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From: Kozo N. <kni...@ri...> - 2011-06-01 11:08:31
|
E-Cell's source code repository has moved to GitHub! E-Cell has been developed using SourceForge's subversion repository since its inception, but we think that now is a good time to switch to a distributed version control system, and we chose GitHub. All the source code from E-Cell project is now available on https://github.com/ecell. You will also find the source code of the E-Cell 3 project under the same organization. The development of E-Cell now continues on GitHub. The previous Subversion repository will be abandoned. We think that migration to GitHub will make it much easier for users to contribute to our project and also help us reach our next milestone more gracefully. -- Kozo Nishida Laboratory for Biochemical Simulation OLABB, Osaka University 6-2-3, Furuedai, Suita, Osaka 565-0874, JAPAN kni...@ri... |
|
From: Michele M. <mat...@eb...> - 2010-06-16 07:10:10
|
Dear ecell-developers,
I've updated Ecell to the latest release for the series 3.1 --> 3.1.108.
Unfortunately my model does not run properly anymore and I receive this error:
gsl: lu.c:147: ERROR: matrix is singular
Default GSL error handler invoked.
Aborted
Any idea how to go about this?
This is my solver conf:
Stepper ODEStepper( DE1 )
{
AbsoluteEpsilon 0.1;
StateToleranceFactor 1.0;
MinStepInterval 2e-300;
RelativeEpsilon 0.1;
Tolerance 1e-06;
StepInterval 1e-08;
DerivativeToleranceFactor 1.0;
MaxStepInterval 1.0;
IsEpsilonChecked 0;
AbsoluteToleranceFactor 1.0;
}
Thanks,
Michele.
|
|
From: Erin <she...@um...> - 2010-04-05 21:45:27
|
Hello,
I think I've found another bug in the session monitor. When I try to load
an ".ess" file into the monitor I get the following error:
Loading Script file
/home/erin/Desktop/Mitochondrion-20100316/modelingFiles/seahorseExperiment.ess
Can't load
[/home/erin/Desktop/Mitochondrion-20100316/modelingFiles/seahorseExperiment.ess]
Traceback (most recent call last):
File "/usr/lib/python2.6/dist-packages/ecell/ui/osogo/MainWindow.py", line
537, in __loadData
self.theSession.loadScript( aFileName )
File
"/usr/lib/python2.6/dist-packages/ecell/ui/osogo/GtkSessionMonitor.py", line
552, in loadScript
Session.loadScript (self, ecs, parameters )
AttributeError: class Session has no attribute 'loadScript'
I'm using E-Cell 3.2.0p2 and Ubuntu Linux 9.10.
Thanks,
Erin
--
Erin Rachael Shellman
The University of Michigan
Bioinformatics PhD Candidate
http://www.erinshellman.com
she...@um...
(937) 321.1129
|
|
From: Moriyoshi K. <mo...@ri...> - 2010-04-02 10:01:37
|
The GUI interface apparently got stuck because the step interval of
the stepper ended up being excessively large with little activities of
the associated processes. You need to set MaxStepInterval to a value
large enough in such cases.
-- moriyoshi
On Tue, Mar 30, 2010 at 12:47 AM, Erin <she...@um...> wrote:
> Hello,
>
> I'm having a lot of problems developing models because when I try to
> test them the Osogo session monitor hangs and crashes. To simplify I
> tried to use the sample em file from page 10 of the E-Cell handbook
> ("ecell3-users-manual-0606.pdf"), however this simple em also crashes
> the Osago session monitor when I try to run the model. I get no
> errors when loading the model. I'm not sure how to get an error log
> when this happens so I can't be more specific, but I recommend that
> you try to run the sample em also and see whether it causes the
> monitor to hang.
>
> I am using E-Cell 3.2.0p1 on Ubuntu 9.10.
>
> Thank you,
>
> Erin
>
> The em I'm using from page 10 is below:
>
> Stepper ODEStepper( ODE_1 )
> {
> # no property
> }
> System System( / )
> {
> StepperID ODE_1;
>
> Variable Variable( SIZE )
> {
> Value 1e-18;
> }
>
> Variable Variable( S )
> {
> Value 10000;
> }
>
> Variable Variable( P )
> {
> Value 0;
> }
>
> Process MassActionFluxProcess( E )
> {
> Name "A mass action from S to P."
> k 1.0;
>
> VariableReferenceList [ S0 :.:S -1 ]
> [ P0 :.:P 1 ];
> }
> }
>
> --
> Erin Rachael Shellman
> The University of Michigan
> Bioinformatics PhD Candidate
> http://www.erinshellman.com
> she...@um...
> (937) 321.1129
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Ecell-devel mailing list
> Ece...@li...
> https://lists.sourceforge.net/lists/listinfo/ecell-devel
>
|
|
From: Moriyoshi K. <mo...@sf...> - 2010-03-31 10:30:14
|
Hi, Sorry for the delay. I just identified the cause of the problem, and I am going to release the fixed version shortly as this is critical. If you are in hurry, check out the subversion repository. Thanks. -- moriyoshi On Mon, Mar 29, 2010 at 11:13 PM, Erin <she...@um...> wrote: > Hello, > > I posted this to ecell-users but I think it's actually a bug, so I'll > repost here. After running a simulation via an ess file, I get the > following errors: > > erin@bobby:~/modelingFiles$ ecell3-session experiment.py > Running for a minute > Simulation complete! > Traceback (most recent call last): > File \"/usr/bin/ecell3-session\", line 234, in <module> > main() > File \"/usr/bin/ecell3-session\", line 229, in main > aConsole.loadScript( anEssFile, aParameters ) > File \"/usr/bin/ecell3-session\", line 56, in loadScript > execfile( ecsFile, aContext ) > File \"experiment.py\", line 68, in <module> > malateResults.save( \'malateResults.ecd\' ) > File \"/usr/lib/python2.6/dist-packages/ecell/ECDDataFile.py\", line 91, > in save > TableIO.writeArray( self.theFileName, self.theData, 1 ) > File \"/usr/lib/python2.6/dist-packages/ecell/TableIO.py\", line 79, in > writeArray > t[\'rows\'] = data.shape[0] > AttributeError: \'ecell._ecs.DataPointVector\' object has no attribute > \'shape\' > > The file "malateResults" is created however, it contains only headers > and no data. > > I am using E-Cell 3.2.0p1 on Ubuntu 9.10. > > Thanks, > > Erin > > -- > Erin Rachael Shellman > The University of Michigan > Bioinformatics PhD Candidate > http://www.erinshellman.com > she...@um... > (937) 321.1129 > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Ecell-devel mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-devel > |
|
From: Erin <she...@um...> - 2010-03-29 15:47:22
|
Hello,
I'm having a lot of problems developing models because when I try to
test them the Osogo session monitor hangs and crashes. To simplify I
tried to use the sample em file from page 10 of the E-Cell handbook
("ecell3-users-manual-0606.pdf"), however this simple em also crashes
the Osago session monitor when I try to run the model. I get no
errors when loading the model. I'm not sure how to get an error log
when this happens so I can't be more specific, but I recommend that
you try to run the sample em also and see whether it causes the
monitor to hang.
I am using E-Cell 3.2.0p1 on Ubuntu 9.10.
