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From: Eric F. <efe...@ph...> - 2009-08-19 16:28:31
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Hi,
I have a build problem with latest stable verion 3.1.107:
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 -pipe
-Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4
-fomit-frame-pointer -march=i586 -mtune=generic
-fasynchronous-unwind-tables -Wno-pmf-conversions -I../libecs -I../..
-I.. -I../../libltdl -I/usr/include/python2.6 ' MassActionFluxPr
ocess.cpp
../../dmtool/dmcompile -v -I/usr/include -O2 -g -pipe -Wformat
-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -fomit-frame-poi
nter -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=MassActionFluxProcess
MassActionFluxProcess.cpp
Traceback (most recent call last):
File "../../dmtool/dmcompile", line 158, in <module>
sys.exit( main() )
File "../../dmtool/dmcompile", line 56, in main
opts , args = getopt.gnu_getopt( sys.argv[1:],
"hvI:L:l:o:D:f:m:O:W:g", ["help", "verbose", "output=" ])
File "/usr/lib/python2.6/getopt.py", line 134, in gnu_getopt
opts, args = do_shorts(opts, args[0][1:], shortopts, args[1:])
File "/usr/lib/python2.6/getopt.py", line 191, in do_shorts
if short_has_arg(opt, shortopts):
File "/usr/lib/python2.6/getopt.py", line 207, in short_has_arg
raise GetoptError('option -%s not recognized' % opt, opt)
getopt.GetoptError: option -p not recognized
ecell3-dmc: ../../dmtool/dmcompile returned error status: 1
Any idea ?
Thanks,
Eric
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From: Moriyoshi K. <mo...@sf...> - 2009-08-19 20:03:34
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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
On Thu, Aug 20, 2009 at 1:16 AM, Eric
Fernandez<efe...@ph...> wrote:
> Hi,
>
> I have a build problem with latest stable verion 3.1.107:
>
> 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 -pipe
> -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4
> -fomit-frame-pointer -march=i586 -mtune=generic
> -fasynchronous-unwind-tables -Wno-pmf-conversions -I../libecs -I../..
> -I.. -I../../libltdl -I/usr/include/python2.6 ' MassActionFluxPr
> ocess.cpp
> ../../dmtool/dmcompile -v -I/usr/include -O2 -g -pipe -Wformat
> -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -fomit-frame-poi
> nter -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=MassActionFluxProcess
> MassActionFluxProcess.cpp
> Traceback (most recent call last):
> File "../../dmtool/dmcompile", line 158, in <module>
> sys.exit( main() )
> File "../../dmtool/dmcompile", line 56, in main
> opts , args = getopt.gnu_getopt( sys.argv[1:],
> "hvI:L:l:o:D:f:m:O:W:g", ["help", "verbose", "output=" ])
> File "/usr/lib/python2.6/getopt.py", line 134, in gnu_getopt
> opts, args = do_shorts(opts, args[0][1:], shortopts, args[1:])
> File "/usr/lib/python2.6/getopt.py", line 191, in do_shorts
> if short_has_arg(opt, shortopts):
> File "/usr/lib/python2.6/getopt.py", line 207, in short_has_arg
> raise GetoptError('option -%s not recognized' % opt, opt)
> getopt.GetoptError: option -p not recognized
> ecell3-dmc: ../../dmtool/dmcompile returned error status: 1
>
> Any idea ?
>
> Thanks,
> Eric
>
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|
|
From: Eric F. <efe...@ph...> - 2009-08-20 09:24:15
|
> -----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
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