Hello,
It looks like the compilation is working but when you are trying to run
the program from the command line it is picking a v1 PYTHONPATH instead of
the v2 one. Is there a bin/analysis? If so, does that mention 1.0 or 2.0
inside it? And if it mentions 2.0, what happens if you run it?
Wayne
On Mon, 18 Aug 2008, Jo Claridge wrote:
> Hi,
>
> I am having trouble installing v2 of analysis, I get some odd compilation messages even
> after copying the ccpnmr1.0 environment.txt and using that.
>
> below is a print out from the terminal window.
>
> ######################################################
>
> Create environment file (y or n) (answer y unless you know otherwise)? n
> cd memops/global; make
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math utility.c
> gcc -c -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math python_util.c
> python_util.c: In function ‘valid_py_object’:
> python_util.c:54: warning: passing argument 1 of ‘equal_strings’ discards qualifiers from
> pointer target type
> python_util.c:54: warning: passing argument 2 of ‘equal_strings’ discards qualifiers from
> pointer target type
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math hash_list.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math hash_table.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math mem_cache.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math mutex.c
> gcc -c -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math py_mem_cache.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math block_file.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math int_array.c
> gcc -c -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math py_block_file.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> BlockFile.so utility.o python_util.o hash_list.o hash_table.o mem_cache.o mutex.o
> py_mem_cache.o block_file.o int_array.o py_block_file.o
> gcc -c -DNEED_GLUT_INIT -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -
> I/sw/include -I/usr/X11R6/include -I/sw/include -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-
> common -ffast-math gl_handler.c
> gcc -c -DUSE_GL_TRUE -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -
> I/sw/include -I/usr/X11R6/include -I/sw/include -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-
> common -ffast-math py_gl_handler.c
> gcc -c -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -I/sw/include -O3 -
> DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math py_tk_util.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math w32func.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> GlHandler.so -L/usr/X11R6/lib -L/sw/lib -L/sw/lib -L/usr/X11R6/lib -L/sw/lib \
> utility.o python_util.o gl_handler.o py_gl_handler.o py_tk_util.o w32func.o -
> lfreeglut -lGLU -lGL -ltk -ltcl -lX11 -lXext -lm
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> MemCache.so utility.o python_util.o hash_list.o hash_table.o mem_cache.o mutex.o
> py_mem_cache.o
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math pdf_handler.c
> gcc -c -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math py_pdf_handler.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> PdfHandler.so \
> utility.o python_util.o pdf_handler.o py_pdf_handler.o
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math ps_handler.c
> gcc -c -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math py_ps_handler.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> PsHandler.so \
> utility.o python_util.o ps_handler.o py_ps_handler.o
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math fit.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math gamma.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math gauss_jordan.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math line_fit.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math nonlinear_model.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math random.c
> gcc -c -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math py_fit.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> FitMethod.so fit.o gamma.o gauss_jordan.o line_fit.o nonlinear_model.o random.o utility.o
> python_util.o py_fit.o
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math color.c
> gcc -c -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -I/sw/include -O3 -
> DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math tk_handler.c
> gcc -c -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -I/sw/include -O3 -
> DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math py_tk_handler.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> TkHandler.so -L/sw/lib -L/usr/X11R6/lib \
> utility.o python_util.o color.o tk_handler.o py_tk_handler.o py_tk_util.o
> w32func.o -ltk -lX11 -lXext
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math store_file.c
> gcc -c -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math py_store_file.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> StoreFile.so \
> utility.o python_util.o store_file.o py_store_file.o
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math store_handler.c
> gcc -c -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math py_store_handler.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> StoreHandler.so \
> utility.o python_util.o store_handler.o py_store_handler.o
> cd ccp/structure; make
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math atom.c
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math bond.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_atom.c
> cd ../../memops/global; make py_util_objects
> make[2]: Nothing to be done for `py_util_objects'.
> cd ../../memops/global; make color_objects
> make[2]: Nothing to be done for `color_objects'.
