Re: [scikit-image] Error during env setup

Thanks for those outputs. They were good at eliminating sources of problems. What Linux distribution are you using and what compilers do you have installed? On Wed, Aug 29, 2018 at 7:36 AM Juan Nunez-Iglesias wrote:

Hmmm. Unfortunately I have no ideas right now about what is going wrong there. One question: can you try running "make clean" and then the pip command again? Sometimes I get weird behaviour where Cython files don't get rebuilt. But other than that I have no idea. I don't see this on my Linux machine. Anyone else?

On Wed, Aug 29, 2018, at 11:09 PM, Sena Agezo wrote:

These are the outputs for pip install -e . --no-deps and build_versions.py .

-Sena

On Aug 28, 2018, at 2:15 PM, Mark Harfouche wrote:

I meant the full output of your build pip install -e . --no-deps

On Tue, Aug 28, 2018 at 11:14 AM Mark Harfouche wrote:

Hi Sena,

Please run

pip install requirements-parser python tools/build_versions.py

Please provide the output of build_versions.py

Can you somehow post the full output of the command? Maybe to pastebin?

Mark

On Tue, Aug 28, 2018 at 10:54 AM Sena Agezo wrote:

Hi Juan,

Yes, I did install Cython first before attempting to “pip install -e .”

-Sena

On Aug 27, 2018, at 8:45 PM, Juan Nunez-Iglesias wrote:

Hi Sena, thanks for wanting to contribute!

I believe you need install Cython first, and then it should work. Can you give that a try and report back?

Juan.

On Tue, Aug 28, 2018, at 7:31 AM, Sena Agezo wrote:

Hi,

I am trying to make a contribution to the scikit-image documentation. In my attempt to setup the environment after creating it, I keep getting an error(see below). This error happens when I do "pip install -e ." in the cloned scikit-image. I’m doing this on a linux machine.

*error: Command "gcc -pthread -B /home/liulab/anaconda3/envs/skimage/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -c _extrema_cy.c -o build/temp.linux-x86_64-3.6/_extrema_cy.o -MMD -MF build/temp.linux-x86_64-3.6/_extrema_cy.o.d" failed with exit status 1* * gcc: error: _extrema_cy.c: No such file or directory* * gcc: error: _extrema_cy.c: No such file or directory*

* ----------------------------------------* *Command "/home/liulab/anaconda3/envs/skimage/bin/python -c "import setuptools, tokenize;__file__='/home/liulab/Documents/scikit-image/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps" failed with error code 1 in /home/liulab/Documents/scikit-image/*

Please advise on what I should do to solve the issue and let me know if you have any questions.

Thanks, Sena

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