[R-SIG-Mac] JGR not working on Snow Leopard
Erich Neuwirth
erich.neuwirth at univie.ac.at
Fri Sep 11 15:08:54 CEST 2009
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)
>>
>> _______________________________________________
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>> R-SIG-Mac at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
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