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> StructAtom.so \
> atom.o bond.o py_atom.o ../../memops/global/python_util.o
> ../../memops/global/utility.o ../../memops/global/color.o
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_bond.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> StructBond.so \
> atom.o bond.o py_atom.o py_bond.o ../../memops/global/python_util.o
> ../../memops/global/utility.o ../../memops/global/color.o
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math structure.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -
> I/sw/include -I/usr/X11R6/include -I/sw/include -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-
> common -ffast-math py_structure.c
> cd ../../memops/global; make sorts_objects
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math sorts.c
> cd ../../memops/global; make geometry_objects
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math geometry.c
> cd ../../memops/global; make py_drawing_objects
> gcc -c -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -I/sw/include -
> I/usr/X11R6/include -I/sw/include -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -
> ffast-math py_draw_handler.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> StructStructure.so -L/usr/X11R6/lib -L/sw/lib -L/sw/lib -L/usr/X11R6/lib -L/sw/lib \
> atom.o bond.o py_atom.o py_bond.o structure.o py_structure.o
> ../../memops/global/python_util.o ../../memops/global/utility.o
> ../../memops/global/color.o \
> ../../memops/global/sorts.o ../../memops/global/geometry.o
> ../../memops/global/gl_handler.o ../../memops/global/pdf_handler.o
> ../../memops/global/ps_handler.o ../../memops/global/store_handler.o
> ../../memops/global/tk_handler.o ../../memops/global/w32func.o
> ../../memops/global/py_draw_handler.o ../../memops/global/py_gl_handler.o
> ../../memops/global/py_pdf_handler.o ../../memops/global/py_ps_handler.o
> ../../memops/global/py_store_handler.o ../../memops/global/py_tk_handler.o
> ../../memops/global/py_tk_util.o -lfreeglut -lGLU -lGL -ltk -ltcl -lX11 -lXext -lm
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math struct_util.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_struct_util.c
> cd ../../memops/global; make linalg_objects
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math eigenvalue.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math linalg.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> StructUtil.so \
> struct_util.o py_struct_util.o ../../memops/global/python_util.o
> ../../memops/global/utility.o \
> ../../memops/global/geometry.o ../../memops/global/eigenvalue.o
> ../../memops/global/linalg.o
> cd ccpnmr/analysis; make
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math contour_data.c
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math contour_levels.c
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math contour_style.c
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math contour_file.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -
> I/sw/include -I/usr/X11R6/include -I/sw/include -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-
> common -ffast-math py_contour_levels.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -
> I/sw/include -I/usr/X11R6/include -I/sw/include -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-
> common -ffast-math py_contour_style.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -
> I/sw/include -I/usr/X11R6/include -I/sw/include -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-
> common -ffast-math py_contour_file.c
> cd ../../memops/global; make py_block_file_objects
> make[2]: Nothing to be done for `py_block_file_objects'.
> cd ../../memops/global; make py_store_file_objects
> make[2]: Nothing to be done for `py_store_file_objects'.
> cd ../../memops/global; make contour_objects
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math contourer.c
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math list.c
> cd ../../memops/global; make py_drawing_objects
> make[2]: Nothing to be done for `py_drawing_objects'.
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> ContourFile.so -L/usr/X11R6/lib -L/sw/lib -L/sw/lib -L/usr/X11R6/lib -L/sw/lib \
> contour_data.o contour_levels.o contour_style.o contour_file.o
> py_contour_levels.o py_contour_style.o py_contour_file.o
> ../../memops/global/python_util.o ../../memops/global/utility.o
> ../../memops/global/hash_list.o ../../memops/global/hash_table.o
> ../../memops/global/mem_cache.o ../../memops/global/mutex.o
> ../../memops/global/py_mem_cache.o ../../memops/global/block_file.o
> ../../memops/global/int_array.o ../../memops/global/py_block_file.o \
> ../../memops/global/store_file.o ../../memops/global/py_store_file.o \
> ../../memops/global/contourer.o ../../memops/global/list.o
> ../../memops/global/gl_handler.o ../../memops/global/pdf_handler.o
> ../../memops/global/ps_handler.o ../../memops/global/store_handler.o
> ../../memops/global/tk_handler.o ../../memops/global/w32func.o
> ../../memops/global/py_draw_handler.o ../../memops/global/py_gl_handler.o
> ../../memops/global/py_pdf_handler.o ../../memops/global/py_ps_handler.o
> ../../memops/global/py_store_handler.o ../../memops/global/py_tk_handler.o
> ../../memops/global/py_tk_util.o -lfreeglut -lGLU -lGL -ltk -ltcl -lX11 -lXext -lm
> cd ../../memops/global; make py_mem_cache_objects
> make[2]: Nothing to be done for `py_mem_cache_objects'.
