[Phylobase-devl] [phylobase-Bugs][165] Configure fails on 2.6.2 patched

[phylobase-bugs at r-forge.r-project.org]

Bugs item #165, was opened at 2008-06-30 09:38
Status: Open
Priority: 3
Submitted By: Marguerite Butler (mbutler)
Assigned to: Brian O'Meara (bcomeara)
Summary: Configure fails on 2.6.2 patched 
Component: None
>Resolution: Fixed
Severity: None
Version: None
Operating System: None
URL: 


Initial Comment:
Installing from source no longer works on R version 2.6.2 patched. Error encountered at:

checking for gcc option to produce PIC... ./configure: line 7412: syntax error near unexpected token `_compilerhppa*64*'
./configure: line 7412: `      case "$host_cpu" _compilerhppa*64*|ia64*)'
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
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
: ignoring unknown tag 
../libtool: line 1: /bin/sed: No such file or directory
*** Warning: inferring the mode of operation is deprecated.
*** Future versions of Libtool will require -mode=MODE be specified.
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
../libtool: line 1: /bin/sed: No such file or directory
: compile: cannot determine name of library object from `'
make[2]: *** [nxsassumptionsblock.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch - i386
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IRcppSrc -Incl/ncl -fPIC  -g -O2 -march=nocona -c NCLInterface.cpp -o NCLInterface.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IRcppSrc -Incl/ncl -fPIC  -g -O2 -march=nocona -c ReadWithNCL.cpp -o ReadWithNCL.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o phylobase.so NCLInterface.o ReadWithNCL.o -LRcppSrc -lRcpp -Lncl/ncl/.libs -lncl  -F/Library/Frameworks/R.framework/.. -framework R 
/usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: can't locate file for: -lncl
/usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: file: -lncl is not an object file (not allowed in a library)
make: *** [phylobase.so] Error 1
chmod: /Library/Frameworks/R.framework/Versions/2.6/Resources/library/phylobase/libs/i386/*: No such file or directory
ERROR: compilation failed for package 'phylobase'


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>Comment By: Brian O'Meara (bcomeara)
Date: 2008-12-03 15:44

Message:
Fixed by Ben Bolker

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