latex geospiza text html latex example hasSingles text html latex example multiPhylo-class text html latex example pdata-class text html latex pdata text html latex phylo4-accessors text html latex example Note: removing empty section \usage in file 'phylo4-class.Rd' Note: removing empty section \value in file 'phylo4-class.Rd' Note: removing empty section \arguments in file 'phylo4-class.Rd' Note: removing empty section \examples in file 'phylo4-class.Rd' phylo4-class text html latex phylo4-display text html latex example phylo4-labels text html latex example phylo4 text html latex example Note: removing empty section \usage in file 'phylo4d-class.Rd' Note: removing empty section \value in file 'phylo4d-class.Rd' phylo4d-class text html latex example Note: removing empty section \examples in file 'phylo4d-display.Rd' phylo4d-display text html latex phylo4d-hasData text html latex example phylo4d text html latex example phyloXXYY text html latex example phylobase-package text html latex phylobubbles text html latex example phylog text html latex phylomat-class text html latex example plotOneTree text html latex example printphylo4 text html latex example read.nexustreestring text html latex readNexus text html latex reorder-methods text html latex example subset-methods text html latex example tdata text html latex example tip.data.plot text html latex treePlot-methods text html latex example treewalk text html latex example ** building package indices ... * DONE (phylobase) _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