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> ContourStyle.so \
> contour_style.o py_contour_style.o ../../memops/global/python_util.o
> ../../memops/global/utility.o ../../memops/global/hash_list.o
> ../../memops/global/hash_table.o ../../memops/global/mem_cache.o
> ../../memops/global/mutex.o ../../memops/global/py_mem_cache.o
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> ContourLevels.so \
> contour_levels.o py_contour_levels.o ../../memops/global/python_util.o
> ../../memops/global/utility.o ../../memops/global/hash_list.o
> ../../memops/global/hash_table.o ../../memops/global/mem_cache.o
> ../../memops/global/mutex.o ../../memops/global/py_mem_cache.o
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math method.c
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math peak.c
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math peak_list.c
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math symbol.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_peak.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_peak_list.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> PeakList.so \
> method.o peak.o peak_list.o symbol.o py_peak.o py_peak_list.o
> ../../memops/global/python_util.o ../../memops/global/utility.o
> ../../memops/global/hash_list.o ../../memops/global/hash_table.o
> ../../memops/global/mem_cache.o ../../memops/global/mutex.o
> ../../memops/global/py_mem_cache.o ../../memops/global/block_file.o
> ../../memops/global/int_array.o ../../memops/global/py_block_file.o -lm
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math slice_file.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -
> I/sw/include -I/usr/X11R6/include -I/sw/include -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-
> common -ffast-math py_slice_file.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> SliceFile.so -L/usr/X11R6/lib -L/sw/lib -L/sw/lib -L/usr/X11R6/lib -L/sw/lib \
> slice_file.o py_slice_file.o ../../memops/global/python_util.o
> ../../memops/global/utility.o ../../memops/global/hash_list.o
> ../../memops/global/hash_table.o ../../memops/global/mem_cache.o
> ../../memops/global/mutex.o ../../memops/global/py_mem_cache.o
> ../../memops/global/block_file.o ../../memops/global/int_array.o
> ../../memops/global/py_block_file.o \
> ../../memops/global/gl_handler.o ../../memops/global/pdf_handler.o
> ../../memops/global/ps_handler.o ../../memops/global/store_handler.o
> ../../memops/global/tk_handler.o ../../memops/global/w32func.o
> ../../memops/global/py_draw_handler.o ../../memops/global/py_gl_handler.o
> ../../memops/global/py_pdf_handler.o ../../memops/global/py_ps_handler.o
> ../../memops/global/py_store_handler.o ../../memops/global/py_tk_handler.o
> ../../memops/global/py_tk_util.o -lfreeglut -lGLU -lGL -ltk -ltcl -lX11 -lXext -lm
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math win_peak_list.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -I/usr/X11R6/include -I/sw/include -
> I/sw/include -I/usr/X11R6/include -I/sw/include -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-
> common -ffast-math py_win_peak_list.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> WinPeakList.so -L/usr/X11R6/lib -L/sw/lib -L/sw/lib -L/usr/X11R6/lib -L/sw/lib \
> method.o peak.o peak_list.o symbol.o win_peak_list.o py_peak.o
> py_peak_list.o py_win_peak_list.o ../../memops/global/python_util.o
> ../../memops/global/utility.o ../../memops/global/hash_list.o
> ../../memops/global/hash_table.o ../../memops/global/mem_cache.o
> ../../memops/global/mutex.o ../../memops/global/py_mem_cache.o
> ../../memops/global/block_file.o ../../memops/global/int_array.o
> ../../memops/global/py_block_file.o \
> ../../memops/global/gl_handler.o ../../memops/global/pdf_handler.o
> ../../memops/global/ps_handler.o ../../memops/global/store_handler.o
> ../../memops/global/tk_handler.o ../../memops/global/w32func.o
> ../../memops/global/py_draw_handler.o ../../memops/global/py_gl_handler.o
> ../../memops/global/py_pdf_handler.o ../../memops/global/py_ps_handler.o
> ../../memops/global/py_store_handler.o ../../memops/global/py_tk_handler.o
> ../../memops/global/py_tk_util.o -lfreeglut -lGLU -lGL -ltk -ltcl -lX11 -lXext -lm
> cd ccpnmr/clouds; make
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math atom_coord.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_atom_coord.c
> cd ../../memops/global; make py_util_objects
> make[2]: Nothing to be done for `py_util_objects'.
