JGR not working on Snow Leopard
I am experiencing problems with JGR on Snow Leopard. After looking for similar messaged I found that I should start JGR from the command line. Further down is the output. I also rebuilt rJava from the source package and this did not help. JGR gives me an error message: Cannot find Java/R (JR) library (libjri.jnilib) Please make sure you start by double clicking the JGR application. 91-115-197-166:~ neuwirth$ /Applications/JGR.app/Contents/MacOS/ JGRLoading preferences from /Users/neuwirth/.JGRprefsrcJGR R_HOME: / Library/Frameworks/R.framework/Resourceslibroot: /Library/Frameworks/ R.framework/Resources/library/Attempting to load jnilib: /Library/ Frameworks/R.framework/Resources/library/rJava/jri/libjri.jnilib Succeeded in loading jnilib, looks good. JGR DYLD_LIBRARY_PATH: /Library/Frameworks/R.framework/Resources/ library/rJava/jri Loading class file... result -1 RCP: JGR CLASSPATH: -Drjava.class.path=/Applications/JGR.app:/Library/ Frameworks/R.framework/Resources/library/rJava/jri/JRI.jar:/Library/ Frameworks/R.framework/Resources/library/iplots/java/iplots.jar:/ Library/Frameworks/R.framework/Resources/library/JGR/java/JGR.jar R_ARCH=/i386 arguments to java: java -cp /Library/Frameworks/R.framework/Resources/library/rJava/java/boot -Xmx512m -Xdock:icon=/Applications/JGR.app/Contents/Resources/JGR.icns -Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=JGR -Dmain.class=org.rosuda.JGR.JGR -Djgr.loader.ver=1.61 -Djgr.load.pkgs=yes -Drjava.class.path=/Applications/JGR.app:/Library/Frameworks/ R.framework/Resources/library/rJava/jri/JRI.jar:/Library/Frameworks/ R.framework/Resources/library/iplots/java/iplots.jar:/Library/ Frameworks/R.framework/Resources/library/JGR/java/JGR.jar -Drjava.path=/Library/Frameworks/R.framework/Resources/library/rJava RJavaClassLoader
On Sep 11, 2009, at 2:25 AM, Simon Urbanek wrote:
Peter, you have probably compiled ncl in 64-bit (default on SL) but you're using 32-bit R, so it won't work. Either use 64-bit R or compile ncl for 32-bit. Cheers, Simon On Sep 10, 2009, at 7:58 PM, Peter Cowan wrote:
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... GNU checking dependency style of g++... gcc3 checking for ranlib... ranlib checking build system type... i686-apple-darwin10.0.0 checking host system type... i686-apple-darwin10.0.0 checking for gcc... gcc 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 checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ld used by gcc... /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 for /usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm checking how to recognise dependent libraries... pass_all checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking how to run the C++ preprocessor... g++ -E checking for g77... no checking for xlf... no checking for f77... no checking for frt... no checking for pgf77... no checking for cf77... no checking for fort77... no checking for fl32... no checking for af77... no checking for xlf90... no checking for f90... no checking for pgf90... no checking for pghpf... no checking for epcf90... no checking for gfortran... gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking the maximum length of command line arguments... 196608 checking command to parse /usr/bin/nm output from gcc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... (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... (cached) yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking whether struct tm is in sys/time.h or time.h... time.h checking whether time.h and sys/time.h may both be included... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for alarm... yes checking for working mktime... no checking for working strtod... yes checking for memmove... yes checking for strchr... yes checking for strtol... yes checking for python... /usr/bin/python checking python module: subprocess... yes checking whether make sets $(MAKE)... (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++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsblock.lo -MD -MP -MF .deps/nxsblock.Tpo -c -o nxsblock.lo nxsblock.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsblock.lo -MD -MP -MF .deps/nxsblock.Tpo -c nxsblock.cpp -fno-common -DPIC -o .libs/nxsblock.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsblock.lo -MD -MP -MF .deps/nxsblock.Tpo -c nxsblock.cpp -o nxsblock.o
/dev/null 2>&1
mv -f .deps/nxsblock.Tpo .deps/nxsblock.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxscharactersblock.lo -MD -MP -MF .deps/nxscharactersblock.Tpo -c -o nxscharactersblock.lo nxscharactersblock.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxscharactersblock.lo -MD -MP -MF .deps/nxscharactersblock.Tpo -c nxscharactersblock.cpp -fno-common -DPIC -o .libs/nxscharactersblock.o nxscharactersblock.cpp: In member function 'virtual void NxsCharactersBlock::Report(std::ostream&)': nxscharactersblock.cpp:2559: warning: deprecated conversion from string constant to 'char*' g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxscharactersblock.lo -MD -MP -MF .deps/nxscharactersblock.Tpo -c nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1 mv -f .deps/nxscharactersblock.Tpo .deps/nxscharactersblock.