Re: [scikit-image] Error during env setup
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@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@fastmail.com <mailto:jni@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@gmail.com <mailto:mark.harfouche@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@gmail.com <mailto:mark.harfouche@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@gmail.com <mailto:senaagezo@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@fastmail.com <mailto:jni@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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We should definitely document that! On Wed, Aug 29, 2018 at 1:36 PM Sena Agezo <senaagezo@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@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@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@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@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@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@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
*_______________________________________________* scikit-image mailing list scikit-image@python.org https://mail.python.org/mailman/listinfo/scikit-image
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_______________________________________________ scikit-image mailing list scikit-image@python.org https://mail.python.org/mailman/listinfo/scikit-image
_______________________________________________ scikit-image mailing list scikit-image@python.org https://mail.python.org/mailman/listinfo/scikit-image
*_______________________________________________* scikit-image mailing list scikit-image@python.org https://mail.python.org/mailman/listinfo/scikit-image
Email had 2 attachments:
- build_version.py_output.pdf 27k (application/pdf) - Pip_install_output.pdf 49k (application/pdf)
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participants (2)
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Mark Harfouche -
Sena Agezo