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> AtomCoord.so atom_coord.o py_atom_coord.o ../../memops/global/python_util.o
> ../../memops/global/utility.o
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math atom_coord_list.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_atom_coord_list.c
> py_atom_coord_list.c:316: warning: initialization from incompatible pointer type
> py_atom_coord_list.c:319: warning: initialization from incompatible pointer type
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> AtomCoordList.so atom_coord.o py_atom_coord.o atom_coord_list.o
> py_atom_coord_list.o ../../memops/global/python_util.o ../../memops/global/utility.o
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math dist_force.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_dist_force.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> DistForce.so dist_force.o py_dist_force.o ../../memops/global/python_util.o
> ../../memops/global/utility.o
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math dist_constraint.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_dist_constraint.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> DistConstraint.so dist_constraint.o py_dist_constraint.o ../../memops/global/python_util.o
> ../../memops/global/utility.o
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math dist_constraint_list.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_dist_constraint_list.c
> py_dist_constraint_list.c:321: warning: initialization from incompatible pointer type
> py_dist_constraint_list.c:324: warning: initialization from incompatible pointer type
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> DistConstraintList.so dist_constraint.o py_dist_constraint.o dist_constraint_list.o
> py_dist_constraint_list.o ../../memops/global/python_util.o ../../memops/global/utility.o
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math dynamics.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_dynamics.c
> cd ../../memops/global; make random_objects
> make[2]: Nothing to be done for `random_objects'.
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> Dynamics.so atom_coord.o atom_coord_list.o dist_constraint.o dist_constraint_list.o
> dist_force.o dynamics.o py_atom_coord.o py_atom_coord_list.o py_dist_constraint.o
> py_dist_constraint_list.o py_dist_force.o py_dynamics.o \
> ../../memops/global/python_util.o ../../memops/global/utility.o
> ../../memops/global/random.o -lm
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math midge.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_midge.c
> cd ../../memops/global; make diag_objects
> gcc -c -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-math diag_dbl.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> Midge.so midge.o py_midge.o \
> ../../memops/global/python_util.o ../../memops/global/utility.o
> ../../memops/global/diag_dbl.o -lm
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_cloud_util.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> CloudUtil.so py_cloud_util.o -lm
> gcc -c -I../../memops/global -O3 -DDO_NOT_HAVE_MALLOC -fPIC -fno-common -ffast-
> math bacus.c
> gcc -c -I../../memops/global -I/sw/include/python2.5 -O3 -DDO_NOT_HAVE_MALLOC -fPIC
> -fno-common -ffast-math py_bacus.c
> gcc -L/sw/lib -bundle -bundle_loader /sw/bin/python2.5 "-Wl,-
> dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dyli
> b:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -o
> Bacus.so bacus.o py_bacus.o \
> ../../memops/global/python_util.o ../../memops/global/utility.o -lm
> rm: *.so: No such file or directory
> rm: *.so: No such file or directory
> rm: *.so: No such file or directory
>
> #######################################################
>
> the program does not start so I tried running AnalysisGui.py from the command line and
> got this:
>
> Traceback (most recent call last):
> File "AnalysisGui.py", line 70, in <module>
> from memops.general.Io import loadProject
> ImportError: cannot import name loadProject
>
> I notice there are some memops related problems in the compilation process...
> This happens on both my OS X box and a Linux box.
>
> cheers,
> Jo Claridge
>
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