Thank you,
Erin
The em I'm using from page 10 is below:
Stepper ODEStepper( ODE_1 )
{
# no property
}
System System( / )
{
StepperID ODE_1;
Variable Variable( SIZE )
{
Value 1e-18;
}
Variable Variable( S )
{
Value 10000;
}
Variable Variable( P )
{
Value 0;
}
Process MassActionFluxProcess( E )
{
Name "A mass action from S to P."
k 1.0;
VariableReferenceList [ S0 :.:S -1 ]
[ P0 :.:P 1 ];
}
}
--
Erin Rachael Shellman
The University of Michigan
Bioinformatics PhD Candidate
http://www.erinshellman.com
she...@um...
(937) 321.1129
|
|
From: Erin <she...@um...> - 2010-03-29 14:19:34
|
Hello,
I posted this to ecell-users but I think it's actually a bug, so I'll
repost here. After running a simulation via an ess file, I get the
following errors:
erin@bobby:~/modelingFiles$ ecell3-session experiment.py
Running for a minute
Simulation complete!
Traceback (most recent call last):
File \"/usr/bin/ecell3-session\", line 234, in <module>
main()
File \"/usr/bin/ecell3-session\", line 229, in main
aConsole.loadScript( anEssFile, aParameters )
File \"/usr/bin/ecell3-session\", line 56, in loadScript
execfile( ecsFile, aContext )
File \"experiment.py\", line 68, in <module>
malateResults.save( \'malateResults.ecd\' )
File \"/usr/lib/python2.6/dist-packages/ecell/ECDDataFile.py\", line 91,
in save
TableIO.writeArray( self.theFileName, self.theData, 1 )
File \"/usr/lib/python2.6/dist-packages/ecell/TableIO.py\", line 79, in
writeArray
t[\'rows\'] = data.shape[0]
AttributeError: \'ecell._ecs.DataPointVector\' object has no attribute
\'shape\'
The file "malateResults" is created however, it contains only headers
and no data.
I am using E-Cell 3.2.0p1 on Ubuntu 9.10.
Thanks,
Erin
--
Erin Rachael Shellman
The University of Michigan
Bioinformatics PhD Candidate
http://www.erinshellman.com
she...@um...
(937) 321.1129
|
|
From: Moriyoshi K. <mo...@sf...> - 2010-02-17 17:25:12
|
The command should've been: svn switch --depth infinity http://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/trunk -- moriyoshi On Thu, Feb 18, 2010 at 2:21 AM, Moriyoshi Koizumi <mo...@sf...> wrote: > Hi, > > I've reorganized the subversion repository so trunk is what was called > ecell-3.2 branch. > The original trunk was moved to branches/old-trunk. > > Please update the repository root URL by doing the following: > > svn switch --relocate > https://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/branches/ecell-3.2 > https://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/trunk > > -- moriyoshi > |
|
From: Moriyoshi K. <mo...@sf...> - 2010-02-17 17:21:27
|
Hi, I've reorganized the subversion repository so trunk is what was called ecell-3.2 branch. The original trunk was moved to branches/old-trunk. Please update the repository root URL by doing the following: svn switch --relocate https://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/branches/ecell-3.2 https://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/trunk -- moriyoshi |
|
From: Moriyoshi K. <mo...@sf...> - 2009-12-10 09:02:34
|
Hi, Actually E-Cell's autogen.sh does more; it tries to generate configure.ac from configure.ac.in. I didn't know that autoreconf now has such an option to invoke libtoolze and other commands in the correct order though. -- moriyoshi On Thu, Dec 10, 2009 at 5:54 PM, Eric Fernandez <efe...@ph...> wrote: >> -----Original Message----- >> From: Moriyoshi Koizumi [mailto:mo...@sf...] >> Sent: 10 December 2009 05:04 >> To: Emre Turkay >> Cc: ece...@li... >> Subject: Re: [Ecell-devel] ecell-4 Ubuntu Karmic autogen >> problem (svn head)[Scanned] >> >> Hi, >> >> What are the versions of the following tools? The version >> numbers within parentheses are what I use currently. >> >> >> - libtool (2.2.6) >> - autoconf (2.64) >> - automake (1.11) >> >> I am using Karmic and was able to proceed to configure >> without problems. >> >> Regards, >> Moriyoshi > > Hi, > > I have not compiled ecell from a long time (will do soon, since I am the > Mandriva package maintainer), but I participate to other projects (such > as the SBML solver libray). > > As far as I know, autogen.sh scripts tend to be deprecated now, and a > preferred method is to use: > autoreconf -if > which uses glibtoolize among others and properly updates the GNU build > system files. > > Any thoughts? > > Eric Fernandez > |
|
From: Eric F. <efe...@ph...> - 2009-12-10 08:54:40
|
> -----Original Message----- > From: Moriyoshi Koizumi [mailto:mo...@sf...] > Sent: 10 December 2009 05:04 > To: Emre Turkay > Cc: ece...@li... > Subject: Re: [Ecell-devel] ecell-4 Ubuntu Karmic autogen > problem (svn head)[Scanned] > > Hi, > > What are the versions of the following tools? The version > numbers within parentheses are what I use currently. > > > - libtool (2.2.6) > - autoconf (2.64) > - automake (1.11) > > I am using Karmic and was able to proceed to configure > without problems. > > Regards, > Moriyoshi Hi, I have not compiled ecell from a long time (will do soon, since I am the Mandriva package maintainer), but I participate to other projects (such as the SBML solver libray). As far as I know, autogen.sh scripts tend to be deprecated now, and a preferred method is to use: autoreconf -if which uses glibtoolize among others and properly updates the GNU build system files. Any thoughts? Eric Fernandez |
|
From: Emre T. <emr...@gm...> - 2009-12-10 08:18:03
|
Moryoshi, I have the same version of libtool, autoconf & automake with you. On Thu, Dec 10, 2009 at 02:03:37PM +0900, Moriyoshi Koizumi wrote: > What are the versions of the following tools? The version numbers > within parentheses are what I use currently. > - libtool (2.2.6) > - autoconf (2.64) > - automake (1.11) > > I am using Karmic and was able to proceed to configure without problems. > > Regards, > Moriyoshi |
|
From: Moriyoshi K. <mo...@sf...> - 2009-12-10 05:03:27
|
Hi, What are the versions of the following tools? The version numbers within parentheses are what I use currently. - libtool (2.2.6) - autoconf (2.64) - automake (1.11) I am using Karmic and was able to proceed to configure without problems. Regards, Moriyoshi Emre Turkay wrote: > Hi folks, > > I checked out ecell-4 svn revision 3607. > > When I executed ./autogen.sh there is an error I got: > > --------------------- > Running autotools for . ... libtoolize aclocal autoheader automake autoconf > Running autotools for libltdl ... libtoolize aclocal acinclude.m4:6405: the serial number must appear before any macro definition > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached > ../../lib/autoconf/general.m4:2018: AC_CACHE_VAL is expanded from... > ../../lib/autoconf/general.m4:2039: AC_CACHE_CHECK is expanded from... > acinclude.m4:615: AC_LIBTOOL_COMPILER_OPTION is expanded from... > acinclude.m4:4815: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... > acinclude.m4:2651: _LT_AC_LANG_C_CONFIG is expanded from... > acinclude.m4:2650: AC_LIBTOOL_LANG_C_CONFIG is expanded from... > acinclude.m4:80: AC_LIBTOOL_SETUP is expanded from... > acinclude.m4:60: _AC_PROG_LIBTOOL is expanded from... > acinclude.m4:25: AC_PROG_LIBTOOL is expanded from... > configure.ac:69: the top level > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:660: AC_LIBTOOL_LINKER_OPTION is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:2732: _LT_AC_LANG_CXX_CONFIG is expanded from... > acinclude.m4:2731: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from... > acinclude.m4:1787: _LT_AC_TAGCONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:3899: _LT_AC_LANG_F77_CONFIG is expanded from... > acinclude.m4:3898: