[scikit-image] Error during env setup

[Mark Harfouche]

We should definitely document that!

On Wed, Aug 29, 2018 at 1:36 PM Sena Agezo <senaagezo at gmail.com> wrote:

> The pip install -e . finally worked! I ran the “make clean” first as Juan
> suggested and then the pip command. Mark, to answer your question, I am
> running it on ubuntu-16.04.5 LTS.
>
> Thanks a lot for your help.
>
> -Sena
>
> On Aug 29, 2018, at 11:34 AM, Mark Harfouche <mark.harfouche at gmail.com>
> wrote:
>
> 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 <jni at fastmail.com>
> 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 <mark.harfouche at gmail.com>
>> 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 <mark.harfouche at gmail.com>
>> 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 <senaagezo at gmail.com> 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 <jni at fastmail.com>
>> 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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>> Email had 2 attachments:
>>
>>    - build_version.py_output.pdf
>>      27k (application/pdf)
>>    - Pip_install_output.pdf
>>      49k (application/pdf)
>>
>>
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