Menu
▾
▴
ecell-devel — For developers.
You can subscribe to this list here.
| 2003 |
Jan
|
Feb
(13) |
Mar
(1) |
Apr
(17) |
May
(26) |
Jun
(35) |
Jul
(28) |
Aug
(17) |
Sep
(11) |
Oct
(42) |
Nov
(16) |
Dec
(7) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2004 |
Jan
(11) |
Feb
(3) |
Mar
(4) |
Apr
(9) |
May
(4) |
Jun
(19) |
Jul
(12) |
Aug
(12) |
Sep
(33) |
Oct
(3) |
Nov
(16) |
Dec
(34) |
| 2005 |
Jan
(59) |
Feb
(25) |
Mar
(9) |
Apr
(11) |
May
(8) |
Jun
(30) |
Jul
(18) |
Aug
(8) |
Sep
(12) |
Oct
(13) |
Nov
(29) |
Dec
(14) |
| 2006 |
Jan
(11) |
Feb
(2) |
Mar
(15) |
Apr
(11) |
May
(23) |
Jun
(14) |
Jul
(4) |
Aug
(19) |
Sep
(3) |
Oct
(34) |
Nov
(7) |
Dec
(7) |
| 2007 |
Jan
(2) |
Feb
(11) |
Mar
(15) |
Apr
|
May
(21) |
Jun
(17) |
Jul
(8) |
Aug
(2) |
Sep
|
Oct
|
Nov
|
Dec
(1) |
| 2008 |
Jan
|
Feb
(9) |
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(2) |
Nov
|
Dec
(6) |
| 2009 |
Jan
|
Feb
|
Mar
|
Apr
(3) |
May
|
Jun
|
Jul
|
Aug
(4) |
Sep
|
Oct
|
Nov
|
Dec
(12) |
| 2010 |
Jan
|
Feb
(2) |
Mar
(3) |
Apr
(2) |
May
|
Jun
(1) |
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2011 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
(1) |
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| S | M | T | W | T | F | S |
|---|---|---|---|---|---|---|
|
|
|
|
|
|
|
1
|
|
2
|
3
|
4
(1) |
5
|
6
|
7
|
8
|
|
9
|
10
|
11
|
12
|
13
|
14
|
15
|
|
16
|
17
|
18
|
19
(2) |
20
(1) |
21
|
22
|
|
23
|
24
|
25
|
26
|
27
|
28
|
29
|
|
30
|
31
|
|
|
|
|
|
|
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
|
|
From: Moriyoshi K. <mo...@sf...> - 2009-08-19 20:03:34
|
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
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now. http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Ecell-devel mailing list
> Ece...@li...
> https://lists.sourceforge.net/lists/listinfo/ecell-devel
>
|
|
From: Eric F. <efe...@ph...> - 2009-08-19 16:28:31
|
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
|
|
From: Bin Hu <hub...@gm...> - 2009-08-04 05:54:58
|
Hi,
I am having a problem in installing 3.1.107 on a virtual machine
running Ubuntu. Configure and compile looked fine, but got the
following error in sudo make install:
Making install in doc
make[1]: Entering directory `/home/hu/bak/ecell-3.1.107/doc'
Making install in users-manual
make[2]: Entering directory `/home/hu/bak/ecell-3.1.107/doc/users-
manual'
rm -f -rf users-manual
mkdir users-manual
make[3]: Entering directory `/home/hu/bak/ecell-3.1.107/doc/users-
manual'
make[3]: Nothing to be done for `install-exec-am'.
rm -f -rf users-manual
mkdir users-manual
test -z "/usr/local/share/doc/ecell/users-manual" || /bin/mkdir -p "/
usr/local/share/doc/ecell/users-manual"
/usr/bin/install -c -m 644 './users-manual/*' '/usr/local/share/doc/
ecell/users-manual/*'
/usr/bin/install: cannot stat `./users-manual/*': No such file or
directory
make[3]: *** [install-_htmlDATA] Error 1
make[3]: Leaving directory `/home/hu/bak/ecell-3.1.107/doc/users-manual'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/home/hu/bak/ecell-3.1.107/doc/users-manual'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/hu/bak/ecell-3.1.107/doc'
make: *** [install-recursive] Error 1
Executing ecell3-session generates the following error:
Traceback (most recent call last):
File "/usr/local/bin/ecell3-session", line 8, in <module>
import ecell.config
ImportError: No module named ecell.config
$ ecell3-python
Python 2.6.2 (release26-maint, Apr 19 2009, 01:56:41)
[GCC 4.3.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Can anyone show me how to solve the problem? Thanks.
Regards,
Bin
|