AC_LIBTOOL_LANG_F77_CONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:4001: _LT_AC_LANG_GCJ_CONFIG is expanded from... > acinclude.m4:4000: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached > autoheader configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached > ../../lib/autoconf/general.m4:2018: AC_CACHE_VAL is expanded from... > ../../lib/autoconf/general.m4:2039: AC_CACHE_CHECK is expanded from... > acinclude.m4:615: AC_LIBTOOL_COMPILER_OPTION is expanded from... > acinclude.m4:4815: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... > acinclude.m4:2651: _LT_AC_LANG_C_CONFIG is expanded from... > acinclude.m4:2650: AC_LIBTOOL_LANG_C_CONFIG is expanded from... > acinclude.m4:80: AC_LIBTOOL_SETUP is expanded from... > acinclude.m4:60: _AC_PROG_LIBTOOL is expanded from... > acinclude.m4:25: AC_PROG_LIBTOOL is expanded from... > configure.ac:69: the top level > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:660: AC_LIBTOOL_LINKER_OPTION is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:2732: _LT_AC_LANG_CXX_CONFIG is expanded from... > acinclude.m4:2731: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from... > acinclude.m4:1787: _LT_AC_TAGCONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:3899: _LT_AC_LANG_F77_CONFIG is expanded from... > acinclude.m4:3898: AC_LIBTOOL_LANG_F77_CONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:4001: _LT_AC_LANG_GCJ_CONFIG is expanded from... > acinclude.m4:4000: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached > automake configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached > ../../lib/autoconf/general.m4:2018: AC_CACHE_VAL is expanded from... > ../../lib/autoconf/general.m4:2039: AC_CACHE_CHECK is expanded from... > acinclude.m4:615: AC_LIBTOOL_COMPILER_OPTION is expanded from... > acinclude.m4:4815: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... > acinclude.m4:2651: _LT_AC_LANG_C_CONFIG is expanded from... > acinclude.m4:2650: AC_LIBTOOL_LANG_C_CONFIG is expanded from... > acinclude.m4:80: AC_LIBTOOL_SETUP is expanded from... > acinclude.m4:60: _AC_PROG_LIBTOOL is expanded from... > acinclude.m4:25: AC_PROG_LIBTOOL is expanded from... > configure.ac:69: the top level > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:660: AC_LIBTOOL_LINKER_OPTION is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:2732: _LT_AC_LANG_CXX_CONFIG is expanded from... > acinclude.m4:2731: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from... > acinclude.m4:1787: _LT_AC_TAGCONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:3899: _LT_AC_LANG_F77_CONFIG is expanded from... > acinclude.m4:3898: AC_LIBTOOL_LANG_F77_CONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:4001: _LT_AC_LANG_GCJ_CONFIG is expanded from... > acinclude.m4:4000: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached > autoconf configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached > ../../lib/autoconf/general.m4:2018: AC_CACHE_VAL is expanded from... > ../../lib/autoconf/general.m4:2039: AC_CACHE_CHECK is expanded from... > acinclude.m4:615: AC_LIBTOOL_COMPILER_OPTION is expanded from... > acinclude.m4:4815: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... > acinclude.m4:2651: _LT_AC_LANG_C_CONFIG is expanded from... > acinclude.m4:2650: AC_LIBTOOL_LANG_C_CONFIG is expanded from... > acinclude.m4:80: AC_LIBTOOL_SETUP is expanded from... > acinclude.m4:60: _AC_PROG_LIBTOOL is expanded from... > acinclude.m4:25: AC_PROG_LIBTOOL is expanded from... > configure.ac:69: the top level > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:660: AC_LIBTOOL_LINKER_OPTION is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:2732: _LT_AC_LANG_CXX_CONFIG is expanded from... > acinclude.m4:2731: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from... > acinclude.m4:1787: _LT_AC_TAGCONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:3899: _LT_AC_LANG_F77_CONFIG is expanded from... > acinclude.m4:3898: AC_LIBTOOL_LANG_F77_CONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached > acinclude.m4:4001: _LT_AC_LANG_GCJ_CONFIG is expanded from... > acinclude.m4:4000: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from... > configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached > > Running autotools for dmtool ... libtoolize aclocal autoheader automake autoconf > Running autotools for ecell ... libtoolize aclocal configure.ac:138: warning: macro `AM_PATH_GSL' not found in library > configure.ac:23: error: AC_SUBST: `ECELL_DIRNAME ' is not a valid shell variable name > configure.ac:23: the top level > autom4te: /usr/bin/m4 failed with exit status: 1 > aclocal: autom4te failed with exit status: 1 > Error processing ecell > --------------------- > > Any solution? > > Thanks, > > emre > > ------------------------------------------------------------------------------ > Return on Information: > Google Enterprise Search pays you back > Get the facts. > http://p.sf.net/sfu/google-dev2dev > _______________________________________________ > Ecell-devel mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-devel |
|
From: Emre T. <emr...@gm...> - 2009-12-09 12:48:59
|
Hi folks,
I checked out ecell-4 svn revision 3607.
When I executed ./autogen.sh there is an error I got:
---------------------
Running autotools for . ... libtoolize aclocal autoheader automake autoconf
Running autotools for libltdl ... libtoolize aclocal acinclude.m4:6405: the serial number must appear before any macro definition
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached
../../lib/autoconf/general.m4:2018: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2039: AC_CACHE_CHECK is expanded from...
acinclude.m4:615: AC_LIBTOOL_COMPILER_OPTION is expanded from...
acinclude.m4:4815: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from...
acinclude.m4:2651: _LT_AC_LANG_C_CONFIG is expanded from...
acinclude.m4:2650: AC_LIBTOOL_LANG_C_CONFIG is expanded from...
acinclude.m4:80: AC_LIBTOOL_SETUP is expanded from...
acinclude.m4:60: _AC_PROG_LIBTOOL is expanded from...
acinclude.m4:25: AC_PROG_LIBTOOL is expanded from...
configure.ac:69: the top level
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:660: AC_LIBTOOL_LINKER_OPTION is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:2732: _LT_AC_LANG_CXX_CONFIG is expanded from...
acinclude.m4:2731: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from...
acinclude.m4:1787: _LT_AC_TAGCONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:3899: _LT_AC_LANG_F77_CONFIG is expanded from...
acinclude.m4:3898: AC_LIBTOOL_LANG_F77_CONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:4001: _LT_AC_LANG_GCJ_CONFIG is expanded from...
acinclude.m4:4000: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
autoheader configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached
../../lib/autoconf/general.m4:2018: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2039: AC_CACHE_CHECK is expanded from...
acinclude.m4:615: AC_LIBTOOL_COMPILER_OPTION is expanded from...
acinclude.m4:4815: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from...
acinclude.m4:2651: _LT_AC_LANG_C_CONFIG is expanded from...
acinclude.m4:2650: AC_LIBTOOL_LANG_C_CONFIG is expanded from...
acinclude.m4:80: AC_LIBTOOL_SETUP is expanded from...
acinclude.m4:60: _AC_PROG_LIBTOOL is expanded from...
acinclude.m4:25: AC_PROG_LIBTOOL is expanded from...
configure.ac:69: the top level
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:660: AC_LIBTOOL_LINKER_OPTION is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:2732: _LT_AC_LANG_CXX_CONFIG is expanded from...
