Problem installing scikit-image probably due to blosc

Question

Hi I am trying to install scikit image in a virtual environment on ubuntu 18.04.

It fails when it tries to install imagecodecs, I tried to install imagecodecs separately but it gives the same error which is something due to blosc. I installed blosc separately but somehow this still fails.

    /usr/include/python3.6m/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^~~~~~~
    imagecodecs/_blosc.c:602:10: fatal error: blosc.h: No such file or directory
     #include "blosc.h"
              ^~~~~~~~~
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

    ----------------------------------------
Command "/home/xxxx/im_an/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-ijwkwo7f/imagecodecs/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-4xtori6c-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/xxxx/im_an/include/site/python3.6/imagecodecs" failed with error code 1 in /tmp/pip-build-ijwkwo7f/imagecodecs/

I hope that somebody could help me with this. Thank you

Answer 1

Unfortunately imagecodecs wheels (pre-compiled binaries) are compatible only with pip 19.0 and newer, because they use the newer manylinux2010 standard. Upgrade pip (pip install -U pip) and try again, and things should work!

See these issues for reference:

https://github.com/scikit-image/scikit-image/issues/4673

https://github.com/scikit-image/scikit-image/issues/4674

Answer 2

After struggling for a while, I solved this with:

pip3 install -U pip