[R-SIG-Mac] Building package from source error "file is not of required architecture"
Simon Urbanek
simon.urbanek at r-project.org
Fri Sep 11 02:25:43 CEST 2009
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
>
>
More information about the R-SIG-Mac
mailing list