Error installing 3.5.2 - can't locate install HDF5 library

[Brendan Boerner]

Error installing 3.5.2, I had previously been using 3.5.1 with no problems.

Ubuntu 14.04.

Please advise.

Thanks!

$ pip install --user -U tables

DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.

Collecting tables

  Downloading https://files.pythonhosted.org/packages/73/51/6dabb2b94826e5db3aa2542b80f1382780b96a0cd13e0cfb637b36ede5c5/tables-3.5.2.tar.gz (7.8MB)

     |████████████████████████████████| 7.8MB 4.6MB/s 

    ERROR: Complete output from command python setup.py egg_info:

    ERROR: /tmp/H5closeehIqzt.c:1:1: warning: return type defaults to ‘int’ [-Wimplicit-int]

     main (int argc, char **argv) {

     ^

    /tmp/H5closeehIqzt.c: In function ‘main’:

    /tmp/H5closeehIqzt.c:2:5: warning: implicit declaration of function ‘H5close’ [-Wimplicit-function-declaration]

         H5close();

         ^

    /usr/bin/ld: cannot find -lhdf5

    collect2: error: ld returned 1 exit status

    * Using Python 2.7.12 (default, Nov 12 2018, 14:36:49)

    * USE_PKGCONFIG: False

    .. ERROR:: Could not find a local HDF5 installation.

       You may need to explicitly state where your local HDF5 headers and

       library can be found by setting the ``HDF5_DIR`` environment

       variable or by using the ``--hdf5`` command-line option.

    ----------------------------------------

ERROR: Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-zSNHwh/tables/

$ dpkg -l libhdf5-dev

Desired=Unknown/Install/Remove/Purge/Hold

| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend

|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)

||/ Name                  Version         Architecture    Description

+++-=====================-===============-===============-================================================

ii  libhdf5-dev           1.8.16+docs-4ub amd64           Hierarchical Data Format 5 (HDF5) - development 

[Brendan Boerner]

Correction: Ubuntu 16.04.

Worked around it using

export HDF5_DIR="/usr/lib/x86_64-linux-gnu/hdf5/serial"

pip install --user -U tables

[Brendan Boerner]

This appears to now be fixed - pip install --user tables now installs a wheel.

Thanks,

Brendan