Error installing 3.5.2 - can't locate install HDF5 library

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Brendan Boerner

May 30, 2019, 2:47:28 PM5/30/19
to pytables-users
Error installing 3.5.2, I had previously been using 3.5.1 with no problems.

Ubuntu 14.04.

Please advise.


$ 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
     |████████████████████████████████| 7.8MB 4.6MB/s 
    ERROR: Complete output from command python 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]
    /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 egg_info" failed with error code 1 in /tmp/pip-install-zSNHwh/tables/

$ dpkg -l libhdf5-dev
| 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

May 30, 2019, 2:58:25 PM5/30/19
to pytables-users
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

Jun 2, 2019, 12:40:23 AM6/2/19
to pytables-users
This appears to now be fixed - pip install --user tables now installs a wheel.

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