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

I've been stuck on this all day too. I have a terrible feeling it has to do with some incompatibility with Python3.6 — Monica Heddneck, May 13 '20 at 21:42
@MonicaHeddneck - could you add `pip3 install -U pip` as an answer? Had the same issue and nothing else worked. — Adam Morris, May 20 '20 at 17:31

score 4 · Answer 1 · answered May 14 '20 at 12:47

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

Monica Heddneck · Answer 2 · 2020-05-20T19:41:59.973

2

After struggling for a while, I solved this with:

pip3 install -U pip

edited May 20 '20 at 19:41

answered May 20 '20 at 17:33

Monica Heddneck

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score 1 · Answer 3 · edited May 14 '20 at 09:37

1

The development libraries (those including *h) are missing from your installation. You can install them like:

sudo apt-get install libblosc-dev

You will have issues with other libraries as well:

sudo apt-get install libbrotli-dev

etc.

edited May 14 '20 at 09:37

Nandu Raj

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answered May 14 '20 at 07:11

user6131524

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Thanks for the answer, unfortunately this did not solve the issue. – si_mon May 14 '20 at 08:56

score 0 · Answer 4 · answered May 25 '20 at 15:04

This happens because imagecodecs package relies on too many dependencies that your computer doesn't have, like libblosc and libbrotli as @user6131524 has said.

To install the dependencies:

 sudo apt-get install build-essential python3-dev cython3 python3-setuptools python3-pip python3-wheel python3-numpy python3-pytest python3-blosc python3-brotli python3-snappy python3-lz4 libz-dev libblosc-dev liblzma-dev liblz4-dev libzstd-dev libpng-dev libwebp-dev libbz2-dev libopenjp2-7-dev libjpeg-turbo8-dev libjxr-dev liblcms2-dev libcharls-dev libaec-dev libbrotli-dev libsnappy-dev libzopfli-dev libgif-dev libtiff-dev

I believe this will solve your problem in the most general way.

Problem installing scikit-image probably due to blosc

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