FindHDF5 module fails on Debian Stretch

[cfhammill]

I'm trying to build libminc on debian stretch and it is failing. The FindHDF5 module does not look in the right places to find hdf5 installed through apt.

The serial include and lib directories for 64 bit install are:
/usr/include/hdf5/serial
/usr/lib/x86_64-linux-gnu/hdf5/serial

The cmake module FindHDF5 provided by kitware (https://github.com/Kitware/CMake/blob/master/Modules/FindHDF5.cmake) is able to find it by using the compiler wrappers h5cc/h5pcc, but seems to require SelectLibraryConfigurations.cmake and FindPackageHandleStandardArgs.cmake and their dependencies.

[ghisvail]

Considering that HDF5 detection is provided by CMake via their own FindHDF5.cmake, the embedded version should probably be dropped now.

That's the fix we will be likely to go for in Debian.

[vfonov]

Well, looks like FindHDF5 is not quite working: https://travis-ci.org/BIC-MNI/libminc/jobs/157120684

[ghisvail]

s/HDF5_INCLUDE_DIR/HDF5_INCLUDE_DIRS

[ghisvail]

HDF5_INCLUDE_DIR is broken and deprecated anyway.

[ghisvail]

You have it used in different files though:

https://github.com/BIC-MNI/libminc/search?utf8=%E2%9C%93&q=HDF5_INCLUDE_DIR

So you might want to use a stub like this set(HDF5_INCLUDE_DIR ${HDF5_INCLUDE_DIRS}).

[ghisvail]

Your call.

[vfonov]

Contents of FindHDF5 in Cmake :

This module will define the following variables:

...

HDF5_INCLUDE_DIR - Location of the hdf5 includes (deprecated)

'''

[ghisvail]

I know, I am just saying telling it is currently broken. I recently had to fix a bunch of Debian packages which were relying on HDF5_INCLUDE_DIR and started to FTBFS with CMake 3.6.

The most important word in your quote remains deprecated.

[ghisvail]

Commit d641c4f should have fixed it.

[vfonov]

It did not: https://travis-ci.org/BIC-MNI/libminc/builds/157143153

[ghisvail]

The error is explicit enough.

CMake Error at CMakeLists.txt:25 (CMAKE_MINIMUM_REQUIRED):

  CMake 3.0 or higher is required.  You are running version 2.8.7

-- Configuring incomplete, errors occurred!

[vfonov]

because they don't have modern cmake, that includes FindHDF5

[ghisvail]

They should, CMake 2.8.7 has a FindHDF5 module.

[ghisvail]

FYI, HDF5_INCLUDE_DIRS is available since CMake 2.8.1.

[ghisvail]

Looks like it worked in the end:

https://travis-ci.org/BIC-MNI/libminc/builds/157162205

[gdevenyi]

Hi,

This snippet I patched into ANTs' travis config will get an up-to-date cmake

https://github.com/stnava/ANTs/blob/master/.travis.yml#L18-L22

[shai-ikko]

(Debian Stretch is not very relevant anymore; I don't know if the commits merged finally fixed this issue on Stretch, but there seems to be no problem to build MINC on a modern Debian-based distro)