* checking for file 'pkg/DESCRIPTION' ... OK
* preparing 'pkg':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running cleanup
Making clean in ncl
rm -rf .libs _libs
test -z "libncl.la" || rm -f libncl.la
rm -f "./so_locations"
rm -f *.o
rm -f *.lo
Making clean in .
rm -rf .libs _libs
rm -f *.lo
* installing the package to re-build vignettes
* 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 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 accepts -g... yes
checking how to run the C++ preprocessor... g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -E
Building libRcpp.a in RcppSrc...
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -march=nocona -c Rcpp.cpp -o Rcpp.o
ar crs libRcpp.a Rcpp.o
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-darwin8.11.1
checking host system type... i686-apple-darwin8.11.1
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-darwin8/4.0.1/ld
checking if the linker (/usr/libexec/gcc/i686-apple-darwin8/4.0.1/ld) is GNU ld... no
checking for /usr/libexec/gcc/i686-apple-darwin8/4.0.1/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -p
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
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checking for f77... no
checking for frt... no
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checking for cf77... no
checking for fort77... no
checking for fl32... no
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checking for pghpf... no
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checking for gfortran... no
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checking for fort... no
checking for ifort... no
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checking for lf95... no
checking for ftn... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
checking the maximum length of command line arguments... 196608
checking command to parse /usr/bin/nm -p 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-darwin8/4.0.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin8.11.1 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-darwin8/4.0.1/ld
checking if the linker (/usr/libexec/gcc/i686-apple-darwin8/4.0.1/ld) is GNU ld... no
checking whether the g++ linker (/usr/libexec/gcc/i686-apple-darwin8/4.0.1/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-darwin8/4.0.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin8.11.1 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
appending configuration tag "F77" to libtool
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... yes
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... no
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  -Wno-long-double -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 -Wno-long-double -fPIC -MT nxsassumptionsblock.lo -MD -MP -MF .deps/nxsassumptionsblock.Tpo -c nxsassumptionsblock.cpp  -fno-common -DPIC -o .libs/nxsassumptionsblock.o
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/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxsblock.lo -MD -MP -MF .deps/nxsblock.Tpo -c -o nxsblock.lo nxsblock.cpp
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/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxscharactersblock.lo -MD -MP -MF .deps/nxscharactersblock.Tpo -c -o nxscharactersblock.lo nxscharactersblock.cpp
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/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxsdatablock.lo -MD -MP -MF .deps/nxsdatablock.Tpo -c -o nxsdatablock.lo nxsdatablock.cpp
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/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxsdiscretedatum.lo -MD -MP -MF .deps/nxsdiscretedatum.Tpo -c -o nxsdiscretedatum.lo nxsdiscretedatum.cpp
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/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxsdiscretematrix.lo -MD -MP -MF .deps/nxsdiscretematrix.Tpo -c -o nxsdiscretematrix.lo nxsdiscretematrix.cpp
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/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxsdistancedatum.lo -MD -MP -MF .deps/nxsdistancedatum.Tpo -c -o nxsdistancedatum.lo nxsdistancedatum.cpp
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mv -f .deps/nxsdistancedatum.Tpo .deps/nxsdistancedatum.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxsdistancesblock.lo -MD -MP -MF .deps/nxsdistancesblock.Tpo -c -o nxsdistancesblock.lo nxsdistancesblock.cpp
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mv -f .deps/nxsdistancesblock.Tpo .deps/nxsdistancesblock.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxsexception.lo -MD -MP -MF .deps/nxsexception.Tpo -c -o nxsexception.lo nxsexception.cpp
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/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxsreader.lo -MD -MP -MF .deps/nxsreader.Tpo -c -o nxsreader.lo nxsreader.cpp
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mv -f .deps/nxsreader.Tpo .deps/nxsreader.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxssetreader.lo -MD -MP -MF .deps/nxssetreader.Tpo -c -o nxssetreader.lo nxssetreader.cpp
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mv -f .deps/nxssetreader.Tpo .deps/nxssetreader.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxsstring.lo -MD -MP -MF .deps/nxsstring.Tpo -c -o nxsstring.lo nxsstring.cpp
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mv -f .deps/nxsstring.Tpo .deps/nxsstring.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxstaxablock.lo -MD -MP -MF .deps/nxstaxablock.Tpo -c -o nxstaxablock.lo nxstaxablock.cpp
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mv -f .deps/nxstaxablock.Tpo .deps/nxstaxablock.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxstoken.lo -MD -MP -MF .deps/nxstoken.Tpo -c -o nxstoken.lo nxstoken.cpp
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mv -f .deps/nxstoken.Tpo .deps/nxstoken.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxstreesblock.lo -MD -MP -MF .deps/nxstreesblock.Tpo -c -o nxstreesblock.lo nxstreesblock.cpp
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mv -f .deps/nxstreesblock.Tpo .deps/nxstreesblock.Plo
/bin/sh ../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I..     -O3 -ffast-math  -Wno-long-double -fPIC -MT nxsunalignedblock.lo -MD -MP -MF .deps/nxsunalignedblock.Tpo -c -o nxsunalignedblock.lo nxsunalignedblock.cpp
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mv -f .deps/nxsunalignedblock.Tpo .deps/nxsunalignedblock.Plo
/bin/sh ../libtool --tag=CXX   --mode=link g++  -O3 -ffast-math  -Wno-long-double -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 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IRcppSrc -Incl/ncl -fPIC  -g -O2 -march=nocona -c NCLInterface.cpp -o NCLInterface.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IRcppSrc -Incl/ncl -fPIC  -g -O2 -march=nocona -c ReadWithNCL.cpp -o ReadWithNCL.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -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 phylobase.so NCLInterface.o ReadWithNCL.o -LRcppSrc -lRcpp -Lncl/ncl/.libs -lncl  -F/Library/Frameworks/R.framework/.. -framework R 
** R
** data
** inst
** preparing package for lazy loading
** Removing '/private/tmp/Rinst781622583/phylobase'
 ERROR
Installation failed.
Removing '/tmp/Rinst781622583'