[MINC-users] build almost everything minc Makefile and git repository for EZminc

Mon Apr 4 21:44:40 EDT 2011

Hi Keaser
if you did something like this for vlad's Makefile:

make Display PREFIX=/usr/local/bic TEMP=$HOME/temp

then try this

cd $HOME/src/Display-1.5.0
./configure --prefix=/usr/local/bic --with-build-path=/usr/local/bic
--with-minc2 --with-x
make

(lots of screen output)

The last line for me is:
/bin/bash ./libtool --tag=CC   --mode=link gcc  -g -O2
-L/usr/local/bic/lib -o Display dummy.o main/main.o main/display.o
main/event_loop.o main/graphics.o main/three_d.o main/transforms.o
atlas/atlas.o input_files/input_files.o input_files/volume_file.o
callbacks/atlas.o callbacks/call_globals.o callbacks/colour_coding.o
callbacks/file.o callbacks/line_ops.o callbacks/object_ops.o
callbacks/marker_ops.o callbacks/polygon_ops.o callbacks/quit.o
callbacks/regions.o callbacks/render_ops.o callbacks/segmenting.o
callbacks/surf_segmenting.o callbacks/surface_curves.o
callbacks/surface_extract.o callbacks/view_ops.o
callbacks/volume_ops.o callbacks/volume_transform_ops.o
current_obj/current_obj.o edit_surface/connected.o edit_surface/edit.o
edit_surface/segment.o images/images.o markers/markers.o
surface_extraction/boundary_extraction.o
surface_extraction/data_structs.o surface_extraction/init_surface.o
surface_extraction/extract.o surface_extraction/surface.o
surface_extraction/surface_events.o voxel_scan/scan_objects.o
events/change_markers.o events/clip_plane.o events/film_loop.o
events/magnify.o events/mouse.o events/mouse_trans.o
events/pick_object.o events/pick_view.o events/rotate_slice.o
events/spaceball.o events/virt_sb.o events/window_man.o
events/utilities.o immediate_mode/draw_immed.o
intersect/ray_polygons.o intersect/plane_polygons.o cursor/cursor.o
cursor/cursor_icon.o menu/build_menu.o menu/cursor_pos.o menu/menu.o
menu/input_menu.o menu/selected.o menu/text.o
cursor_contours/contours.o segmenting/cut_neighbours.o
segmenting/painting.o segmenting/segmenting.o
segmenting/segment_polygons.o slice_window/colour_bar.o
slice_window/colour_coding.o slice_window/crop.o
slice_window/draw_slice.o slice_window/histogram.o
slice_window/pick_angle.o slice_window/quadmesh.o slice_window/slice.o
slice_window/slice_3d.o slice_window/slice_events.o
slice_window/undo.o slice_window/view.o surface_curves/closest_line.o
surface_curves/events.o surface_curves/edge_distance.o
tubes/convert_lines.o structures/action_table.o structures/fit_view.o
structures/lights.o structures/render.o structures/view.o
structures/window.o  Graphics/libbicgl.a -lGL  -lm -lGLU -lGL  -lm
-lglut  -lSM -lICE -lXmu -lXi  -lGLU -lGL  -lm  -lbicpl -lvolume_io2
-lminc2 -lhdf5 -lz -lnetcdf -lm -lm   -lbicpl -lvolume_io2 -lminc2
-lhdf5 -lz -lnetcdf -lm -lm