acinclude.m4:2731: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from...
acinclude.m4:1787: _LT_AC_TAGCONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:3899: _LT_AC_LANG_F77_CONFIG is expanded from...
acinclude.m4:3898: AC_LIBTOOL_LANG_F77_CONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:4001: _LT_AC_LANG_GCJ_CONFIG is expanded from...
acinclude.m4:4000: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
automake configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached
../../lib/autoconf/general.m4:2018: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2039: AC_CACHE_CHECK is expanded from...
acinclude.m4:615: AC_LIBTOOL_COMPILER_OPTION is expanded from...
acinclude.m4:4815: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from...
acinclude.m4:2651: _LT_AC_LANG_C_CONFIG is expanded from...
acinclude.m4:2650: AC_LIBTOOL_LANG_C_CONFIG is expanded from...
acinclude.m4:80: AC_LIBTOOL_SETUP is expanded from...
acinclude.m4:60: _AC_PROG_LIBTOOL is expanded from...
acinclude.m4:25: AC_PROG_LIBTOOL is expanded from...
configure.ac:69: the top level
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:660: AC_LIBTOOL_LINKER_OPTION is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:2732: _LT_AC_LANG_CXX_CONFIG is expanded from...
acinclude.m4:2731: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from...
acinclude.m4:1787: _LT_AC_TAGCONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:3899: _LT_AC_LANG_F77_CONFIG is expanded from...
acinclude.m4:3898: AC_LIBTOOL_LANG_F77_CONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:4001: _LT_AC_LANG_GCJ_CONFIG is expanded from...
acinclude.m4:4000: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
autoconf configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached
../../lib/autoconf/general.m4:2018: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2039: AC_CACHE_CHECK is expanded from...
acinclude.m4:615: AC_LIBTOOL_COMPILER_OPTION is expanded from...
acinclude.m4:4815: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from...
acinclude.m4:2651: _LT_AC_LANG_C_CONFIG is expanded from...
acinclude.m4:2650: AC_LIBTOOL_LANG_C_CONFIG is expanded from...
acinclude.m4:80: AC_LIBTOOL_SETUP is expanded from...
acinclude.m4:60: _AC_PROG_LIBTOOL is expanded from...
acinclude.m4:25: AC_PROG_LIBTOOL is expanded from...
configure.ac:69: the top level
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:660: AC_LIBTOOL_LINKER_OPTION is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:2732: _LT_AC_LANG_CXX_CONFIG is expanded from...
acinclude.m4:2731: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from...
acinclude.m4:1787: _LT_AC_TAGCONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:3899: _LT_AC_LANG_F77_CONFIG is expanded from...
acinclude.m4:3898: AC_LIBTOOL_LANG_F77_CONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
acinclude.m4:4001: _LT_AC_LANG_GCJ_CONFIG is expanded from...
acinclude.m4:4000: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from...
configure.ac:69: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached
Running autotools for dmtool ... libtoolize aclocal autoheader automake autoconf
Running autotools for ecell ... libtoolize aclocal configure.ac:138: warning: macro `AM_PATH_GSL' not found in library
configure.ac:23: error: AC_SUBST: `ECELL_DIRNAME ' is not a valid shell variable name
configure.ac:23: the top level
autom4te: /usr/bin/m4 failed with exit status: 1
aclocal: autom4te failed with exit status: 1
Error processing ecell
---------------------
Any solution?
Thanks,
emre
|
|
From: Michele M. <mat...@eb...> - 2009-12-09 10:10:39
|
Ok sorry, my fault. For some reason git-svn bridge didn't work properly and was not fetching the last version from svn. I recreate the repo using the svn, now I can compile the 3.1 branch without any problem and installing it. Thanks for the support! Cheers, Michele. On Wed, Dec 9, 2009 at 1:40 AM, Moriyoshi Koizumi <mo...@sf...>wrote: > Seems weird. The HEAD is 3606 so it is most likely that you haven't > got your local repository up-to-date. > > -- moriyoshi > > > > On Tue, Dec 8, 2009 at 8:02 PM, Michele Mattioni <mat...@eb...> > wrote: > > Yep, > > the failure is from the svn code: > > > > mattions@triton:ecell-3.1(master)$ git svn info > > Path: . > > URL: > > http://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/branches/ecell-3.1 > > Repository Root: http://ecell.svn.sourceforge.net/svnroot/ecell > > Repository UUID: f1531174-cb10-0410-9fe6-89aa7ac3eedb > > Revision: 3464 > > Node Kind: directory > > Schedule: normal > > Last Changed Author: moriyoshi > > Last Changed Rev: 3464 > > Last Changed Date: 2009-04-29 15:27:07 +0100 (Wed, 29 Apr 2009) > > > > (Using git bridge to svn...) > > > > On Tue, Dec 8, 2009 at 10:57 AM, Moriyoshi Koizumi <mo...@sf...> > > wrote: > >> > >> Hi, > >> > >> This should have been fixed at some point. Did you get this when you > >> were trying to use the svn version instead of 3.1.107? > >> > >> -- moriyoshi > >> > >> > >> > >> On Tue, Dec 8, 2009 at 7:50 PM, Michele Mattioni <mat...@eb...> > >> wrote: > >> > Hi Moriyoshi, > >> > > >> > I've managed to compile the version (1.107), commenting the > >> > Gillespie.hpp > >> > > >> > When I try to compile the code from the svn I hit a libtool problem > >> > which I > >> > don't really understand. > >> > > >> > I use the .autogen/sh > >> > ./configure > >> > make > >> > > >> > process > >> > > >> > mattions@triton:ecell-3.1(master)$ make > >> > make all-recursive > >> > make[1]: Entering directory > >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1' > >> > Making all in libltdl > >> > make[2]: Entering directory > >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' > >> > make all-am > >> > make[3]: Entering directory > >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' > >> > /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H > >> > -I. -g -O2 -c -o ltdl.lo ltdl.c > >> > ./libtool: line 463: CDPATH: command not found > >> > ./libtool: line 1141: func_opt_split: command not found > >> > libtool: Version mismatch error. This is libtool 2.2.6 > >> > Debian-2.2.6a-4, > >> > but the > >> > libtool: definition of this LT_INIT comes from an older release. > >> > libtool: You should recreate aclocal.m4 with macros from libtool > >> > 2.2.6 > >> > Debian-2.2.6a-4 > >> > libtool: and run autoconf again. > >> > make[3]: *** [ltdl.lo] Error 63 > >> > make[3]: Leaving directory > >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' > >> > make[2]: *** [all] Error 2 > >> > make[2]: Leaving directory > >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' > >> > make[1]: *** [all-recursive] Error 1 > >> > make[1]: Leaving directory > >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1' > >> > make: *** [all] Error 2 > >> > > >> > BTW, > >> > thanks for Ecell. It's awesome. > >> > > >> > On Mon, Dec 7, 2009 at 10:29 AM, Moriyoshi Koizumi < > mo...@sf...