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

[Michele M. <mat...@eb...>]

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
> >
> >
>