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Problem with libhdf5 dependency

asked 2013-07-14 21:52:06 -0500

Recently I had an issue updating my Fuerte packages. When I ran

$ sudo apt-get upgrade

I received the error

"E: Unable to correct problems, you have held broken packages."

for 12 packages.

After digging into the issue, I found that ros-fuerte-perception-pcl requires libhdf5-serial-dev. However, I had installed Paraview (which has a PCL viewer plugin) and paraview requires libhdf5-openmpi-dev. It appears these two packages are mutually exclusive.

Because I haven't been using Paraview lately, I decided to uninstall it so I could update my ROS Fuerte install. However, since it was coexisting peacefully before I feel something must have changed.

During the uninstall of Paraview and update of perception-pcl, I noticed that libnetcdf6 can use either libhdf5-serial or -openmpi

$ apt-cache depends libnetcdf6 
  Depends: libc6
  Depends: libcurl3-gnutls
  Depends: libgcc1
  Depends: libgfortran3
 |Depends: libhdf5-serial-1.8.4
  Depends: <libhdf5-1.8.4>
  Depends: libstdc++6
  Conflicts: libnetcdf6:i386

Could perception-pcl be modified to accept either also? This would allow Paraview installation again.

Yes, I'm also going to query the Ubuntu package maintainers about doing the same with Paraview.

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1 Answer

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answered 2013-10-14 04:05:21 -0500

peci1 gravatar image

The problem can be overcome by a little hack. Because libhdf5-serial package contains all the files paraview needs, it is just sufficient to tell apt-get that the package libhdf5-openmpi has already been installed. You can download a "fake" package from .

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If you don't trust that file, you can create your own onw using the tutorial at (just the main-package part, without coping with the .conf file).

peci1 gravatar image peci1  ( 2013-10-14 04:09:05 -0500 )edit

To install the downloaded .deb file just double-click it and install it. If that doesn't work for you, you can always do `sudo dpkg -i name_of_file.deb` .

peci1 gravatar image peci1  ( 2013-10-14 04:11:48 -0500 )edit

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Asked: 2013-07-14 21:52:06 -0500

Seen: 914 times

Last updated: Jul 14 '13