Re: [Ecell-devel] build error with dmcompile: getopt.GetoptError: option -p not recognized

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> -----Original Message-----
> From: mor...@gm... [mailto:mor...@gm...] On 
> Behalf Of Moriyoshi Koizumi
> Sent: 19 August 2009 21:03
> To: Eric Fernandez
> Cc: ece...@li...
> Subject: Re: [Ecell-devel] build error with dmcompile: 
> getopt.GetoptError: option -p not recognized[Scanned]
> 
> Hi,
> 
> Looks like the -pipe option that was passed to ecell3-dmc got 
> interpreted as a set of short options -p -i -e, which are of 
> course unsupported by it. Try removing them from CXXFLAGS.
> 
> -- moriyoshi
> 
> 
> 

Thanks a lot, I had to remove --pipe and also --param=ssp-buffer-size=4
from the default rpm compiling options, but got this new error:

make[4]: Entering directory
`/home/zeb/svn/ecell/BUILD/ecell-3.1.107/ecell/dm'
../pyecell/ecell3-python ../bin/ecell3-dmc --verbose
--dmcompile="../../dmtool" --no-stdinclude --no-stdlibdir
--ldflags="-L/home/zeb/svn/ecell/BUILD/ecell-3.1.107/ecell/tmp/usr/lib
-L/usr/lib -lgsl -lgslcblas -lm" --cxxflags='-I/usr/include -O2 -g
-Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector -fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions -I../libecs -I../..
-I.. -I../../libltdl  -I/usr/include/python2.6 '
MassActionFluxProcess.cpp 
../pyecell/ecell3-python ../bin/ecell3-dmc --verbose
--dmcompile="../../dmtool" --no-stdinclude --no-stdlibdir
--ldflags="-L/home/zeb/svn/ecell/BUILD/ecell-3.1.107/ecell/tmp/usr/lib
-L/usr/lib -lgsl -lgslcblas -lm" --cxxflags='-I/usr/include -O2 -g
-Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector -fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions -I../libecs -I../..
-I.. -I../../libltdl  -I/usr/include/python2.6 '
MichaelisUniUniFluxProcess.cpp 
../pyecell/ecell3-python ../bin/ecell3-dmc --verbose
--dmcompile="../../dmtool" --no-stdinclude --no-stdlibdir
--ldflags="-L/home/zeb/svn/ecell/BUILD/ecell-3.1.107/ecell/tmp/usr/lib
-L/usr/lib -lgsl -lgslcblas -lm" --cxxflags='-I/usr/include -O2 -g
-Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector -fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions -I../libecs -I../..
-I.. -I../../libltdl  -I/usr/include/python2.6 ' ConstantFluxProcess.cpp

../pyecell/ecell3-python ../bin/ecell3-dmc --verbose
--dmcompile="../../dmtool" --no-stdinclude --no-stdlibdir
--ldflags="-L/home/zeb/svn/ecell/BUILD/ecell-3.1.107/ecell/tmp/usr/lib
-L/usr/lib -lgsl -lgslcblas -lm" --cxxflags='-I/usr/include -O2 -g
-Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector -fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions -I../libecs -I../..
-I.. -I../../libltdl  -I/usr/include/python2.6 ' DecayFluxProcess.cpp 
cc -fPIC -O2 -g -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector -fomit-frame-pointer -march=i586
-mtune=generic -fasynchronous-unwind-tables -O2 -g -Wformat
-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector -fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions -O2 -g -Wformat
-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector -fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions
-D_ECELL3_DM_CLASSNAME=MassActionFluxProcess -I/usr/include -I../libecs
-I../.. -I.. -I../../libltdl -I/usr/include/python2.6 -c
MassActionFluxProcess.cpp -o MassActionFluxProcess.o
cc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro
-Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -shared
MassActionFluxProcess.o
-L/home/zeb/svn/ecell/BUILD/ecell-3.1.107/ecell/tmp/usr/lib -L/usr/lib
-lgsl -lgslcblas -lm -lecs -lgsl -lboost_python -o MassActionFluxcc
-fPIC -O2 -g -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector -fomit-frame-pointer -march=i586
-mtune=generic -fasynchronous-unwind-tables -O2 -g -Wformat
-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector -fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions -O2 -g -Wformat
-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector -fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions
-D_ECELL3_DM_CLASSNAME=ConstantFluxProcess -I/usr/include -I../libecs
-I../.. -I.. -I../../libltdl -I/usr/include/python2.6 -c
ConstantFluxProcess.cpp -o ConstantFluxProcess.o
cc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro
-Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -shared
ConstantFluxProcess.o
-L/home/zeb/svn/ecell/BUILD/ecell-3.1.107/ecell/tmp/usr/lib -L/usr/lib
-lgsl -lgslcblas -lm -lecs -lgsl -lboost_python -o
ConstantFluxProcess.socc -fPIC -O2 -g -Wformat -Werror=format-security
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
-fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -O2 -g -Wformat -Werror=format-security
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
-fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions -O2 -g -Wformat
-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector -fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions
-D_ECELL3_DM_CLASSNAME=MichaelisUniUniFluxProcess -I/usr/include
-I../libecs -I../.. -I.. -I../../libltdl -I/usr/include/python2.6 -c
MichaelisUniUniFluxProcess.cpp -o MichaelisUniUniFluxProcess.o
cc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro
-Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -shared
MichaelisUniUniFluxProcess.o
-L/home/zeb/svn/ecell/BUILD/ecell-3.1.107/ecell/tmp/usr/lib -L/usr/lib
-lgsl -lgslcblas -lm -lecs -lgsl -lboost_pythMassActionFluxProcess.o: In
function `__gnu_cxx::new_allocator<libecs::Polymorph>::allocate(unsigned
int, void const*)':
/usr/lib/gcc/i586-manbo-linux-gnu/4.4.1/../../../../include/c++/4.4.1/ex
t/new_allocator.h:89: undefined reference to `operator new(unsigned
int)'

[... then many undefined reference errors such as delete, string, STL
etc...]

dmcompile: failed to link the object files:
LinkError(DistutilsExecError("command 'cc' failed with exit status
1",),)
../../dmtool/dmcompile -v -I/usr/include -O2 -g -Wformat
-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector -fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions -I../libecs -I../..
-I.. -I../../libltdl -I/usr/include/python2.6
-L/home/zeb/svn/ecell/BUILD/ecell-3.1.107/ecell/tmp/usr/lib -L/usr/lib
-lgsl -lgslcblas -lm -lecs -lgsl -lboost_python
-D_ECELL3_DM_CLASSNAME=MichaelisUniUniFluxProcess
MichaelisUniUniFluxProcess.cpp
ecell3-dmc: ../../dmtool/dmcompile returned error status: 1
make[4]: *** [MichaelisUniUniFluxProcess.so] Error 1

It seems it should be using g++ instead of cc there ? Or am I doing
something wrong ?

Thanks,
Eric