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

[Moriyoshi K. <mo...@sf...>]

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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>
>