fails to build due to missing H5cpp.h?

[atomoclast]

Hello all,

I'm trying to build these packages, but I'm getting an error on map_creator:

fatal error: H5Cpp.h: No such file or directory
compilation terminated.
make[2]: *** [CMakeFiles/hdf5_dataset.dir/src/hdf5_dataset.cpp.o] Error 1
make[1]: *** [CMakeFiles/hdf5_dataset.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
make: *** [all] Error 2
cd /home/andrew/.../build/map_creator; catkin build --get-env map_creator | catkin env -si  /usr/bin/make --jobserver-fds=6,7 -j; cd -

[jontromanab]

Hello @atomoclast ,

Have you tried installing hdf5 by

sudo apt-get install libhdf5-dev

I just realized the hdf5 library should be mentioned in CMakeLists.txt as a dependency. It will be included in the next PR. For now, it should work. Please let me know.

[atomoclast]

@jontromanab ,

Thank you for the prompt reply! I already have libhdf5-dev installed and it still fails for the same reason...

I am trying to build on ros kinetic on 16.04. That may be an issue?

[atomoclast]

I did read on this page that you need the H5C++ library...
http://askubuntu.com/questions/702145/c-header-files-for-hdf5-are-missing
I tried to build and it still failed....

Gonna try and build it from source...because it could be a version issue. What version of hdf5 lib are you using?
https://support.hdfgroup.org/HDF5/release/obtainsrc.html#src

[atomoclast]

So. I tried to build from source. The most recent release that is.

What version are you using? Gonna try and see if I can find the source for H5C++.

[jontromanab]

my version is 1.8.11
But I think the issue is because of Ubuntu version
Have you tried to build any other program using hdf5 ??
may be take a .h5 file and run h5dump and see the results

[atomoclast]

I think openRAVE uses hdf5. In their source, they're importing header files.

The issue is that it needs the H5Cpp.h. Which i tried to apt-get with

sudo apt-get install libhdf5-cpp-11

Still not working. So it could be a version thing or something I need to build from source.

[jontromanab]

Yes. Openrave uses hdf5. But that is hdf5py which can be installed separately.
Do you want me to write a sample code which uses hdf5cpp. You can run that and let me know if the sample program is also having problem.(it should be if it cannot find hdf5cpp)

Have you tried to build it from source?? Please try to build from source and let me know.

The most probable reason is that the ubuntu and ROS version. We have not imported reuleaux to ros kinetic yet. We are still in indigo. If you can import that you are most welcome.

[atomoclast]

So. I just build it with no issue on an indigo/14.04 machine. I'll look into why it doesn't build and fix it, then get back to you!

[geoffreychiou]

@atomoclast, A few months back I managed to get it to build on Kinetic with these changes:
https://github.com/ros-industrial-consortium/reuleaux/pull/28/files
I don't know if it still works but you might want to start there.

It was through trial and error so you may not need all of those changes.

[atomoclast]

@geoffreychiou

Looks like it's failing now. It did get farther, but still fails. I'm gonna look into it more. This is more of a side project right now between a few other priorities.

Anyways. The output I got is as follows:

Errors << map_creator:make /home/andrew/Development/openrave_ws/logs/map_creator/build.make.000.log CMakeFiles/create_reachability_map.dir/src/create_reachability_map.cpp.o: In function main':
create_reachability_map.cpp:(.text+0x288a): undefined reference to hdf5_dataset::Hdf5Dataset::Hdf5Dataset(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)' create_reachability_map.cpp:(.text+0x28cd): undefined reference to hdf5_dataset::Hdf5Dataset::saveReachMapsToDataset(std::multimap<std::vector<double, std::allocator > const*, std::vector<double, std::allocator > const*, std::less<std::vector<double, std::allocator > const*>, std::allocator<std::pair<std::vector<double, std::allocator > const* const, std::vector<double, std::allocator > const*> > >&, std::map<std::vector<double, std::allocator > const*, double, std::less<std::vector<double, std::allocator > const*>, std::allocator<std::pair<std::vector<double, std::allocator > const* const, double> > >&, float)'
collect2: error: ld returned 1 exit status
make[2]: *** [/home/andrew/Development/openrave_ws/devel/.private/map_creator/lib/map_creator/create_reachability_map] Error 1
make[1]: *** [CMakeFiles/create_reachability_map.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
CMakeFiles/create_capability_map.dir/src/create_capability_map.cpp.o: In function main': create_capability_map.cpp:(.text+0x3676): undefined reference to hdf5_dataset::Hdf5Dataset::Hdf5Dataset(std::__cxx11::basic_string<char, std::char_traits, std::allocator >)'
create_capability_map.cpp:(.text+0x36a5): undefined reference to hdf5_dataset::Hdf5Dataset::saveCapMapsToDataset(std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, float&)' collect2: error: ld returned 1 exit status make[2]: *** [/home/andrew/Development/openrave_ws/devel/.private/map_creator/lib/map_creator/create_capability_map] Error 1 make[1]: *** [CMakeFiles/create_capability_map.dir/all] Error 2 make: *** [all] Error 2

