[ghemical-devel] new releases
Jean Bréfort
jean.brefort at free.fr
Sat Jul 2 04:29:20 EDT 2005
Le vendredi 01 juillet 2005 à 22:45 +0300, Tommi Hassinen a écrit :
> On Fri, 1 Jul 2005, Heinz Hemken wrote:
>
> > Is there an "easy" way to set up 1.90 and the options other than
> > downloading from CVS? I would really like to avoid compiling it! Are
> > there linux x86 binaries?
>
> No need to use CVS anymore ; you should be able to download the sources
> here:
>
> http://www.uku.fi/~thassine/ghemical/download.html
>
> or here:
>
> http://bioinformatics.org/ghemical/download.html
>
> Unfortunately there are no binaries yet. I hope we could build them soon.
> I only have Debian boxes here now.
>
> Compiling the 1.90 version should not be harder than before, now you just
> need to know the order in which the packages are to be installed. I
> suggest an order
>
> mopac7-1.00 (optional)
> openbabel-1.100.2 (optional)
> libghemical-1.90
> ghemical-1.90
>
> to get a similar feature set than the 1.0x series used to have by default.
> But now please remember that mopac7 and openbabel are optional and you can
> leave them out if you wish ; please see the updated INSTALL files at
> libghemical and ghemical source trees for more information.
>
I encountered a problem while compiling mopac7-1.00 on a gentoo amd64
machine. configure runs fine, but make calls autoconf and al. (seems
that configure.ac is more recent than configurea and Makefile.in older
than aclocal.m4, and apparently other such reverse order) and this
fails:
*************************************************************
checking for correct ltmain.sh version... no
*** Gentoo sanity check failed! ***
*** libtool.m4 and ltmain.sh have a version mismatch! ***
*** (libtool.m4 = 1.5.18, ltmain.sh = 1.5.6) ***
Please run:
libtoolize --copy --force
if appropriate, please contact the maintainer of this
package (or your distribution) for help.
*************************************************************
Running libtoolize fixed the problem.
Same problem with libghemical-1.90.
ghemical-1.90 did not configure:configure:
*************************************************************
error: The pkg-config script could not be found or is too old. Make sure it
is in your PATH or set the PKG_CONFIG environment variable to the full
path to pkg-config.
Alternatively you may set the GTK_CFLAGS and GTK_LIBS environment variables
to avoid the need to call pkg-config. See the pkg-config man page for
more details.
To get pkg-config, see <http://www.freedesktop.org/software/pkgconfig>.
See `config.log' for more details.
*************************************************************
I have pkg-config 0.17.2. config.log was not helpful. I had to set the PKG_CONFIG variable to /usr/bin/pkg-config (/usr/bin is in my path) to make it work.
This seems quite mysterious.
Then compilation failed, because of a protected member (gcc is 3.4.4).
Here come the error messages:
In file included from /home/jean/sources/installs/ghemical-1.90/src/project.h:13,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/home/jean/sources/installs/ghemical-1.90/src/appconfig.h:63:1: warning: "PACKAGE_NAME" redefined
In file included from /usr/local/include/ghemical/v3d.h:13,
from /usr/local/include/ghemical/seqbuild.h:33,
from /usr/local/include/ghemical/model.h:39,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:19,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/usr/local/include/ghemical/libconfig.h:71:1: warning: this is the location of the previous definition
In file included from /home/jean/sources/installs/ghemical-1.90/src/project.h:13,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/home/jean/sources/installs/ghemical-1.90/src/appconfig.h:66:1: warning: "PACKAGE_STRING" redefined
In file included from /usr/local/include/ghemical/v3d.h:13,
from /usr/local/include/ghemical/seqbuild.h:33,
from /usr/local/include/ghemical/model.h:39,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:19,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/usr/local/include/ghemical/libconfig.h:74:1: warning: this is the location of the previous definition
In file included from /home/jean/sources/installs/ghemical-1.90/src/project.h:13,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/home/jean/sources/installs/ghemical-1.90/src/appconfig.h:69:1: warning: "PACKAGE_TARNAME" redefined
In file included from /usr/local/include/ghemical/v3d.h:13,
from /usr/local/include/ghemical/seqbuild.h:33,
from /usr/local/include/ghemical/model.h:39,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:19,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/usr/local/include/ghemical/libconfig.h:77:1: warning: this is the location of the previous definition
In file included from /home/jean/sources/installs/ghemical-1.90/src/views.h:13,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:48,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/home/jean/sources/installs/ghemical-1.90/src/appconfig.h:63:1: warning: "PACKAGE_NAME" redefined
In file included from /usr/local/include/ghemical/eng1_sf.h:13,
