[AMBER] Undefined symbols: "___builtin___strcpy_chk" and more

From: Yu Chen <chen.hhmi.umbc.edu>
Date: Fri, 30 Apr 2010 10:10:44 -0400

Hi,

I am trying to recompile Amber10/AmberTools1.2 since we have upgraded from OS X leopard to Snow Leopard. While everything worked on Leopard, now it doesn't compile on Snow leopard. Any help is greatly appreciated!

System: OS X 10.6.2 with Xcode 3.2.2, Intel compiler 10.1.014, Amber 10, AmberTools 1.2:

"./configure_at icc" finished just fine. When I started "make -f Makefile_at", it gives out following errors:
#######################################################################
...
icc -c -wd117,177,266,880,1011 -DBINTRAJ -DSTAND_ALONE eval.c
icc -o ucpp mem.o nhash.o cpp.o lexer.o assert.o macro.o eval.o
Undefined symbols:
  "___builtin___strcpy_chk", referenced from:
      _handle_include in cpp.o
      _handle_include in cpp.o
      _stringify in macro.o
  "___builtin_object_size", referenced from:
      _sdup in mem.o
      _sdup in mem.o
      _sdup in mem.o
      _incmem in mem.o
      _incmem in mem.o
      _incmem in mem.o
      _internal_put in nhash.o
      _internal_put in nhash.o
      _internal_put in nhash.o
      _internal_put in nhash.o
      _internal_put in nhash.o
      _internal_put in nhash.o
      _internal_put in nhash.o
      _internal_put in nhash.o
      _internal_put in nhash.o
      _main in cpp.o
      _main in cpp.o
      _cpp in cpp.o
      _cpp in cpp.o
      _handle_cpp in cpp.o
      _handle_cpp in cpp.o
      _handle_cpp in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _enter_file in cpp.o
      _enter_file in cpp.o
      _handle_line in cpp.o
      _handle_line in cpp.o
      _handle_line in cpp.o
      _handle_line in cpp.o
      ___inline_memmove_chk in cpp.o
      _ucpp_compress_token_list in cpp.o
      _ucpp_compress_token_list in cpp.o
      _ucpp_compress_token_list in cpp.o
      _ucpp_handle_unassert in assert.o
      _ucpp_handle_unassert in assert.o
      _ucpp_handle_unassert in assert.o
      _destroy_assertion in assert.o
      _destroy_assertion in assert.o
      _destroy_assertion in assert.o
      _ucpp_handle_define in macro.o
      _ucpp_handle_define in macro.o
      _ucpp_handle_define in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _stringify in macro.o
      _stringify in macro.o
      _stringify in macro.o
      _init_macros in macro.o
      _init_macros in macro.o
      _init_macros in macro.o
      _init_macros in macro.o
      _init_macros in macro.o
      _init_macros in macro.o
  "___builtin___memmove_chk", referenced from:
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_line in cpp.o
      _handle_line in cpp.o
      ___inline_memmove_chk in cpp.o
      _ucpp_handle_unassert in assert.o
      _ucpp_handle_unassert in assert.o
      _destroy_assertion in assert.o
      _destroy_assertion in assert.o
  "___builtin___memcpy_chk", referenced from:
      _sdup in mem.o
      _incmem in mem.o
      _internal_put in nhash.o
      _internal_put in nhash.o
      _internal_put in nhash.o
      _handle_cpp in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _handle_include in cpp.o
      _ucpp_compress_token_list in cpp.o
      _ucpp_handle_define in macro.o
      _ucpp_handle_define in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _ucpp_substitute_macro in macro.o
      _init_macros in macro.o
      _init_macros in macro.o
      _init_macros in macro.o
      _init_macros in macro.o
  "___builtin___sprintf_chk", referenced from:
      _main in cpp.o
      _main in cpp.o
      _cpp in cpp.o
      _cpp in cpp.o
      _enter_file in cpp.o
      _enter_file in cpp.o
      _ucpp_substitute_macro in macro.o
ld: symbol(s) not found
make[1]: *** [ucpp] Error 1
make: *** [install] Error 2
##################################################################

I couldn't find any information related to this. Any helps are greatly appreciated!

Regards,
Chen


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Received on Fri Apr 30 2010 - 07:30:03 PDT
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