Cannot pip install the python module tables

Question

I am trying to install tables so an existing python script does not complain when it tries to 'import tables'

pip install tables

Here is the output:

Collecting tables
  Using cached tables-3.2.3.1.tar.gz
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.8.0 in ./miniconda/envs/optimus/lib/python2.7/site-packages (from tables)
Requirement already satisfied (use --upgrade to upgrade): numexpr>=2.5.2 in ./miniconda/envs/optimus/lib/python2.7/site-packages (from tables)
Installing collected packages: tables
  Running setup.py install for tables: started
    Running setup.py install for tables: finished with status 'error'
    Complete output from command /home/jonathonhill/miniconda/envs/optimus/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-jcuNfM/tables/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-ofzTc6-record/install-record.txt --single-version-externally-managed --compile:
    * Using Python 2.7.8 |Continuum Analytics, Inc.| (default, Aug 21 2014, 18:22:21)
    * USE_PKGCONFIG: True
    * pkg-config header dirs for HDF5: /usr/include/hdf5/serial
    * pkg-config library dirs for HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial
    * Found HDF5 headers at ``/usr/include/hdf5/serial``, library at ``/usr/lib/x86_64-linux-gnu/hdf5/serial``.
    .. WARNING:: Could not find the HDF5 runtime.
       The HDF5 shared library was *not* found in the default library
       paths. In case of runtime problems, please remember to install it.
    /tmp/lzo_version_dateanObdP.c:1:1: warning: return type defaults to âintâ [-Wimplicit-int]
     main (int argc, char **argv) {
     ^
    /tmp/lzo_version_dateanObdP.c: In function âmainâ:
    /tmp/lzo_version_dateanObdP.c:2:5: warning: implicit declaration of function âlzo_version_dateâ [-Wimplicit-function-declaration]
         lzo_version_date();
         ^
    * Could not find LZO 2 headers and library; disabling support for it.
    /tmp/lzo_version_datedINlTK.c:1:1: warning: return type defaults to âintâ [-Wimplicit-int]
     main (int argc, char **argv) {
     ^
    /tmp/lzo_version_datedINlTK.c: In function âmainâ:
    /tmp/lzo_version_datedINlTK.c:2:5: warning: implicit declaration of function âlzo_version_dateâ [-Wimplicit-function-declaration]
         lzo_version_date();
         ^
    * Could not find LZO 1 headers and library; disabling support for it.
    /tmp/BZ2_bzlibVersionL7B4pC.c:1:1: warning: return type defaults to âintâ [-Wimplicit-int]
     main (int argc, char **argv) {
     ^
    /tmp/BZ2_bzlibVersionL7B4pC.c: In function âmainâ:
    /tmp/BZ2_bzlibVersionL7B4pC.c:2:5: warning: implicit declaration of function âBZ2_bzlibVersionâ [-Wimplicit-function-declaration]
         BZ2_bzlibVersion();
         ^
    * Found bzip2 headers at ``/usr/include``, the library is located in the standard system search dirs.
    /tmp/blosc_list_compressorsQc0Mok.c:1:1: warning: return type defaults to âintâ [-Wimplicit-int]
     main (int argc, char **argv) {
     ^
    /tmp/blosc_list_compressorsQc0Mok.c: In function âmainâ:
    /tmp/blosc_list_compressorsQc0Mok.c:2:5: warning: implicit declaration of function âblosc_list_compressorsâ [-Wimplicit-function-declaration]
         blosc_list_compressors();
         ^
    * Could not find blosc headers and library; using internal sources.

I gather from this that I am missing a HDF5 shared library. How can I fix this error / install any necessary dependencies.

Answer 1

Your log explicitly tell what's wrong:

WARNING:: Could not find the HDF5 runtime.

Try this:

sudo python setup.py build_ext --inplace --hdf5=/opt/local --lzo=/opt/local --bzip2==opt/local

sudo python setup.py install --hdf5=/opt/local --lzo=/opt/local --bzip2==opt/local

Answer 2

Take a look at the project site page . You can download manually the dependeces ( blosc ), maybe the issue is given by a network problem, or can not be satisfy automatically.If you already have the library try to specify during the installation in this way:

python setup.py --blosc=/stuff/blosc-1.8.1

Answer 3

As you can read in the error message in the installation process:

• HDF5 wasn't found: WARNING:: Could not find the HDF5 runtime.

• LZO (neither 2 nor 1) wasn't found: * Could not find LZO 2 headers and library; disabling support for it. * Could not find LZO 2 headers and library; disabling support for it. * Could not find LZO 1 headers and library; disabling support for it.

• Blosc wasn't found but it seems it can use the internal sources packed in with PyTables. * Could not find blosc headers and library; using internal sources. In my case, I also had to install it to make it work.

You have two options:

a) You can install the three libraries with apt and pip by doing:

sudo apt install python-blosc python-lzo
pip install h5py

b) Alternatively, if you're using Conda do:

conda install h5py python-blosc python-lzo 

---

If the python-lzo installation fails, try installing the base library:

sudo apt install liblzo2-dev

Answer 4

I tried all the provided solutions and none worked. I was using python 3.9.2 .

I ended up switching to python 3.8.0 and had no issues just running: pip install tables , which installed tables properly and everything worked as expected.

Just thought I'd add this as an answer for anyone who happens to be in the same situation as me.