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
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