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdatablock.lo -MD -MP -MF .deps/nxsdatablock.Tpo -c -o nxsdatablock.lo nxsdatablock.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdatablock.lo -MD -MP -MF .deps/nxsdatablock.Tpo -c nxsdatablock.cpp -fno-common -DPIC -o .libs/nxsdatablock.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdatablock.lo -MD -MP -MF .deps/nxsdatablock.Tpo -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1 mv -f .deps/nxsdatablock.Tpo .deps/nxsdatablock.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdiscretedatum.lo -MD -MP -MF .deps/nxsdiscretedatum.Tpo -c -o nxsdiscretedatum.lo nxsdiscretedatum.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdiscretedatum.lo -MD -MP -MF .deps/nxsdiscretedatum.Tpo -c nxsdiscretedatum.cpp -fno-common -DPIC -o .libs/nxsdiscretedatum.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdiscretedatum.lo -MD -MP -MF .deps/nxsdiscretedatum.Tpo -c nxsdiscretedatum.cpp -o nxsdiscretedatum.o >/dev/null 2>&1 mv -f .deps/nxsdiscretedatum.Tpo .deps/nxsdiscretedatum.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdiscretematrix.lo -MD -MP -MF .deps/nxsdiscretematrix.Tpo -c -o nxsdiscretematrix.lo nxsdiscretematrix.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdiscretematrix.lo -MD -MP -MF .deps/nxsdiscretematrix.Tpo -c nxsdiscretematrix.cpp -fno-common -DPIC -o .libs/nxsdiscretematrix.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdiscretematrix.lo -MD -MP -MF .deps/nxsdiscretematrix.Tpo -c nxsdiscretematrix.cpp -o nxsdiscretematrix.o >/dev/null 2>&1 mv -f .deps/nxsdiscretematrix.Tpo .deps/nxsdiscretematrix.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdistancedatum.lo -MD -MP -MF .deps/nxsdistancedatum.Tpo -c -o nxsdistancedatum.lo nxsdistancedatum.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdistancedatum.lo -MD -MP -MF .deps/nxsdistancedatum.Tpo -c nxsdistancedatum.cpp -fno-common -DPIC -o .libs/nxsdistancedatum.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdistancedatum.lo -MD -MP -MF .deps/nxsdistancedatum.Tpo -c nxsdistancedatum.cpp -o nxsdistancedatum.o >/dev/null 2>&1 mv -f .deps/nxsdistancedatum.Tpo .deps/nxsdistancedatum.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdistancesblock.lo -MD -MP -MF .deps/nxsdistancesblock.Tpo -c -o nxsdistancesblock.lo nxsdistancesblock.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdistancesblock.lo -MD -MP -MF .deps/nxsdistancesblock.Tpo -c nxsdistancesblock.cpp -fno-common -DPIC -o .libs/nxsdistancesblock.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsdistancesblock.lo -MD -MP -MF .deps/nxsdistancesblock.Tpo -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1 mv -f .deps/nxsdistancesblock.Tpo .deps/nxsdistancesblock.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsexception.lo -MD -MP -MF .deps/nxsexception.Tpo -c -o nxsexception.lo nxsexception.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsexception.lo -MD -MP -MF .deps/nxsexception.Tpo -c nxsexception.cpp -fno-common -DPIC -o .libs/nxsexception.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxsexception.lo -MD -MP -MF .deps/nxsexception.Tpo -c nxsexception.cpp -o nxsexception.o >/dev/null 2>&1 mv -f .deps/nxsexception.Tpo .deps/nxsexception.Plo /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 nxsstring.cpp -o nxsstring.o
/dev/null 2>&1
mv -f .deps/nxsstring.Tpo .deps/nxsstring.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxstaxablock.lo -MD -MP -MF .deps/nxstaxablock.Tpo -c -o nxstaxablock.lo nxstaxablock.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxstaxablock.lo -MD -MP -MF .deps/nxstaxablock.Tpo -c nxstaxablock.cpp -fno-common -DPIC -o .libs/nxstaxablock.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxstaxablock.lo -MD -MP -MF .deps/nxstaxablock.Tpo -c nxstaxablock.cpp -o nxstaxablock.o >/dev/null 2>&1 mv -f .deps/nxstaxablock.Tpo .deps/nxstaxablock.Plo /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxstoken.lo -MD -MP -MF .deps/nxstoken.Tpo -c -o nxstoken.lo nxstoken.cpp g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxstoken.lo -MD -MP -MF .deps/nxstoken.Tpo -c nxstoken.cpp -fno-common -DPIC -o .libs/nxstoken.o g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT nxstoken.lo -MD -MP -MF .deps/nxstoken.Tpo -c nxstoken.cpp -o nxstoken.o
/dev/null 2>&1
mv -f .deps/nxstoken.Tpo .deps/nxstoken.Plo
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I.
-I.. -O3 -ffast-math -fPIC -MT nxstreesblock.lo -MD -MP -MF
.deps/nxstreesblock.Tpo -c -o nxstreesblock.lo nxstreesblock.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT
nxstreesblock.lo -MD -MP -MF .deps/nxstreesblock.Tpo -c
nxstreesblock.cpp -fno-common -DPIC -o .libs/nxstreesblock.o
g++ -DHAVE_CONFIG_H -I. -I.. -O3 -ffast-math -fPIC -MT
nxstreesblock.lo -MD -MP -MF .deps/nxstreesblock.Tpo -c
nxstreesblock.cpp -o nxstreesblock.o >/dev/null 2>&1
mv -f .deps/nxstreesblock.Tpo .deps/nxstreesblock.Plo
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I.
-I.. -O3 -ffast-math -fPIC -MT nxsunalignedblock.lo -MD -MP -MF
.deps/nxsunalignedblock.Tpo -c -o nxsunalignedblock.lo
nxsunalignedblock.cpp
g++ -DHAVE_CONFIG_H -I. -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 R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac