[MINC-users] Problem building Display

Tanweer Rashid trash001 at odu.edu
Fri Mar 2 13:12:18 EST 2012 

Hi,

I did have two minc2 libs, but I removed one of them, and after that, this
is what we're seeing...


trash001 at ubuntu:~/Desktop/hassemlal-Display-305f573Build$ make clean
trash001 at ubuntu:~/Desktop/hassemlal-Display-305f573Build$ make VERBOSE=1
/usr/bin/cmake -H/home/trash001/Desktop/hassemlal-Display-305f573
-B/home/trash001/Desktop/hassemlal-Display-305f573Build
--check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start
/home/trash001/Desktop/hassemlal-Display-305f573Build/CMakeFiles
/home/trash001/Desktop/hassemlal-Display-305f573Build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory
`/home/trash001/Desktop/hassemlal-Display-305f573Build'
make -f CMakeFiles/Display.dir/build.make CMakeFiles/Display.dir/depend
make[2]: Entering directory
`/home/trash001/Desktop/hassemlal-Display-305f573Build'
cd /home/trash001/Desktop/hassemlal-Display-305f573Build && /usr/bin/cmake
-E cmake_depends "Unix Makefiles"
/home/trash001/Desktop/hassemlal-Display-305f573
/home/trash001/Desktop/hassemlal-Display-305f573
/home/trash001/Desktop/hassemlal-Display-305f573Build
/home/trash001/Desktop/hassemlal-Display-305f573Build
/home/trash001/Desktop/hassemlal-Display-305f573Build/CMakeFiles/Display.dir/DependInfo.cmake
--color=
make[2]: Leaving directory
`/home/trash001/Desktop/hassemlal-Display-305f573Build'
make -f CMakeFiles/Display.dir/build.make CMakeFiles/Display.dir/build
make[2]: Entering directory
`/home/trash001/Desktop/hassemlal-Display-305f573Build'
/usr/bin/cmake -E cmake_progress_report
/home/trash001/Desktop/hassemlal-Display-305f573Build/CMakeFiles
[  0%] Building C object CMakeFiles/Display.dir/atlas/atlas.c.o
/usr/bin/gcc  -DMINC2
-I/home/trash001/Desktop/hassemlal-Display-305f573Build
-I/home/trash001/Desktop/hassemlal-Display-305f573/Graphics/OpenGL_graphics/Include
-I/home/trash001/Desktop/hassemlal-Display-305f573/Graphics/Include
-I/home/trash001/Desktop/hassemlal-Display-305f573/Graphics/GLUT_windows/Include
-I/home/trash001/Desktop/hassemlal-Display-305f573/Include
-I/usr/local/include    -o CMakeFiles/Display.dir/atlas/atlas.c.o   -c
/home/trash001/Desktop/hassemlal-Display-305f573/atlas/atlas.c
/usr/bin/cmake -E cmake_progress_report
/home/trash001/Desktop/hassemlal-Display-305f573Build/CMakeFiles 1

...

[100%] Building C object CMakeFiles/Display.dir/dummy.c.o
/usr/bin/gcc  -DMINC2
-I/home/trash001/Desktop/hassemlal-Display-305f573Build
-I/home/trash001/Desktop/hassemlal-Display-305f573/Graphics/OpenGL_graphics/Include
-I/home/trash001/Desktop/hassemlal-Display-305f573/Graphics/Include
-I/home/trash001/Desktop/hassemlal-Display-305f573/Graphics/GLUT_windows/Include
-I/home/trash001/Desktop/hassemlal-Display-305f573/Include
-I/usr/local/include    -o CMakeFiles/Display.dir/dummy.c.o   -c
/home/trash001/Desktop/hassemlal-Display-305f573/dummy.c
Linking C executable Display
/usr/bin/cmake -E cmake_link_script CMakeFiles/Display.dir/link.txt
--verbose=1
/usr/bin/gcc      CMakeFiles/Display.dir/atlas/atlas.c.o
CMakeFiles/Display.dir/input_files/input_files.c.o
CMakeFiles/Display.dir/input_files/volume_file.c.o
CMakeFiles/Display.dir/tubes/convert_lines.c.o
CMakeFiles/Display.dir/callbacks/volume_ops.c.o
CMakeFiles/Display.dir/callbacks/surf_segmenting.c.o
CMakeFiles/Display.dir/callbacks/file.c.o
CMakeFiles/Display.dir/callbacks/view_ops.c.o
CMakeFiles/Display.dir/callbacks/regions.c.o
CMakeFiles/Display.dir/callbacks/polygon_ops.c.o
CMakeFiles/Display.dir/callbacks/surface_curves.c.o
CMakeFiles/Display.dir/callbacks/call_globals.c.o
CMakeFiles/Display.dir/callbacks/quit.c.o
CMakeFiles/Display.dir/callbacks/marker_ops.c.o
CMakeFiles/Display.dir/callbacks/colour_coding.c.o
CMakeFiles/Display.dir/callbacks/render_ops.c.o
CMakeFiles/Display.dir/callbacks/segmenting.c.o
CMakeFiles/Display.dir/callbacks/atlas.c.o
CMakeFiles/Display.dir/callbacks/object_ops.c.o
CMakeFiles/Display.dir/callbacks/surface_extract.c.o
CMakeFiles/Display.dir/callbacks/line_ops.c.o
CMakeFiles/Display.dir/callbacks/volume_transform_ops.c.o
CMakeFiles/Display.dir/callbacks/georges.c.o
CMakeFiles/Display.dir/main/event_loop.c.o
CMakeFiles/Display.dir/main/transforms.c.o
CMakeFiles/Display.dir/main/three_d.c.o
CMakeFiles/Display.dir/main/graphics.c.o
CMakeFiles/Display.dir/main/display.c.o
CMakeFiles/Display.dir/main/main.c.o
CMakeFiles/Display.dir/cursor_contours/contours.c.o
CMakeFiles/Display.dir/markers/markers.c.o
CMakeFiles/Display.dir/images/images.c.o
CMakeFiles/Display.dir/segmenting/segment_polygons.c.o
CMakeFiles/Display.dir/segmenting/painting.c.o
CMakeFiles/Display.dir/segmenting/segmenting.c.o
CMakeFiles/Display.dir/segmenting/cut_neighbours.c.o
CMakeFiles/Display.dir/menu/text.c.o
CMakeFiles/Display.dir/menu/build_menu.c.o
CMakeFiles/Display.dir/menu/selected.c.o
CMakeFiles/Display.dir/menu/cursor_pos.c.o
CMakeFiles/Display.dir/menu/input_menu.c.o
CMakeFiles/Display.dir/menu/menu.c.o
CMakeFiles/Display.dir/structures/fit_view.c.o
CMakeFiles/Display.dir/structures/action_table.c.o
CMakeFiles/Display.dir/structures/lights.c.o
CMakeFiles/Display.dir/structures/window.c.o
CMakeFiles/Display.dir/structures/render.c.o
CMakeFiles/Display.dir/structures/view.c.o
CMakeFiles/Display.dir/voxel_scan/scan_objects.c.o
CMakeFiles/Display.dir/surface_extraction/surface.c.o
CMakeFiles/Display.dir/surface_extraction/extract.c.o
CMakeFiles/Display.dir/surface_extraction/surface_events.c.o
CMakeFiles/Display.dir/surface_extraction/init_surface.c.o
CMakeFiles/Display.dir/surface_extraction/data_structs.c.o
CMakeFiles/Display.dir/surface_extraction/boundary_extraction.c.o
CMakeFiles/Display.dir/immediate_mode/draw_immed.c.o
CMakeFiles/Display.dir/cursor/cursor_icon.c.o
CMakeFiles/Display.dir/cursor/cursor.c.o
CMakeFiles/Display.dir/Graphics/G_graphics/event_loop.c.o
CMakeFiles/Display.dir/Graphics/G_graphics/lights.c.o
CMakeFiles/Display.dir/Graphics/G_graphics/draw_objects.c.o
CMakeFiles/Display.dir/Graphics/G_graphics/windows.c.o
CMakeFiles/Display.dir/Graphics/G_graphics/graphics_structs.c.o
CMakeFiles/Display.dir/Graphics/G_graphics/render.c.o
CMakeFiles/Display.dir/Graphics/G_graphics/draw.c.o
CMakeFiles/Display.dir/Graphics/G_graphics/view.c.o
CMakeFiles/Display.dir/Graphics/G_graphics/random_order.c.o
CMakeFiles/Display.dir/Graphics/GLUT_windows/glut_windows.c.o
CMakeFiles/Display.dir/Graphics/GLUT_windows/copy_x_colours.c.o
CMakeFiles/Display.dir/Graphics/dummy.c.o
CMakeFiles/Display.dir/Graphics/OpenGL_graphics/event_loop.c.o
CMakeFiles/Display.dir/Graphics/OpenGL_graphics/lights.c.o
CMakeFiles/Display.dir/Graphics/OpenGL_graphics/windows.c.o
CMakeFiles/Display.dir/Graphics/OpenGL_graphics/colour_def.c.o
CMakeFiles/Display.dir/Graphics/OpenGL_graphics/render.c.o
CMakeFiles/Display.dir/Graphics/OpenGL_graphics/draw.c.o
CMakeFiles/Display.dir/Graphics/OpenGL_graphics/view.c.o
CMakeFiles/Display.dir/edit_surface/segment.c.o
CMakeFiles/Display.dir/edit_surface/connected.c.o
CMakeFiles/Display.dir/edit_surface/edit.c.o
CMakeFiles/Display.dir/surface_curves/edge_distance.c.o
CMakeFiles/Display.dir/surface_curves/closest_line.c.o
CMakeFiles/Display.dir/surface_curves/events.c.o
CMakeFiles/Display.dir/current_obj/current_obj.c.o
CMakeFiles/Display.dir/intersect/ray_polygons.c.o
CMakeFiles/Display.dir/intersect/plane_polygons.c.o
CMakeFiles/Display.dir/events/mouse.c.o
CMakeFiles/Display.dir/events/utilities.c.o
CMakeFiles/Display.dir/events/clip_plane.c.o
CMakeFiles/Display.dir/events/rotate_slice.c.o
CMakeFiles/Display.dir/events/mouse_trans.c.o
CMakeFiles/Display.dir/events/magnify.c.o
CMakeFiles/Display.dir/events/change_markers.c.o
CMakeFiles/Display.dir/events/pick_object.c.o
CMakeFiles/Display.dir/events/virt_sb.c.o
CMakeFiles/Display.dir/events/pick_view.c.o
CMakeFiles/Display.dir/events/window_man.c.o
CMakeFiles/Display.dir/events/spaceball.c.o
CMakeFiles/Display.dir/events/film_loop.c.o
CMakeFiles/Display.dir/slice_window/slice_3d.c.o
CMakeFiles/Display.dir/slice_window/slice_events.c.o
CMakeFiles/Display.dir/slice_window/quadmesh.c.o
CMakeFiles/Display.dir/slice_window/pick_angle.c.o
CMakeFiles/Display.dir/slice_window/slice.c.o
CMakeFiles/Display.dir/slice_window/colour_coding.c.o
CMakeFiles/Display.dir/slice_window/crop.c.o
CMakeFiles/Display.dir/slice_window/histogram.c.o
CMakeFiles/Display.dir/slice_window/colour_bar.c.o
CMakeFiles/Display.dir/slice_window/undo.c.o
CMakeFiles/Display.dir/slice_window/draw_slice.c.o
CMakeFiles/Display.dir/slice_window/view.c.o
CMakeFiles/Display.dir/dummy.c.o  -o Display -rdynamic
/usr/local/lib/libminc2.so /usr/local/lib/libvolume_io2.so -lnetcdf
/usr/local/lib/libbicpl.a -lglut -lGL -Wl,-rpath,/usr/local/lib:
/usr/local/lib/libvolume_io2.so: undefined reference to `MI2dimdef'
/usr/local/lib/libvolume_io2.so: undefined reference to `miicv_get'
/usr/local/lib/libvolume_io2.so: undefined reference to `miattputdbl'
/usr/local/lib/libvolume_io2.so: undefined reference to `miicv_free'
/usr/local/lib/libvolume_io2.so: undefined reference to `MI2varinq'
/usr/local/lib/libvolume_io2.so: undefined reference to `miattgetstr'
/usr/local/lib/libvolume_io2.so: undefined reference to `miicv_put'
/usr/local/lib/libvolume_io2.so: undefined reference to `MI2attput'
/usr/local/lib/libvolume_io2.so: undefined reference to `miget_valid_range'
/usr/local/lib/libvolume_io2.so: undefined reference to
`micopy_all_var_values'
/usr/local/lib/libvolume_io2.so: undefined reference to `micopy_all_atts'
/usr/local/lib/libvolume_io2.so: undefined reference to `miicv_inqdbl'
/usr/local/lib/libvolume_io2.so: undefined reference to `miicv_detach'
/usr/local/lib/libvolume_io2.so: undefined reference to `MI2attinq'
/usr/local/lib/libvolume_io2.so: undefined reference to `mivarput'
/usr/local/lib/libvolume_io2.so: undefined reference to `miicv_setint'
/usr/local/lib/libvolume_io2.so: undefined reference to `MI2endef'
/usr/local/lib/libvolume_io2.so: undefined reference to `miicv_setdbl'
/usr/local/lib/libvolume_io2.so: undefined reference to `miattget'
/usr/local/lib/libvolume_io2.so: undefined reference to `miclose'
/usr/local/lib/libvolume_io2.so: undefined reference to `mivarput1'
/usr/local/lib/libvolume_io2.so: undefined reference to `MI2attdel'
/usr/local/lib/libvolume_io2.so: undefined reference to
`micreate_std_variable'
/usr/local/lib/libvolume_io2.so: undefined reference to `micreate'
/usr/local/lib/libvolume_io2.so: undefined reference to `miicv_setstr'
/usr/local/lib/libvolume_io2.so: undefined reference to `miattputstr'
/usr/local/lib/libvolume_io2.so: undefined reference to `MI2varid'
/usr/local/lib/libvolume_io2.so: undefined reference to `miicv_create'
/usr/local/lib/libvolume_io2.so: undefined reference to `micreate_tempfile'
/usr/local/lib/libvolume_io2.so: undefined reference to `miicv_attach'
/usr/local/lib/libvolume_io2.so: undefined reference to `mivarget'
/usr/local/lib/libvolume_io2.so: undefined reference to
`micopy_all_var_defs'
/usr/local/lib/libvolume_io2.so: undefined reference to `MI2diminq'
/usr/local/lib/libvolume_io2.so: undefined reference to `miset_valid_range'
/usr/local/lib/libvolume_io2.so: undefined reference to `miattget1'
/usr/local/lib/libvolume_io2.so: undefined reference to `miopen'
collect2: ld returned 1 exit status


