pytables installation failed

conda install pytables
pip install pytables
pip install hdf5
install hdf5 ubuntu
conda install h5py
error:: could not find a local hdf5 installation.
missing optional dependency 'tables'. use pip or conda to install tables.
how to install pytables on ubuntu

I do:

sudo pip install --upgrade tables

I get:

    /usr/bin/ld: cannot find -lhdf5
collect2: ld returned 1 exit status
.. 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.
Complete output from command python setup.py egg_info:
/usr/bin/ld: cannot find -lhdf5

however:

$ echo $HDF5_DIR 
/opt/hdf5/
$ ls /opt/hdf5/
bin  include  lib  share
$ ls /opt/hdf5/lib/
libhdf5.a     libhdf5_hl.la  libhdf5_hl.so.8      libhdf5.la        libhdf5.so libhdf5.so.8.0.1
libhdf5_hl.a  libhdf5_hl.so  libhdf5_hl.so.8.0.1  libhdf5.settings  libhdf5.so.8

What's wrong? How to debug? I already tried to set HDF5_DIR to /opt/ or to /opt/hdf5/lib.

I also had the same error on Debian sid trying to work in a local virtualenv. To work around it I did:

apt-get build-dep python-tables
HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/serial/ && pip install tables

... now it's working.

pytables installation failed, I also had the same error on Debian sid trying to work in a local virtualenv. To work around it I did: apt-get build-dep python-tables� pytables installation failed. Ask Question Asked 6 years, 5 months ago. Active 1 year, 4 months ago. Viewed 8k times 4. 1. I do: sudo pip install --upgrade tables

I was able to fix this easily in OSX with virtual environments using the following code:

    $ brew install hdf5
    $ pyvenv test
    $ workon myvenv # to get pytables working within the virtual environment myvenv
    $ pip install numpy numexpr cython
    $ pip install tables

(taken from andreabedini post in https://github.com/PyTables/PyTables/issues/385)

pip tables install fails, HDF5 library not found � Issue #219 � PyTables , I've been trying install pytables via pip using pip install tables , however, it fails with an error Could not find a local HDF5 installation. : We've tested this PyTables version with HDF5 1.8.4/1.8.12, NumPy 1.7.1/1.8.0 and Numexpr 2.4, and you need to use these versions, or higher, to make use of PyTables. Installation The Python Distutils are used to build and install PyTables, so it is fairly simple to get things ready to go.

I'm having a similar problem, but I'm using the leading edge not the pip release (see Aside). I also tried pointing to the library itself

export HDF5_DIR=/usr/lib/libhdf5.so.6

but it did not work.

Aside: You can try the leading edge of PyTables if you think your bug may have been addressed recently:

sudo pip install git+https://github.com/PyTables/PyTables

.

The build (that was caused by pip install...) seemed to progress further after I installed the dev version of the hdf5 library (libhdf5-openmpi-dev). The build still failed for other reasons, but it's another direction you could try.

same old, same old: pip install fails � Issue #385 � PyTables , Must be the most searched topic about hdf5. I have installed: numpy 1.8.2, numexpr 2.4, hdf5 1.8.13. I have exported the environment variable� during the installation of PyTables I had 4 tests which have failed. Here ist the full output of tables.test(): Python 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2] on linux2 Type "help&q

I tried everything without success. The only way I could I achieved was using nehalecky's answer I got here:

https://github.com/PyTables/PyTables/issues/219

In a nutshell, you should do these 2 commands, correcting the path, of course:

sudo python3 setup.py build_ext --inplace --hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial/
sudo python3 setup.py install --hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial/

Hope it helps!

same old, same old: pip install fails - PyTables, Must be the most searched topic about hdf5. I have installed: numpy 1.8.2, numexpr 2.4, hdf5 1.8.13. I have exported the environment variable� PyTables 3.1.1 (as well as HEAD) attempts to import both numpy and numexpr, otherwise erroring out. This behavior is a problem for anyone building deployment requirements in bulk, for example with

Unable to install Pytables on Mac OS 10.6 using easy_install, When trying to install Pytables on Mac OS 10.6 using easy_install, I run into the following error: mleblanc-vm:~ adriano$ easy_install tables. Searching for tables 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.

Installation — PyTables 3.0.0rc2 documentation, The Python Distutils are used to build and install PyTables, so it is fairly simple to And last, but not least, in case a test fails, please run the failing test module� PyTables - Hierarchical datasets Mailing Lists Brought to you by: a_valentino , falted , ivilata , joshmoore

Failed to reinstall PyTables for Python 2.7, The hdf5 command line option was not specified correctly (--hdf5 = '/ usr / local / hdf5'). Dropping print statements in setup.py simplified the problem. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large

Comments
  • sudo apt-get build-dep python-tables was sufficient for me! (Ubuntu 14.04)
  • All I had to do was sudo apt-get install hdf5-serial-dev, then pip install tables.
  • A lot has changed since 2014, good to know the -dev package works for pytables out of the box now :)
  • sudo apt-get install libhdf5-serial-dev for me, on a debian-based docker image in 2019
  • Python 3.6.9 on Ubuntu 16.04 required install of libhdf5-dev followed by: HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/serial/ pip install tables
  • HDF5_DIR requires a directory not a file, export HDF5_DIR=/local/johndoe/hdf5