from /usr/local/include/ghemical/moldyn.h:26,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:43,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/usr/local/include/ghemical/libconfig.h:71:1: warning: this is the location of the previous definition
In file included from /home/jean/sources/installs/ghemical-1.90/src/views.h:13,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:48,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/home/jean/sources/installs/ghemical-1.90/src/appconfig.h:66:1: warning: "PACKAGE_STRING" redefined
In file included from /usr/local/include/ghemical/eng1_sf.h:13,
from /usr/local/include/ghemical/moldyn.h:26,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:43,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/usr/local/include/ghemical/libconfig.h:74:1: warning: this is the location of the previous definition
In file included from /home/jean/sources/installs/ghemical-1.90/src/views.h:13,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:48,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/home/jean/sources/installs/ghemical-1.90/src/appconfig.h:69:1: warning: "PACKAGE_TARNAME" redefined
In file included from /usr/local/include/ghemical/eng1_sf.h:13,
from /usr/local/include/ghemical/moldyn.h:26,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:43,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/usr/local/include/ghemical/libconfig.h:77:1: warning: this is the location of the previous definition
In file included from /home/jean/sources/installs/ghemical-1.90/src/camera.h:32,
from /home/jean/sources/installs/ghemical-1.90/src/mtools.h:41,
from /home/jean/sources/installs/ghemical-1.90/src/views.h:39,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:48,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/home/jean/sources/installs/ghemical-1.90/src/objects.h:92: error: `obj_loc_data* dummy_object::GetLocDataRW() const' is protected
/home/jean/sources/installs/ghemical-1.90/src/objects.h:179: error: within this context
In file included from /home/jean/sources/installs/ghemical-1.90/src/filetrans.h:16,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:50,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/home/jean/sources/installs/ghemical-1.90/src/appconfig.h:63:1: warning: "PACKAGE_NAME" redefined
In file included from /home/jean/sources/installs/ghemical-1.90/src/filetrans.h:13,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:50,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/usr/local/include/ghemical/libconfig.h:71:1: warning: this is the location of the previous definition
In file included from /home/jean/sources/installs/ghemical-1.90/src/filetrans.h:16,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:50,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/home/jean/sources/installs/ghemical-1.90/src/appconfig.h:66:1: warning: "PACKAGE_STRING" redefined
In file included from /home/jean/sources/installs/ghemical-1.90/src/filetrans.h:13,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:50,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/usr/local/include/ghemical/libconfig.h:74:1: warning: this is the location of the previous definition
In file included from /home/jean/sources/installs/ghemical-1.90/src/filetrans.h:16,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:50,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/home/jean/sources/installs/ghemical-1.90/src/appconfig.h:69:1: warning: "PACKAGE_TARNAME" redefined
In file included from /home/jean/sources/installs/ghemical-1.90/src/filetrans.h:13,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:50,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/usr/local/include/ghemical/libconfig.h:77:1: warning: this is the location of the previous definition
In file included from /usr/local/include/openbabel/mol.h:51,
from /home/jean/sources/installs/ghemical-1.90/src/filetrans.h:26,
from /home/jean/sources/installs/ghemical-1.90/src/project.h:50,
from /home/jean/sources/installs/ghemical-1.90/src/gtk_project.h:21,
from ./trajview_dialog.h:16,
from ./trajview_dialog.cpp:10:
/usr/local/include/openbabel/data.h: In constructor `OpenBabel::OBElement::OBElement(int, const char*, double, double, double, int, double, double)':
/usr/local/include/openbabel/data.h:102: warning: `OpenBabel::OBElement::_maxbonds' will be initialized after
/usr/local/include/openbabel/data.h:101: warning: `double OpenBabel::OBElement::_mass'
/usr/local/include/openbabel/data.h:109: warning: when initialized here
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.4/include/g++-v3/backward/strstream:51,
from ./trajview_dialog.cpp:13:
/usr/lib/gcc/x86_64-pc-linux-gnu/3.4.4/include/g++-v3/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
./trajview_dialog.cpp: In static member function `static void trajview_dialog::handler_Destroy(GtkWidget*, void*)':
./trajview_dialog.cpp:47: warning: unused variable 'ref'
make[1]: *** [trajview_dialog.o] Error 1
make: *** [all] Error 1
Even after I removed the protected flag, compilation failed in filetrans.cpp because I installed openbabel 2.0.0b2-20050701, but this is more an openbabel problem than a ghemical problem
Best regards,
Jean
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