[geoffreychiou]

Do you have a fork of the repo I could take a look at?

[atomoclast]

@geoffreychiou, I can make and push one, but all I did was take the current master branch and just update the cmake files and package.xmls with the changes you showed me.

My forked changes are here: https://github.com/atomoclast/reuleaux/tree/kinetic-devel

[willcbaker]

tried using h5c++ compiler https://github.com/willcbaker/reuleaux/tree/feature/kinetic-devel; aborted compilation after 3 hrs and no errors printed to screen

[geoffreychiou]

@atomoclast, I believe you may have copied the files over directly instead of just pasting over the changes.

https://github.com/geoffreychiou/reuleaux/tree/kinetic-build
Here is my fork with the changes applied.

I was able to get your fork to build by adding hdf5_dataset to the target_link_libraries of create_reachability_map and create_capability_map in map_creator/CMakeLists.txt

Example:
Old:

target_link_libraries(create_reachability_map sphere_discretization kinematics -lhdf5 -lhdf5_cpp ${catkin_LIBRARIES})

target_link_libraries(create_capability_map sphere_discretization kinematics -lhdf5 -lhdf5_cpp ${catkin_LIBRARIES})

New:

target_link_libraries(create_reachability_map sphere_discretization kinematics -lhdf5 -lhdf5_cpp hdf5_dataset ${catkin_LIBRARIES})

target_link_libraries(create_capability_map sphere_discretization kinematics -lhdf5 -lhdf5_cpp hdf5_dataset ${catkin_LIBRARIES})

I have not tested if it actually runs correctly on kinetic.

[atomoclast]

@geoffreychiou

I just tested it. Everything but base_placement plugin builds on my end.

The error message i got was:

Errors << base_placement_plugin:make /home/andrew/Development/openrave_ws/logs/base_placement_plugin/build.make.000.log /home/andrew/Development/openrave_ws/src/reuleaux/base_placement_plugin/include/base_placement_plugin/point_tree_item.h:30: Note: No relevant classes found. No output generated. /home/andrew/Development/openrave_ws/src/reuleaux/base_placement_plugin/src/widgets/base_placement_widget.ui: Warning: Z-order assignment: 'horizontalSpacer' is not a valid widget. /usr/bin/ld: cannot find -lhdf5_dataset /usr/bin/ld: cannot find -lhdf5_dataset /usr/bin/ld: cannot find -lsphere_discretization /usr/bin/ld: cannot find -lkinematics /usr/bin/ld: cannot find -lhdf5_dataset /usr/bin/ld: cannot find -lsphere_discretization /usr/bin/ld: cannot find -lkinematics collect2: error: ld returned 1 exit status make[2]: *** [/home/andrew/Development/openrave_ws/devel/.private/base_placement_plugin/lib/libbase_placement_plugin.so] Error 1 make[1]: *** [CMakeFiles/base_placement_plugin.dir/all] Error 2 make: *** [all] Error 2

[jontromanab]

@atomoclast are your sphere_discretization, kinematics and hdf5_Dataset libraries properly built from map_creator package? Have tried creating any maps and visualizing them in rviz?

It looks I have to create a kinetic branch to replicate the problems. (It is fine in indigo so far)
I am installing kinetic now. May be can tell you the results by tomorrow.

[geoffreychiou]

@atomoclast, Have you tried doing a clean build?