> > >> > wrote: > >> >> > >> >> Hi, > >> >> > >> >> This is due to an *inappropriate* change in the recent glibc that > >> >> defines "getc" as a preprocessor macro in place of a weak alias to > the > >> >> actual function name. You can checkout the latest source code from > >> >> the ecell's subversion repository which already includes workaround > >> >> for this problem (plus several crucial fixes). > >> >> > >> >> > >> >> > http://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/branches/ecell-3.1 > >> >> > >> >> -- moriyoshi > >> >> > >> >> > >> >> > >> >> On Mon, Dec 7, 2009 at 6:50 PM, Michele Mattioni <mat...@eb... > > > >> >> wrote: > >> >> > Hello ecell-3 devs, > >> >> > > >> >> > I'm trying to compile the final version of Ecell-3 (1.107) on a > >> >> > Ubuntu > >> >> > Karmic (9.10) and unfortunaly the compilation fail: > >> >> > > >> >> > cc -fPIC -g -O2 -g -O2 -Wno-pmf-conversions -g -O2 > >> >> > -Wno-pmf-conversions > >> >> > -D_ECELL3_DM_CLASSNAME= > >> >> > GillespieProcess -I/usr/include -I../libecs -I../.. -I.. > >> >> > -I../../libltdl > >> >> > -I/usr/include/python2.6 -c GillespieProcess.cpp -o > >> >> > GillespieProcess.o > >> >> > In file included from GillespieProcess.cpp:28: > >> >> > GillespieProcess.hpp: In static member function ‘static void > >> >> > > >> >> > > GillespieProcess::initializePropertyInterface(libecs::Type2Type<TT>)’: > >> >> > GillespieProcess.hpp:59: error: ‘getc’ is not a member of > >> >> > ‘GillespieProcess’ > >> >> > GillespieProcess.hpp:59: error: ‘getc’ is not a member of > >> >> > ‘GillespieProcess’ > >> >> > dmcompile: failed to compile the specified source files: > >> >> > CompileError(DistutilsExecError("command 'cc' failed with exit > status > >> >> > 1",),) > >> >> > ecell3-dmc: ../../dmtool/dmcompile returned error status: 1 > >> >> > make[4]: *** [GillespieProcess.so] Error 1 > >> >> > make[4]: Leaving directory > >> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell/dm' > >> >> > make[3]: *** [all-recursive] Error 1 > >> >> > make[3]: Leaving directory > >> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell' > >> >> > make[2]: *** [all] Error 2 > >> >> > make[2]: Leaving directory > >> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell' > >> >> > make[1]: *** [all-recursive] Error 1 > >> >> > make[1]: Leaving directory > >> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107' > >> >> > make: *** [all] Error 2 > >> >> > > >> >> > The problem seems to be the line 59 of the > >> >> > ecell/dm/GillespieProcess.hpp > >> >> > file, which is: > >> >> > > >> >> > PROPERTYSLOT_GET_NO_LOAD_SAVE( Real, c ); > >> >> > > >> >> > Any suggestions? > >> >> > > >> >> > (Are you thinking to provide deb package for karmic? (maybe using > >> >> > launchpad... :) ) > >> >> > > >> >> > Regards, > >> >> > Michele Mattioni > >> >> > > >> >> > > >> >> > > >> >> > > ------------------------------------------------------------------------------ > >> >> > Join us December 9, 2009 for the Red Hat Virtual Experience, > >> >> > a free event focused on virtualization and cloud computing. > >> >> > Attend in-depth sessions from your desk. Your couch. Anywhere. > >> >> > http://p.sf.net/sfu/redhat-sfdev2dev > >> >> > _______________________________________________ > >> >> > Ecell-devel mailing list > >> >> > Ece...@li... > >> >> > https://lists.sourceforge.net/lists/listinfo/ecell-devel > >> >> > > >> >> > > >> > > >> > > > > > > |
|
From: Moriyoshi K. <mo...@sf...> - 2009-12-09 01:48:32
|
Seems weird. The HEAD is 3606 so it is most likely that you haven't got your local repository up-to-date. -- moriyoshi On Tue, Dec 8, 2009 at 8:02 PM, Michele Mattioni <mat...@eb...> wrote: > Yep, > the failure is from the svn code: > > mattions@triton:ecell-3.1(master)$ git svn info > Path: . > URL: > http://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/branches/ecell-3.1 > Repository Root: http://ecell.svn.sourceforge.net/svnroot/ecell > Repository UUID: f1531174-cb10-0410-9fe6-89aa7ac3eedb > Revision: 3464 > Node Kind: directory > Schedule: normal > Last Changed Author: moriyoshi > Last Changed Rev: 3464 > Last Changed Date: 2009-04-29 15:27:07 +0100 (Wed, 29 Apr 2009) > > (Using git bridge to svn...) > > On Tue, Dec 8, 2009 at 10:57 AM, Moriyoshi Koizumi <mo...@sf...> > wrote: >> >> Hi, >> >> This should have been fixed at some point. Did you get this when you >> were trying to use the svn version instead of 3.1.107? >> >> -- moriyoshi >> >> >> >> On Tue, Dec 8, 2009 at 7:50 PM, Michele Mattioni <mat...@eb...> >> wrote: >> > Hi Moriyoshi, >> > >> > I've managed to compile the version (1.107), commenting the >> > Gillespie.hpp >> > >> > When I try to compile the code from the svn I hit a libtool problem >> > which I >> > don't really understand. >> > >> > I use the .autogen/sh >> > ./configure >> > make >> > >> > process >> > >> > mattions@triton:ecell-3.1(master)$ make >> > make all-recursive >> > make[1]: Entering directory >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1' >> > Making all in libltdl >> > make[2]: Entering directory >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' >> > make all-am >> > make[3]: Entering directory >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' >> > /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H >> > -I. -g -O2 -c -o ltdl.lo ltdl.c >> > ./libtool: line 463: CDPATH: command not found >> > ./libtool: line 1141: func_opt_split: command not found >> > libtool: Version mismatch error. This is libtool 2.2.6 >> > Debian-2.2.6a-4, >> > but the >> > libtool: definition of this LT_INIT comes from an older release. >> > libtool: You should recreate aclocal.m4 with macros from libtool >> > 2.2.6 >> > Debian-2.2.6a-4 >> > libtool: and run autoconf again. >> > make[3]: *** [ltdl.lo] Error 63 >> > make[3]: Leaving directory >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' >> > make[2]: *** [all] Error 2 >> > make[2]: Leaving directory >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' >> > make[1]: *** [all-recursive] Error 1 >> > make[1]: Leaving directory >> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1' >> > make: *** [all] Error 2 >> > >> > BTW, >> > thanks for Ecell. It's awesome. >> > >> > On Mon, Dec 7, 2009 at 10:29 AM, Moriyoshi Koizumi <mo...@sf...> >> > wrote: >> >> >> >> Hi, >> >> >> >> This is due to an *inappropriate* change in the recent glibc that >> >> defines "getc" as a preprocessor macro in place of a weak alias to the >> >> actual function name. You can checkout the latest source code from >> >> the ecell's subversion repository which already includes workaround >> >> for this problem (plus several crucial fixes). >> >> >> >> >> >> http://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/branches/ecell-3.1 >> >> >> >> -- moriyoshi >> >> >> >> >> >> >> >> On Mon, Dec 7, 2009 at 6:50 PM, Michele Mattioni <mat...@eb...