Thank you for your help.

- - - Tanweer Rashid


On Thu, Mar 1, 2012 at 6:37 PM, Audette, Michel A. <maudette at odu.edu> wrote:

> Hi Haz-edine,
>
> I'll ask my student Tanweer to get in touch with you with this output.
>
> Thanks for your kind support.
>
> Michel
> Michel Audette, Ph.D.
> Assistant Professor,
> Department of Modeling, Simulation and Visualization Engineering,
> Old Dominion University,
> Norfolk, VA.
> ________________________________________
> From: minc-users-bounces at bic.mni.mcgill.ca [
> minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Haz-Edine Assemlal [
> assemlal at cim.mcgill.ca]
> Sent: Thursday, March 01, 2012 5:04 PM
> To: MINC users mailing list
> Subject: Re: [MINC-users] Problem building Display
>
> Hi Audette,
>
> This error is typical of incoherency between the header and the shared
> library. Maybe you have two MINC2 libraries (maybe headers only)
> installed in your system.
>
> Can you go the Display source directory and do:
> $ make clean
> $ make VERBOSE=1
>
> and send me the output.
>
> Thanks,
> Haz-Edine
>
>
> On Thu, 2012-03-01 at 16:21 -0500, Audette, Michel A. wrote:
> > Hi Haz-Edine,
> >
> > we're trying your solution, but we're having a build problem...
> > Linking C executable Display
> > /usr/local/lib/libvolume_io2.so: undefined reference to `MI2dimdef'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miicv_get'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miattputdbl'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miicv_free'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `MI2varinq'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miattgetstr'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miicv_put'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `MI2attput'
> > /usr/local/lib/libvolume_io2.so: undefined reference to
> `miget_valid_range'
> > /usr/local/lib/libvolume_io2.so: undefined reference to
> `micopy_all_var_values'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `micopy_all_atts'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miicv_inqdbl'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miicv_detach'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `MI2attinq'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `mivarput'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miicv_setint'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `MI2endef'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miicv_setdbl'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miattget'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miclose'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `mivarput1'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `MI2attdel'
> > /usr/local/lib/libvolume_io2.so: undefined reference to
> `micreate_std_variable'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `micreate'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miicv_setstr'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miattputstr'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `MI2varid'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miicv_create'
> > /usr/local/lib/libvolume_io2.so: undefined reference to
> `micreate_tempfile'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miicv_attach'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `mivarget'
> > /usr/local/lib/libvolume_io2.so: undefined reference to
> `micopy_all_var_defs'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `MI2diminq'
> > /usr/local/lib/libvolume_io2.so: undefined reference to
> `miset_valid_range'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miattget1'
> > /usr/local/lib/libvolume_io2.so: undefined reference to `miopen'
> > collect2: ld returned 1 exit status
> >
> > I've tried both static and shared minc2 libraries. We're using ccmake as
> follows...
> >
> >  MINC_INCLUDE_DIR                 /usr/local/include
> >  MINC_minc2_LIBRARY               /usr/local/lib/libminc2.a
> >  MINC_volume_io2_LIBRARY          /usr/local/lib/libvolume_io2.so
> >
> > Thanks for your kind support.
> >
> > Michel
> >
> > Michel Audette, Ph.D.
> > Assistant Professor,
> > Department of Modeling, Simulation and Visualization Engineering,
> > Old Dominion University,
> > Norfolk, VA.
> > ________________________________________
> > From: minc-users-bounces at bic.mni.mcgill.ca [
> minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Haz-Edine Assemlal [
> assemlal at cim.mcgill.ca]
> > Sent: Thursday, March 01, 2012 1:29 PM
> > To: MINC users mailing list
> > Subject: Re: [MINC-users] Problem building Display
> >
> > Hi,
> >
> > Alternatively, I've been working a bit on Display recently. You are
> > welcome give it a try. The latest version is using CMake in place of
> > autotools:
> >
> > https://github.com/hassemlal/Display/tags
> >
> > Haz-Edine
> >
> >
> >
> > On Fri, 2012-03-02 at 03:35 +1000, Andrew Janke wrote:
> > > On 29 February 2012 14:40, Claude LEPAGE <claude at bic.mni.mcgill.ca>
> wrote:
> > > > This is probably the known bug that Andrew and I know how to
> > > > fix but haven't taken the time to do so.
> > >
> > > Probably guilty as charged, but from what I can see this "bug" is not
> > > a bug in minc, it seems to be in libtool.
> > >
> > > I'd be very curious to know if running
> > >
> > >    $ libtoolize --automake --copy
> > >
> > > In the Display directory and then re-running:
> > >
> > >    $ ./autogen.sh
> > >
> > > and
> > >
> > >    $ ./configure --with-build-path=/usr/local/bic ...
> > >
> > > fixes things.
> > >
> > > ta
> > >
> > >
> > > a
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
> > --
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
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-- 
Tanweer Rashid
Graduate Teaching & Research Assistant
Department of Modeling, Simulation and Visualization Engineering
Old Dominion University

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