If you have, push your latest changes to your git and let me see if I can replicate.

[jontromanab]

@atomoclast have you been able to solve the problem of running reuleaux on Kinetic yet. Please let me know. I have not been able to find any computer to install kinetic yet. All my work is in indigo and and can't update it now. But if you have not solved it I can borrow a computer and install kinetic there and reproduce your problems.

[atomoclast]

Hi guys, sorry for the late reply. Let me look and see, then I'll let you guys know. I have it forked on my page right now. Will update in a few.

[atomoclast]

So. I made some changes to the package XML and CMakeLists.txt file, got really close. Seems like there's some issues with HDF5 or something related. I pushed my changes to my fork for you to look at. I can start to delve into some of the issues tomorrow maybe if you don't get a chance to look at it soon.

My fork and changes can be found: https://github.com/atomoclast/reuleaux/tree/kinetic-devel

[ 67%] Generating include/base_placement_plugin/moc_place_base.cxx
Scanning dependencies of target base_placement_plugin
[ 69%] Building CXX object reuleaux/base_placement_plugin/CMakeFiles/base_placement_plugin.dir/src/add_way_point.cpp.o
[ 70%] Building CXX object reuleaux/base_placement_plugin/CMakeFiles/base_placement_plugin.dir/src/point_tree_item.cpp.o
[ 72%] Building CXX object reuleaux/base_placement_plugin/CMakeFiles/base_placement_plugin.dir/src/point_tree_model.cpp.o
[ 74%] Linking CXX executable /home/andrew/Development/manip_ws/devel/lib/map_creator/create_capability_map
[ 75%] Linking CXX executable /home/andrew/Development/manip_ws/devel/lib/map_creator/create_inverse_reachability_map
[ 77%] Linking CXX executable /home/andrew/Development/manip_ws/devel/lib/map_creator/create_reachability_map
[ 79%] Building CXX object reuleaux/base_placement_plugin/CMakeFiles/base_placement_plugin.dir/src/widgets/base_placement_widget.cpp.o
[ 79%] Built target create_inverse_reachability_map
Scanning dependencies of target workspace_visualization
[ 80%] Building CXX object reuleaux/workspace_visualization/CMakeFiles/workspace_visualization.dir/src/reachability_map_visual.cpp.o
CMakeFiles/create_reachability_map.dir/src/create_reachability_map.cpp.o: In function `main':
create_reachability_map.cpp:(.text+0x288a): undefined reference to `hdf5_dataset::Hdf5Dataset::Hdf5Dataset(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
create_reachability_map.cpp:(.text+0x28cd): undefined reference to `hdf5_dataset::Hdf5Dataset::saveReachMapsToDataset(std::multimap<std::vector<double, std::allocator<double> > const*, std::vector<double, std::allocator<double> > const*, std::less<std::vector<double, std::allocator<double> > const*>, std::allocator<std::pair<std::vector<double, std::allocator<double> > const* const, std::vector<double, std::allocator<double> > const*> > >&, std::map<std::vector<double, std::allocator<double> > const*, double, std::less<std::vector<double, std::allocator<double> > const*>, std::allocator<std::pair<std::vector<double, std::allocator<double> > const* const, double> > >&, float)'
collect2: error: ld returned 1 exit status
reuleaux/map_creator/CMakeFiles/create_reachability_map.dir/build.make:326: recipe for target '/home/andrew/Development/manip_ws/devel/lib/map_creator/create_reachability_map' failed
make[2]: *** [/home/andrew/Development/manip_ws/devel/lib/map_creator/create_reachability_map] Error 1
CMakeFiles/Makefile2:2072: recipe for target 'reuleaux/map_creator/CMakeFiles/create_reachability_map.dir/all' failed
make[1]: *** [reuleaux/map_creator/CMakeFiles/create_reachability_map.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 82%] Building CXX object reuleaux/workspace_visualization/CMakeFiles/workspace_visualization.dir/src/reachability_map_display.cpp.o
CMakeFiles/create_capability_map.dir/src/create_capability_map.cpp.o: In function `main':
create_capability_map.cpp:(.text+0x3676): undefined reference to `hdf5_dataset::Hdf5Dataset::Hdf5Dataset(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
create_capability_map.cpp:(.text+0x36a5): undefined reference to `hdf5_dataset::Hdf5Dataset::saveCapMapsToDataset(std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, float&)'
collect2: error: ld returned 1 exit status
reuleaux/map_creator/CMakeFiles/create_capability_map.dir/build.make:326: recipe for target '/home/andrew/Development/manip_ws/devel/lib/map_creator/create_capability_map' failed
make[2]: *** [/home/andrew/Development/manip_ws/devel/lib/map_creator/create_capability_map] Error 1
CMakeFiles/Makefile2:682: recipe for target 'reuleaux/map_creator/CMakeFiles/create_capability_map.dir/all' failed
make[1]: *** [reuleaux/map_creator/CMakeFiles/create_capability_map.dir/all] Error 2
[ 83%] Building CXX object reuleaux/workspace_visualization/CMakeFiles/workspace_visualization.dir/src/capability_map_visual.cpp.o
[ 85%] Building CXX object reuleaux/workspace_visualization/CMakeFiles/workspace_visualization.dir/src/capability_map_display.cpp.o
[ 87%] Building CXX object reuleaux/workspace_visualization/CMakeFiles/workspace_visualization.dir/workspace_visualization_automoc.cpp.o
[ 88%] Building CXX object reuleaux/base_placement_plugin/CMakeFiles/base_placement_plugin.dir/src/place_base.cpp.o
[ 90%] Building CXX object reuleaux/base_placement_plugin/CMakeFiles/base_placement_plugin.dir/include/base_placement_plugin/moc_add_way_point.cxx.o
[ 91%] Building CXX object reuleaux/base_placement_plugin/CMakeFiles/base_placement_plugin.dir/include/base_placement_plugin/moc_point_tree_item.cxx.o
[ 93%] Building CXX object reuleaux/base_placement_plugin/CMakeFiles/base_placement_plugin.dir/include/base_placement_plugin/moc_point_tree_model.cxx.o
[ 95%] Building CXX object reuleaux/base_placement_plugin/CMakeFiles/base_placement_plugin.dir/include/base_placement_plugin/widgets/moc_base_placement_widget.cxx.o
[ 96%] Linking CXX shared library /home/andrew/Development/manip_ws/devel/lib/libworkspace_visualization.so
[ 96%] Built target workspace_visualization
[ 98%] Building CXX object reuleaux/base_placement_plugin/CMakeFiles/base_placement_plugin.dir/include/base_placement_plugin/moc_place_base.cxx.o
[100%] Linking CXX shared library /home/andrew/Development/manip_ws/devel/lib/libbase_placement_plugin.so
[100%] Built target base_placement_plugin
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2
Invoking "make -j4 -l4" failed