> >> >> wrote: >> >> > Hello ecell-3 devs, >> >> > >> >> > I'm trying to compile the final version of Ecell-3 (1.107) on a >> >> > Ubuntu >> >> > Karmic (9.10) and unfortunaly the compilation fail: >> >> > >> >> > cc -fPIC -g -O2 -g -O2 -Wno-pmf-conversions -g -O2 >> >> > -Wno-pmf-conversions >> >> > -D_ECELL3_DM_CLASSNAME= >> >> > GillespieProcess -I/usr/include -I../libecs -I../.. -I.. >> >> > -I../../libltdl >> >> > -I/usr/include/python2.6 -c GillespieProcess.cpp -o >> >> > GillespieProcess.o >> >> > In file included from GillespieProcess.cpp:28: >> >> > GillespieProcess.hpp: In static member function ‘static void >> >> > >> >> > GillespieProcess::initializePropertyInterface(libecs::Type2Type<TT>)’: >> >> > GillespieProcess.hpp:59: error: ‘getc’ is not a member of >> >> > ‘GillespieProcess’ >> >> > GillespieProcess.hpp:59: error: ‘getc’ is not a member of >> >> > ‘GillespieProcess’ >> >> > dmcompile: failed to compile the specified source files: >> >> > CompileError(DistutilsExecError("command 'cc' failed with exit status >> >> > 1",),) >> >> > ecell3-dmc: ../../dmtool/dmcompile returned error status: 1 >> >> > make[4]: *** [GillespieProcess.so] Error 1 >> >> > make[4]: Leaving directory >> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell/dm' >> >> > make[3]: *** [all-recursive] Error 1 >> >> > make[3]: Leaving directory >> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell' >> >> > make[2]: *** [all] Error 2 >> >> > make[2]: Leaving directory >> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell' >> >> > make[1]: *** [all-recursive] Error 1 >> >> > make[1]: Leaving directory >> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107' >> >> > make: *** [all] Error 2 >> >> > >> >> > The problem seems to be the line 59 of the >> >> > ecell/dm/GillespieProcess.hpp >> >> > file, which is: >> >> > >> >> > PROPERTYSLOT_GET_NO_LOAD_SAVE( Real, c ); >> >> > >> >> > Any suggestions? >> >> > >> >> > (Are you thinking to provide deb package for karmic? (maybe using >> >> > launchpad... :) ) >> >> > >> >> > Regards, >> >> > Michele Mattioni >> >> > >> >> > >> >> > >> >> > ------------------------------------------------------------------------------ >> >> > Join us December 9, 2009 for the Red Hat Virtual Experience, >> >> > a free event focused on virtualization and cloud computing. >> >> > Attend in-depth sessions from your desk. Your couch. Anywhere. >> >> > http://p.sf.net/sfu/redhat-sfdev2dev >> >> > _______________________________________________ >> >> > Ecell-devel mailing list >> >> > Ece...@li... >> >> > https://lists.sourceforge.net/lists/listinfo/ecell-devel >> >> > >> >> > >> > >> > > > |
|
From: Michele M. <mat...@eb...> - 2009-12-08 11:02:33
|
Yep,
the failure is from the svn code:
mattions@triton:ecell-3.1(master)$ git svn info
Path: .
URL:
http://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/branches/ecell-3.1
Repository Root: http://ecell.svn.sourceforge.net/svnroot/ecell
Repository UUID: f1531174-cb10-0410-9fe6-89aa7ac3eedb
Revision: 3464
Node Kind: directory
Schedule: normal
Last Changed Author: moriyoshi
Last Changed Rev: 3464
Last Changed Date: 2009-04-29 15:27:07 +0100 (Wed, 29 Apr 2009)
(Using git bridge to svn...)
On Tue, Dec 8, 2009 at 10:57 AM, Moriyoshi Koizumi <mo...@sf...>wrote:
> Hi,
>
> This should have been fixed at some point. Did you get this when you
> were trying to use the svn version instead of 3.1.107?
>
> -- moriyoshi
>
>
>
> On Tue, Dec 8, 2009 at 7:50 PM, Michele Mattioni <mat...@eb...>
> wrote:
> > Hi Moriyoshi,
> >
> > I've managed to compile the version (1.107), commenting the Gillespie.hpp
> >
> > When I try to compile the code from the svn I hit a libtool problem which
> I
> > don't really understand.
> >
> > I use the .autogen/sh
> > ./configure
> > make
> >
> > process
> >
> > mattions@triton:ecell-3.1(master)$ make
> > make all-recursive
> > make[1]: Entering directory
> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1'
> > Making all in libltdl
> > make[2]: Entering directory
> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl'
> > make all-am
> > make[3]: Entering directory
> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl'
> > /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
> > -I. -g -O2 -c -o ltdl.lo ltdl.c
> > ./libtool: line 463: CDPATH: command not found
> > ./libtool: line 1141: func_opt_split: command not found
> > libtool: Version mismatch error. This is libtool 2.2.6
> Debian-2.2.6a-4,
> > but the
> > libtool: definition of this LT_INIT comes from an older release.
> > libtool: You should recreate aclocal.m4 with macros from libtool
> 2.2.6
> > Debian-2.2.6a-4
> > libtool: and run autoconf again.
> > make[3]: *** [ltdl.lo] Error 63
> > make[3]: Leaving directory
> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl'
> > make[2]: *** [all] Error 2
> > make[2]: Leaving directory
> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl'
> > make[1]: *** [all-recursive] Error 1
> > make[1]: Leaving directory
> > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1'
> > make: *** [all] Error 2
> >
> > BTW,
> > thanks for Ecell. It's awesome.
> >
> > On Mon, Dec 7, 2009 at 10:29 AM, Moriyoshi Koizumi <mo...@sf...>
> > wrote:
> >>
> >> Hi,
> >>
> >> This is due to an *inappropriate* change in the recent glibc that
> >> defines "getc" as a preprocessor macro in place of a weak alias to the
> >> actual function name. You can checkout the latest source code from
> >> the ecell's subversion repository which already includes workaround
> >> for this problem (plus several crucial fixes).
> >>
> >>
> http://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/branches/ecell-3.1
> >>
> >> -- moriyoshi
> >>
> >>
> >>
> >> On Mon, Dec 7, 2009 at 6:50 PM, Michele Mattioni <mat...@eb...>
> >> wrote:
> >> > Hello ecell-3 devs,
> >> >
> >> > I'm trying to compile the final version of Ecell-3 (1.107) on a
> Ubuntu
> >> > Karmic (9.10) and unfortunaly the compilation fail:
> >> >
> >> > cc -fPIC -g -O2 -g -O2 -Wno-pmf-conversions -g -O2
> >> > -Wno-pmf-conversions
> >> > -D_ECELL3_DM_CLASSNAME=
> >> > GillespieProcess -I/usr/include -I../libecs -I../.. -I..
> -I../../libltdl
> >> > -I/usr/include/python2.6 -c GillespieProcess.cpp -o GillespieProcess.o
> >> > In file included from GillespieProcess.cpp:28:
> >> > GillespieProcess.hpp: In static member function ‘static void
> >> > GillespieProcess::initializePropertyInterface(libecs::Type2Type<TT>)’:
> >> > GillespieProcess.hpp:59: error: ‘getc’ is not a member of
> >> > ‘GillespieProcess’
> >> > GillespieProcess.hpp:59: error: ‘getc’ is not a member of
> >> > ‘GillespieProcess’
> >> > dmcompile: failed to compile the specified source files:
> >> > CompileError(DistutilsExecError("command 'cc' failed with exit status
> >> > 1",),)
> >> > ecell3-dmc: ../../dmtool/dmcompile returned error status: 1
> >> > make[4]: *** [GillespieProcess.so] Error 1
> >> > make[4]: Leaving directory
> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell/dm'
> >> > make[3]: *** [all-recursive] Error 1
> >> > make[3]: Leaving directory
> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell'
> >> > make[2]: *** [all] Error 2
> >> > make[2]: Leaving directory
> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell'
> >> > make[1]: *** [all-recursive] Error 1
> >> > make[1]: Leaving directory
> >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107'
> >> > make: *** [all] Error 2
> >> >
> >> > The problem seems to be the line 59 of the
> ecell/dm/GillespieProcess.hpp
> >> > file, which is:
> >> >
> >> > PROPERTYSLOT_GET_NO_LOAD_SAVE( Real, c );
> >> >
> >> > Any suggestions?
