[R-SIG-Mac] JGR not working on Snow Leopard
Erich Neuwirth
erich.neuwirth at univie.ac.at
Sat Sep 12 18:41:05 CEST 2009
It seems I have been able to install 64bit R.
R version 2.9.2 Patched (2009-09-05 r49613)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
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[R.app GUI 1.28 (5399) x86_64-apple-darwin9.8.0]
I could not, however, find a newer installer version of R.app (or
R64.app)
Trying to install JGR still does not work.
I downloaded 64bit JGR as I was told,
but on start it tells me it needs to install some additional
libraries, and then tells ,e
that it could not finish its work.
the JGR packages is missing.
So I try
188-23-83-195:devel neuwirth$ sudo R --arch x86_64 CMD INSTALL JGR
* Installing to library ‘/Library/Frameworks/R.framework/Resources/
library’
* Installing *source* package ‘JGR’ ...
** R
** inst
** preparing package for lazy loading
Error in library(CarbonEL) : there is no package called 'CarbonEL'
Error : package 'iplots' could not be loaded
ERROR: lazy loading failed for package ‘JGR’
* Removing ‘/Library/Frameworks/R.framework/Resources/library/JGR’
188-23-83-195:devel neuwirth$
How can I get past this problem?
On Sep 11, 2009, at 4:19 PM, Simon Urbanek wrote:
> Erich,
>
> On Sep 11, 2009, at 9:08 AM, Erich Neuwirth wrote:
>
>> I am experiencing problems with JGR on Snow Leopard.
>
> Apple only provides 64-bit Java in Snow Leopard, so you can only use
> 64-bit R. In addition, you'll need 64-bit JGR launcher which you can
> download from
> http://urbanek.info/JGR-1.6-SL.dmg
> (despite the name it is compatible with both JGR 1.6 and 1.7 [I
> tested is with the latter])
>
> (When installing packages from sources for 64-bir R, please make
> sure you use --arch x86_64 to build the 64-bit version).
>
> Cheers,
> Simon
>
>
>> 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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