[hemangchawla]

@atomoclast modify the link directories in the CMakeLists.txt to

link_directories("/usr/lib/x86_64-linux-gnu/hdf5/openmpi" "~/catkin_ws/devel/lib")

Not the best of ways, but that worked for me. The base_placement plugin compiles as well.

However when I add it in rviz panel, it crashes.

[jontromanab]

Hello @atomoclast @geoffreychiou @willcbaker @hemangchawla
Sorry for the delay in the solution. But here is the solution to run Reuleaux on Kinetic.

https://github.com/jontromanab/reuleaux/tree/kinetic-devel

I am not very familiar with Kinetic. So please test this on your systems, before I ask @akgoins to merge it in the main repository and please let me know about the results.

Thank you everybody for your patience.

[skohlbr]

Just also ran into this on Kinetic. Will try the fork with the kinetic-devel branch posted by @jontromanab once I find some spare time. Anybody merged those changes with current master? :)

[jontromanab]

@skohlbr please let me know if the solution works.

[Maverobot]

@jontromanab The kinect-devel branch from your fork works! Thanks!

[vajrag]

Hey @jontromanab!

I did follow this, reinstalled hdf5 using this command sudo apt-get install libhdf5-dev and it is the newest version.
I have cloned this version https://github.com/jontromanab/reuleaux/tree/kinetic-devel of the repo. But I still face the issue

[jontromanab]

@vajrag Do you have any way to test if the hdf5 library is working separately. Most of the forks from the kinetic branch generally work. Is there any way to see your fork?

[blubbi321]

Hey @jontromanab!

