xdmf I/O HDF5 linking error on MacOS: libhdf5.101.dylib not found

[Ruben Di Battista]

Ehi Ryan, 

Thank you. I looked in all the computer and there is not any libhdf5.101.dylib. I also tried with the trace mode, but I got an error like “bin/ps operation not permitted” before it reached the actual point where the previous error was given. Can I somehow overcome the sandboxing? 

Thanks!

          _   
-.     .´  |∞∞∞∞
  ',  ;    |∞∞∞∞∞∞
    ˜˜     |∞∞∞∞∞∞∞∞∞ RdB
    ,.,    |∞∞∞∞∞∞
  .'   '.  |∞∞∞∞
-'       `’

https://rdb.is

On 17 novembre 2018 a 03:24:40, Ryan Schmidt (ryandesign at macports.org) scritto:



On Nov 16, 2018, at 18:00, Ruben Di Battista wrote:  

> I tested again the build (with also rev-upgrade). No luck, same error. Does anyone here can try to install: vtk +hdf5 +python27 +mpich to see if it’s just a misconfiguration for me or it’s a general problem?  

Some file on your system that is being used by the vtk build is linked with /opt/local/lib/libhdf5.101.dylib. We need to identify that file and rebuild it so that it is linked with /opt/local/lib/libhdf5.103.dylib instead.  

That's what running "sudo port rev-upgrade" does, so I'm surprised that didn't fix the problem for you.  

Maybe rev-upgrade is failing, but isn't printing an error message. You could run it with debug output: "sudo port -d rev-upgrade".  

If the output doesn't look like an error is happening, then maybe the problem is that the file that is linked with /opt/local/lib/libhdf5.101.dylib is not in MacPorts, but the vtk build is finding it for some reason. (For example, maybe it is in /usr/local.) If so, you could use trace mode, which tells MacPorts to ignore any files not explicitly listed as dependencies: "sudo port clean vtk && sudo port -t install vtk +hdf5 +python27 +mpich".  


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.macports.org/pipermail/macports-dev/attachments/20181117/1db52cfe/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 833 bytes
Desc: Message signed with OpenPGP using AMPGpg
URL: <http://lists.macports.org/pipermail/macports-dev/attachments/20181117/1db52cfe/attachment.sig>