Hi, I found other build issues: In file included from ./filetrans.h:16, from ./filetrans.cpp:10: ./appconfig.h:63:1: warning: "PACKAGE_NAME" redefined In file included from ./filetrans.h:13, from ./filetrans.cpp:10: /usr/local/include/ghemical/libconfig.h:71:1: warning: this is the location of the previous definition I think that including a *config.h file in headers is generally a very bad idea and should be done only if absolutely necessary. If necessary (seems it is the case for some files), it is possible to use a solution like the one used in openbabel: AM_CONFIG_HEADER(src/config.h) ... AC_CONFIG_COMMANDS([src/libconfig.h], [cat src/config.h | grep -v PACKAGE >src/libconfig.h]) and add #include <config.h> in cpp files when the PACKAGE* variables are needed (i.e. nowhere in libghemical). When compiling ghemical on an amd64, I get lot of messages like this one: ./project.cpp:2804: warning: cast from pointer to integer of different size. This MUST be fixed. It is quite unsafe. If you try to convert the 32 bits int back to a pointer, you will probably have crashes (it will occur if the object is on the stack). I also think you should use openbabel-2 for gchemical-2. I can help with that if needed. Best regards, Jean