missing dependencies

[jamestwebber]

Hey, I'm running make install on a fresh Ubuntu16 AMI and I've been wrestling with getting various dependencies installed. I don't know if these things can be automated but it would be good to at least put them in the install instructions.

Or maybe I'm not building this correctly, in which case please let me know!

• libz-dev to get zlib.h
• libncurses5-dev for ncurses.h
• [WIP] libhdf5-dev for hdf5.h but it still isn't finding the file, possibly because Ubuntu has a different naming scheme. Working on this one

[jamestwebber]

And more:

Fixed the hdf5.h issue with judicious application of CFLAGS:

~/pomoxis$ CFLAGS="-I/usr/include/hdf5/serial" CPPFLAGS="-I/usr/include/hdf5/serial"  make install

And then needed to apt-get libblas-* (or potentially some subset of that) to get cblas.h.

[cjw85]

Hi @jamestwebber

Thanks for this reminder! We do aim to list these dependencies (at least for Ubuntu) in the README but in this case it must have slipped. We too have noticed that the include path for hdf on Ubuntu16 needs to be appended.

We'll try to get around to adding a "Ubuntu Dependencies" section to the README, or feel free to send a pull request.

For reference, a list of prerequisite Ubuntu (14.04, though 16.04 will be broadly similar) packages can currently be found in the https://github.com/nanoporetech/pomoxis/blob/master/.travis.yml file:

      - gcc-4.9
      - g++-4.9
      - zlib1g-dev
      - libncurses5-dev
      - python3-all-dev
      - libhdf5-dev
      - libatlas-base-dev
      - libopenblas-base
      - libopenblas-dev
      - libbz2-dev
      - liblzma-dev
      - libffi-dev