> >> >
> >> > (Are you thinking to provide deb package for karmic? (maybe using
> >> > launchpad... :) )
> >> >
> >> > Regards,
> >> > Michele Mattioni
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------------
> >> > Join us December 9, 2009 for the Red Hat Virtual Experience,
> >> > a free event focused on virtualization and cloud computing.
> >> > Attend in-depth sessions from your desk. Your couch. Anywhere.
> >> > http://p.sf.net/sfu/redhat-sfdev2dev
> >> > _______________________________________________
> >> > Ecell-devel mailing list
> >> > Ece...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/ecell-devel
> >> >
> >> >
> >
> >
>
|
|
From: Moriyoshi K. <mo...@sf...> - 2009-12-08 10:57:30
|
Hi, This should have been fixed at some point. Did you get this when you were trying to use the svn version instead of 3.1.107? -- moriyoshi On Tue, Dec 8, 2009 at 7:50 PM, Michele Mattioni <mat...@eb...> wrote: > Hi Moriyoshi, > > I've managed to compile the version (1.107), commenting the Gillespie.hpp > > When I try to compile the code from the svn I hit a libtool problem which I > don't really understand. > > I use the .autogen/sh > ./configure > make > > process > > mattions@triton:ecell-3.1(master)$ make > make all-recursive > make[1]: Entering directory > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1' > Making all in libltdl > make[2]: Entering directory > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' > make all-am > make[3]: Entering directory > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' > /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H > -I. -g -O2 -c -o ltdl.lo ltdl.c > ./libtool: line 463: CDPATH: command not found > ./libtool: line 1141: func_opt_split: command not found > libtool: Version mismatch error. This is libtool 2.2.6 Debian-2.2.6a-4, > but the > libtool: definition of this LT_INIT comes from an older release. > libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6 > Debian-2.2.6a-4 > libtool: and run autoconf again. > make[3]: *** [ltdl.lo] Error 63 > make[3]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' > make[2]: *** [all] Error 2 > make[2]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1' > make: *** [all] Error 2 > > BTW, > thanks for Ecell. It's awesome. > > On Mon, Dec 7, 2009 at 10:29 AM, Moriyoshi Koizumi <mo...@sf...> > wrote: >> >> Hi, >> >> This is due to an *inappropriate* change in the recent glibc that >> defines "getc" as a preprocessor macro in place of a weak alias to the >> actual function name. You can checkout the latest source code from >> the ecell's subversion repository which already includes workaround >> for this problem (plus several crucial fixes). >> >> http://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/branches/ecell-3.1 >> >> -- moriyoshi >> >> >> >> On Mon, Dec 7, 2009 at 6:50 PM, Michele Mattioni <mat...@eb...> >> wrote: >> > Hello ecell-3 devs, >> > >> > I'm trying to compile the final version of Ecell-3 (1.107) on a Ubuntu >> > Karmic (9.10) and unfortunaly the compilation fail: >> > >> > cc -fPIC -g -O2 -g -O2 -Wno-pmf-conversions -g -O2 >> > -Wno-pmf-conversions >> > -D_ECELL3_DM_CLASSNAME= >> > GillespieProcess -I/usr/include -I../libecs -I../.. -I.. -I../../libltdl >> > -I/usr/include/python2.6 -c GillespieProcess.cpp -o GillespieProcess.o >> > In file included from GillespieProcess.cpp:28: >> > GillespieProcess.hpp: In static member function ‘static void >> > GillespieProcess::initializePropertyInterface(libecs::Type2Type<TT>)’: >> > GillespieProcess.hpp:59: error: ‘getc’ is not a member of >> > ‘GillespieProcess’ >> > GillespieProcess.hpp:59: error: ‘getc’ is not a member of >> > ‘GillespieProcess’ >> > dmcompile: failed to compile the specified source files: >> > CompileError(DistutilsExecError("command 'cc' failed with exit status >> > 1",),) >> > ecell3-dmc: ../../dmtool/dmcompile returned error status: 1 >> > make[4]: *** [GillespieProcess.so] Error 1 >> > make[4]: Leaving directory >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell/dm' >> > make[3]: *** [all-recursive] Error 1 >> > make[3]: Leaving directory >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell' >> > make[2]: *** [all] Error 2 >> > make[2]: Leaving directory >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell' >> > make[1]: *** [all-recursive] Error 1 >> > make[1]: Leaving directory >> > `/home/mattions/Work/progs/ecell/ecell-3.1.107' >> > make: *** [all] Error 2 >> > >> > The problem seems to be the line 59 of the ecell/dm/GillespieProcess.hpp >> > file, which is: >> > >> > PROPERTYSLOT_GET_NO_LOAD_SAVE( Real, c ); >> > >> > Any suggestions? >> > >> > (Are you thinking to provide deb package for karmic? (maybe using >> > launchpad... :) ) >> > >> > Regards, >> > Michele Mattioni >> > >> > >> > ------------------------------------------------------------------------------ >> > Join us December 9, 2009 for the Red Hat Virtual Experience, >> > a free event focused on virtualization and cloud computing. >> > Attend in-depth sessions from your desk. Your couch. Anywhere. >> > http://p.sf.net/sfu/redhat-sfdev2dev >> > _______________________________________________ >> > Ecell-devel mailing list >> > Ece...@li... >> > https://lists.sourceforge.net/lists/listinfo/ecell-devel >> > >> > > > |
|
From: Michele M. <mat...@eb...> - 2009-12-08 10:50:50
|
Hi Moriyoshi,
I've managed to compile the version (1.107), commenting the Gillespie.hpp
When I try to compile the code from the svn I hit a libtool problem which I
don't really understand.
I use the .autogen/sh
./configure
make
process
mattions@triton:ecell-3.1(master)$ make
make all-recursive
make[1]: Entering directory
`/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1'
Making all in libltdl
make[2]: Entering directory
`/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl'
make all-am
make[3]: Entering directory
`/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl'
/bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -g -O2 -c -o ltdl.lo ltdl.c
./libtool: line 463: CDPATH: command not found
./libtool: line 1141: func_opt_split: command not found
libtool: Version mismatch error. This is libtool 2.2.6 Debian-2.2.6a-4,
but the
libtool: definition of this LT_INIT comes from an older release.
libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6
Debian-2.2.6a-4
libtool: and run autoconf again.
make[3]: *** [ltdl.lo] Error 63
make[3]: Leaving directory
`/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl'
make[2]: *** [all] Error 2
make[2]: Leaving directory
`/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1/libltdl'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/home/mattions/Work/progs/ecell/ecell3/branches/ecell-3.1'
make: *** [all] Error 2
BTW,
thanks for Ecell. It's awesome.
On Mon, Dec 7, 2009 at 10:29 AM, Moriyoshi Koizumi <mo...@sf...>wrote:
> Hi,
>
> This is due to an *inappropriate* change in the recent glibc that
> defines "getc" as a preprocessor macro in place of a weak alias to the
> actual function name. You can checkout the latest source code from
> the ecell's subversion repository which already includes workaround
> for this problem (plus several crucial fixes).
