Thread: [Ecell-devel] Failure compiling Ecell-3 on Ubuntu Karmic

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Brought to you by: kozo2, moriyoshi, shafi

ecell-devel

[Ecell-devel] Failure compiling Ecell-3 on Ubuntu Karmic

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

Re: [Ecell-devel] Failure compiling Ecell-3 on Ubuntu Karmic

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
>
>

Re: [Ecell-devel] Failure compiling Ecell-3 on Ubuntu Karmic

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
> >
> >
>

Re: [Ecell-devel] Failure compiling Ecell-3 on Ubuntu Karmic

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
>> >
>> >
>
>

Re: [Ecell-devel] Failure compiling Ecell-3 on Ubuntu Karmic

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
> >> >
> >> >
> >
> >
>

Re: [Ecell-devel] Failure compiling Ecell-3 on Ubuntu Karmic

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
>> >> >
>> >> >
>> >
>> >
>
>

Re: [Ecell-devel] Failure compiling Ecell-3 on Ubuntu Karmic

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
> >> >> >
> >> >> >
> >> >
> >> >
> >
> >
>