So you would just do:
gcc  -g -O2  -L/usr/local/bic/lib -o Display dummy.o main/main.o
main/display.o main/event_loop.o main/graphics.o main/three_d.o
main/transforms.o atlas/atlas.o input_files/input_files.o
input_files/volume_file.o callbacks/atlas.o callbacks/call_globals.o
callbacks/colour_coding.o callbacks/file.o callbacks/line_ops.o
callbacks/object_ops.o callbacks/marker_ops.o callbacks/polygon_ops.o
callbacks/quit.o callbacks/regions.o callbacks/render_ops.o
callbacks/segmenting.o callbacks/surf_segmenting.o
callbacks/surface_curves.o callbacks/surface_extract.o
callbacks/view_ops.o callbacks/volume_ops.o
callbacks/volume_transform_ops.o current_obj/current_obj.o
edit_surface/connected.o edit_surface/edit.o edit_surface/segment.o
images/images.o markers/markers.o
surface_extraction/boundary_extraction.o
surface_extraction/data_structs.o surface_extraction/init_surface.o
surface_extraction/extract.o surface_extraction/surface.o
surface_extraction/surface_events.o voxel_scan/scan_objects.o
events/change_markers.o events/clip_plane.o events/film_loop.o
events/magnify.o events/mouse.o events/mouse_trans.o
events/pick_object.o events/pick_view.o events/rotate_slice.o
events/spaceball.o events/virt_sb.o events/window_man.o
events/utilities.o immediate_mode/draw_immed.o
intersect/ray_polygons.o intersect/plane_polygons.o cursor/cursor.o
cursor/cursor_icon.o menu/build_menu.o menu/cursor_pos.o menu/menu.o
menu/input_menu.o menu/selected.o menu/text.o
cursor_contours/contours.o segmenting/cut_neighbours.o
segmenting/painting.o segmenting/segmenting.o
segmenting/segment_polygons.o slice_window/colour_bar.o
slice_window/colour_coding.o slice_window/crop.o
slice_window/draw_slice.o slice_window/histogram.o
slice_window/pick_angle.o slice_window/quadmesh.o slice_window/slice.o
slice_window/slice_3d.o slice_window/slice_events.o
slice_window/undo.o slice_window/view.o surface_curves/closest_line.o
surface_curves/events.o surface_curves/edge_distance.o
tubes/convert_lines.o structures/action_table.o structures/fit_view.o
structures/lights.o structures/render.o structures/view.o
structures/window.o  Graphics/libbicgl.a -lGL  -lm -lGLU -lGL  -lm
-lglut  -lSM -lICE -lXmu -lXi  -lGLU -lGL  -lm  -lbicpl -lvolume_io2
-lminc2 -lhdf5 -lz -lnetcdf -lm -lm   -lbicpl -lvolume_io2 -lminc2
-lhdf5 -lz -lnetcdf -lm -lm

Unfortunately, I still get an error and there is no executable
slice_window/crop.o: In function `crop_and_load_volume':
/home/mishkin/src/Display-1.5.0/slice_window/crop.c:165: warning: the
use of `tmpnam' is dangerous, better use `mkstemp'
/usr/local/bic/lib/libbicpl.a(rgb_io.o): In function `output_rgb_file':
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:95: undefined
reference to `ppm_writeppminit'
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:98: undefined
reference to `ppm_allocrow'
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:116: undefined
reference to `ppm_writeppmrow'
/usr/local/bic/lib/libbicpl.a(rgb_io.o): In function `input_rgb_file':
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:29: undefined
reference to `ppm_readppminit'
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:31: undefined
reference to `ppm_allocrow'
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:44: undefined
reference to `ppm_readppmrow'
collect2: ld returned 1 exit status

Maybe you will have better luck, or maybe the people much smarter than
me will be able to help you.

mishkin

On Mon, Apr 4, 2011 at 12:52 PM, Keaser, Michael L
<MKeaser at umaryland.edu> wrote:
> Andrew,
>
> I'm still having trouble installing Display.
>
> When you say "copy and paste the last line of the build (when Display is made) and then run it without the liibtool part", which specific "build" file are you referring to where we can make this edit?
>
> Thanks,
>
> Michael
>
> ________________________________________
> From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Andrew Janke [a.janke at gmail.com]
> Sent: Tuesday, March 29, 2011 8:16 AM
> To: MINC users mailing list
> Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc
>
> If this is the same "bug" that I have been bitten by it's to do with
> libtool and the way bicpl is linked (or not as the case often turns
> out to be) with libnetpbm.
>
> If you run make in the Display directory, copy and paste the last line
> of the build (when Display is made) and then run it without the
> libtool part.  turn
>
>   $ libtool <blah> gcc <blah>
>
> into
>
>   $ gcc <blah>
>
> and in most cases Display will be made.
>
> YMMV but this is what I have seen but haven't got to the bottom of yet.
>
> a
>
> On Tue, Mar 29, 2011 at 09:34, Mishkin Derakhshan <mishkind at gmail.com> wrote:
>> Then I tried debugging:
>> Inside the source dir of Display-1.5.0
>> ./configure --prefix=/usr/local/bic --with-build-path=/usr/local/bic
>> --with-minc2 --with-x
>> make
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>