>
> http://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/branches/ecell-3.1
>
> -- moriyoshi
>
>
>
> On Mon, Dec 7, 2009 at 6:50 PM, Michele Mattioni <mat...@eb...>
> wrote:
> > Hello ecell-3 devs,
> >
> > I'm trying to compile the final version of Ecell-3 (1.107) on a Ubuntu
> > Karmic (9.10) and unfortunaly the compilation fail:
> >
> > cc -fPIC -g -O2 -g -O2 -Wno-pmf-conversions -g -O2
> -Wno-pmf-conversions
> > -D_ECELL3_DM_CLASSNAME=
> > GillespieProcess -I/usr/include -I../libecs -I../.. -I.. -I../../libltdl
> > -I/usr/include/python2.6 -c GillespieProcess.cpp -o GillespieProcess.o
> > In file included from GillespieProcess.cpp:28:
> > GillespieProcess.hpp: In static member function ‘static void
> > GillespieProcess::initializePropertyInterface(libecs::Type2Type<TT>)’:
> > GillespieProcess.hpp:59: error: ‘getc’ is not a member of
> > ‘GillespieProcess’
> > GillespieProcess.hpp:59: error: ‘getc’ is not a member of
> > ‘GillespieProcess’
> > dmcompile: failed to compile the specified source files:
> > CompileError(DistutilsExecError("command 'cc' failed with exit status
> 1",),)
> > ecell3-dmc: ../../dmtool/dmcompile returned error status: 1
> > make[4]: *** [GillespieProcess.so] Error 1
> > make[4]: Leaving directory
> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell/dm'
> > make[3]: *** [all-recursive] Error 1
> > make[3]: Leaving directory
> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell'
> > make[2]: *** [all] Error 2
> > make[2]: Leaving directory
> > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell'
> > make[1]: *** [all-recursive] Error 1
> > make[1]: Leaving directory
> > `/home/mattions/Work/progs/ecell/ecell-3.1.107'
> > make: *** [all] Error 2
> >
> > The problem seems to be the line 59 of the ecell/dm/GillespieProcess.hpp
> > file, which is:
> >
> > PROPERTYSLOT_GET_NO_LOAD_SAVE( Real, c );
> >
> > Any suggestions?
> >
> > (Are you thinking to provide deb package for karmic? (maybe using
> > launchpad... :) )
> >
> > Regards,
> > Michele Mattioni
> >
> >
> ------------------------------------------------------------------------------
> > Join us December 9, 2009 for the Red Hat Virtual Experience,
> > a free event focused on virtualization and cloud computing.
> > Attend in-depth sessions from your desk. Your couch. Anywhere.
> > http://p.sf.net/sfu/redhat-sfdev2dev
> > _______________________________________________
> > Ecell-devel mailing list
> > Ece...@li...
> > https://lists.sourceforge.net/lists/listinfo/ecell-devel
> >
> >
>
|
|
From: Moriyoshi K. <mo...@sf...> - 2009-12-07 10:29:38
|
Hi, This is due to an *inappropriate* change in the recent glibc that defines "getc" as a preprocessor macro in place of a weak alias to the actual function name. You can checkout the latest source code from the ecell's subversion repository which already includes workaround for this problem (plus several crucial fixes). http://ecell.svn.sourceforge.net/svnroot/ecell/ecell3/branches/ecell-3.1 -- moriyoshi On Mon, Dec 7, 2009 at 6:50 PM, Michele Mattioni <mat...@eb...> wrote: > Hello ecell-3 devs, > > I'm trying to compile the final version of Ecell-3 (1.107) on a Ubuntu > Karmic (9.10) and unfortunaly the compilation fail: > > cc -fPIC -g -O2 -g -O2 -Wno-pmf-conversions -g -O2 -Wno-pmf-conversions > -D_ECELL3_DM_CLASSNAME= > GillespieProcess -I/usr/include -I../libecs -I../.. -I.. -I../../libltdl > -I/usr/include/python2.6 -c GillespieProcess.cpp -o GillespieProcess.o > In file included from GillespieProcess.cpp:28: > GillespieProcess.hpp: In static member function ‘static void > GillespieProcess::initializePropertyInterface(libecs::Type2Type<TT>)’: > GillespieProcess.hpp:59: error: ‘getc’ is not a member of > ‘GillespieProcess’ > GillespieProcess.hpp:59: error: ‘getc’ is not a member of > ‘GillespieProcess’ > dmcompile: failed to compile the specified source files: > CompileError(DistutilsExecError("command 'cc' failed with exit status 1",),) > ecell3-dmc: ../../dmtool/dmcompile returned error status: 1 > make[4]: *** [GillespieProcess.so] Error 1 > make[4]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell/dm' > make[3]: *** [all-recursive] Error 1 > make[3]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell' > make[2]: *** [all] Error 2 > make[2]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory > `/home/mattions/Work/progs/ecell/ecell-3.1.107' > make: *** [all] Error 2 > > The problem seems to be the line 59 of the ecell/dm/GillespieProcess.hpp > file, which is: > > PROPERTYSLOT_GET_NO_LOAD_SAVE( Real, c ); > > Any suggestions? > > (Are you thinking to provide deb package for karmic? (maybe using > launchpad... :) ) > > Regards, > Michele Mattioni > > ------------------------------------------------------------------------------ > Join us December 9, 2009 for the Red Hat Virtual Experience, > a free event focused on virtualization and cloud computing. > Attend in-depth sessions from your desk. Your couch. Anywhere. > http://p.sf.net/sfu/redhat-sfdev2dev > _______________________________________________ > Ecell-devel mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-devel > > |
|
From: Michele M. <mat...@eb...> - 2009-12-07 09:50:26
|
Hello ecell-3 devs,
I'm trying to compile the final version of Ecell-3 (1.107) on a Ubuntu
Karmic (9.10) and unfortunaly the compilation fail:
cc -fPIC -g -O2 -g -O2 -Wno-pmf-conversions -g -O2 -Wno-pmf-conversions
-D_ECELL3_DM_CLASSNAME=
GillespieProcess -I/usr/include -I../libecs -I../.. -I.. -I../../libltdl
-I/usr/include/python2.6 -c GillespieProcess.cpp -o GillespieProcess.o
In file included from GillespieProcess.cpp:28:
GillespieProcess.hpp: In static member function ‘static void
GillespieProcess::initializePropertyInterface(libecs::Type2Type<TT>)’:
GillespieProcess.hpp:59: error: ‘getc’ is not a member of
‘GillespieProcess’
GillespieProcess.hpp:59: error: ‘getc’ is not a member of
‘GillespieProcess’
dmcompile: failed to compile the specified source files:
CompileError(DistutilsExecError("command 'cc' failed with exit status 1",),)
ecell3-dmc: ../../dmtool/dmcompile returned error status: 1
make[4]: *** [GillespieProcess.so] Error 1
make[4]: Leaving directory
`/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell/dm'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell'
make[2]: *** [all] Error 2
make[2]: Leaving directory
`/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/home/mattions/Work/progs/ecell/ecell-3.1.107'
make: *** [all] Error 2
The problem seems to be the line 59 of the ecell/dm/GillespieProcess.hpp
file, which is:
PROPERTYSLOT_GET_NO_LOAD_SAVE( Real, c );
Any suggestions?
(Are you thinking to provide deb package for karmic? (maybe using
launchpad... :) )
Regards,
Michele Mattioni
|
|
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
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> _______________________________________________
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>
|
|
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
|
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