[R-SIG-Mac] JGR not working on Snow Leopard
Simon Urbanek
simon.urbanek at r-project.org
Fri Sep 11 16:19:35 CEST 2009
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)
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
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