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

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

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
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------------
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> >> >
> >> >
> >
> >
>