I did follow this, reinstalled hdf5 using this command sudo apt-get install libhdf5-dev and it is the newest version.
I have cloned this version https://github.com/jontromanab/reuleaux/tree/kinetic-devel of the repo. But I still face the issue

I had the same issue and it turned out I just forgot to change the branch after checkout ;)

[JuliusSustarevas]

This issue appears again in melodic, any advice?
https://github.com/jontromanab/reuleaux/tree/kinetic-devel did not work.

[tunguyenmta]

This issue appears again in melodic, any advice?
https://github.com/jontromanab/reuleaux/tree/kinetic-devel did not work.

Hey @jontromanab!
I did follow this, reinstalled hdf5 using this command sudo apt-get install libhdf5-dev and it is the newest version.
I have cloned this version https://github.com/jontromanab/reuleaux/tree/kinetic-devel of the repo. But I still face the issue

I had the same issue and it turned out I just forgot to change the branch after checkout ;)

As a long time searching on the internet I have just built the package 100%
firstly, you need to find the path to the H5Cpp.h in my case it is /usr/include/hdf5/serial/
then you can use terminal and export or add export CPATH=/usr/include/hdf5/serial/ in bashrc
and when compile you will face another issue that is about /usr/bin/ld: cannot find -lhdf5
in my case once again we need to find the path of libhdf5.so and use terminal sudo cp yourpath/libhdf5.so /usr/lib
Hope it's useful
Tu_Mo

[daominhson]

This issue appears again in melodic, any advice?
https://github.com/jontromanab/reuleaux/tree/kinetic-devel did not work.

Hey @jontromanab!
I did follow this, reinstalled hdf5 using this command sudo apt-get install libhdf5-dev and it is the newest version.
I have cloned this version https://github.com/jontromanab/reuleaux/tree/kinetic-devel of the repo. But I still face the issue

I had the same issue and it turned out I just forgot to change the branch after checkout ;)

As a long time searching on the internet I have just built the package 100%
firstly, you need to find the path to the H5Cpp.h in my case it is /usr/include/hdf5/serial/
then you can use terminal and export or add export CPATH=/usr/include/hdf5/serial/ in bashrc
and when compile you will face another issue that is about /usr/bin/ld: cannot find -lhdf5
in my case once again we need to find the path of libhdf5.so and use terminal sudo cp yourpath/libhdf5.so /usr/lib
Hope it's useful
Tu_Mo

huhuhu

[sidml]

I got this error in melodic. I resolved it by linking both hdf5 and hdf5_cpp.

In cmake file i added the following
target_link_libraries(basic_shapes hdf5 hdf5_cpp ${catkin_LIBRARIES} )

[Kaushik093]

In file included from /home/kaushik/catkin_ws/src/reuleaux/map_creator/src/hdf5_dataset.cpp:1: /home/kaushik/catkin_ws/src/reuleaux/map_creator/include/map_creator/hdf5_dataset.h:3:10: fatal error: H5cpp.h: No such file or directory 3 | #include "H5cpp.h" | ^~~~~~~~~ compilation terminated. make[2]: *** No rule to make target '/opt/ros/noetic/lib/liboctomap.so.1.9.8', needed by '/home/kaushik/catkin_ws/devel/lib/libsphere_discretization.so'. Stop. make[2]: *** [reuleaux/map_creator/CMakeFiles/hdf5_dataset.dir/build.make:63: reuleaux/map_creator/CMakeFiles/hdf5_dataset.dir/src/hdf5_dataset.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:4923: reuleaux/map_creator/CMakeFiles/sphere_discretization.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:4869: reuleaux/map_creator/CMakeFiles/hdf5_dataset.dir/all] Error 2 [ 2%] Built target pcl_msgs_generate_messages_eus [ 2%] Built target _map_creator_generate_messages_check_deps_WorkSpace [ 2%] Built target _map_creator_generate_messages_check_deps_capShape [ 2%] Built target _map_creator_generate_messages_check_deps_WsSphere [ 2%] Built target _map_creator_generate_messages_check_deps_capability make: *** [Makefile:141: all] Error 2 Invoking "make -j8 -l8" failed

This was the error I faced on map_creator
I am trying to build on ROS-noetic
How do I rectify this?