Closed garretstuber closed 9 years ago
It looks like the problem is with installing guiqwt. (We recommend installing this package separately before attempting to install roibuddy with pip http://www.losonczylab.org/sima/1.2/roi_buddy.html#mac-os-x.) Looking through the error messages, the root of the problem appears to be that the Cython compilation of the histogram2d.pyx file into histogram2d.c has failed. If you download the zip file from the guidata downloads site (see link above, which in turn has a link to there), then it already contains a compiled histogram2d.c file, and so this step should be avoidable. Please let us know if that fixes your issue.
also - it guidata installs fine. the problem with histogram2d.pyx is coming from the guiqwt install. I get that cython compiler error every which way I try it.
On May 7, 2015, at 10:02 AM, Garret Stuber gstuber@gmail.com wrote:
Thanks for your help Patrick - unfortunately, there is still the issue with histogram2d, even when I installed directly from the .zip file. Here is the new log, if you have any other though
On May 6, 2015, at 9:26 PM, Patrick Kaifosh notifications@github.com wrote:
It looks like the problem is with installing guiqwt. (We recommend installing this package separately before attempting to install roibuddy with pip http://www.losonczylab.org/sima/1.2/roi_buddy.html#mac-os-x. http://www.losonczylab.org/sima/1.2/roi_buddy.html#mac-os-x.) Looking through the error messages, the root of the problem appears to be that the Cython compilation of the histogram2d.pyx file into histogram2d.c has failed. If you download the zip file from the guidata downloads site (see link above, which in turn has a link to there), then it already contains a compiled histogram2d.c file, and so this step should be avoidable. Please let us know if that fixes your issue.
— Reply to this email directly or view it on GitHub https://github.com/losonczylab/roibuddy/issues/16#issuecomment-99669235.
Can you please confirm that you get this error when downloading the installing guiqwt zip file separately from the pip install sima, and then installing it by running setup.py?
@nbdanielson @jzaremba How have you installed guiqwt on your Mac laptops?
I think I finally found the culprit - guiqwt is installing to my system python, not to anaconda for some reason. I am working on fixing that, and will let you know if that works. We were able to get everything running on a linux box, so we are hopefully good to go. Thanks again - I really appreciate your help.
Garret
On May 7, 2015, at 12:02 PM, Patrick Kaifosh notifications@github.com wrote:
Can you please confirm that you get this error when downloading the installing guiqwt zip file separately from the pip install sima, and then installing it by running setup.py?
@nbdanielson https://github.com/nbdanielson @jzaremba https://github.com/jzaremba How have you installed guiqwt on your Mac laptops?
— Reply to this email directly or view it on GitHub https://github.com/losonczylab/roibuddy/issues/16#issuecomment-99922440.
Did this work? Can we close the issue?
Yes, it working great now. Thanks for your help.
Garret
On Aug 13, 2015, at 9:03 AM, Patrick Kaifosh notifications@github.com wrote:
Did this work? Can we close the issue?
— Reply to this email directly or view it on GitHub.
When trying to install roibuddy via pip, errors always appear to be generated. here is the output. Any ideas on how to solve this would be greatly appreciated. Thanks.
wire152019015140:~ gstuber$ pip install roibuddy --allow-unverified guiqwt Collecting roibuddy Using cached roibuddy-1.0.0-py2-none-any.whl Collecting guiqwt>=2.1.6 (from roibuddy) guiqwt is potentially insecure and unverifiable. Downloading http://guiqwt.googlecode.com/files/guiqwt-2.3.1.zip (3.1MB) 100% |████████████████████████████████| 3.1MB 11.8MB/s Requirement already satisfied (use --upgrade to upgrade): guidata>=1.4.1 in ./anaconda/lib/python2.7/site-packages (from roibuddy) Requirement already satisfied (use --upgrade to upgrade): sima in ./anaconda/lib/python2.7/site-packages (from roibuddy) Requirement already satisfied (use --upgrade to upgrade): numpy>=1.8 in ./anaconda/lib/python2.7/site-packages (from sima->roibuddy) Requirement already satisfied (use --upgrade to upgrade): scipy>=0.13.0 in ./anaconda/lib/python2.7/site-packages (from sima->roibuddy) Requirement already satisfied (use --upgrade to upgrade): scikit-image>=0.9.3 in ./anaconda/lib/python2.7/site-packages (from sima->roibuddy) Requirement already satisfied (use --upgrade to upgrade): shapely>=1.2.14 in ./anaconda/lib/python2.7/site-packages (from sima->roibuddy) Requirement already satisfied (use --upgrade to upgrade): scikit-learn>=0.11 in ./anaconda/lib/python2.7/site-packages (from sima->roibuddy) Requirement already satisfied (use --upgrade to upgrade): pillow>=2.6.1 in ./anaconda/lib/python2.7/site-packages (from sima->roibuddy) Requirement already satisfied (use --upgrade to upgrade): future>=0.14 in ./.local/lib/python2.7/site-packages (from sima->roibuddy) Requirement already satisfied (use --upgrade to upgrade): six>=1.3 in ./anaconda/lib/python2.7/site-packages (from scikit-image>=0.9.3->sima->roibuddy) Installing collected packages: guiqwt, roibuddy Running setup.py install for guiqwt Complete output from command /Users/gstuber/anaconda/bin/python -c "import setuptools, tokenize;file='/private/var/folders/pf/kc8qz5m12gb2w3c0dmt5mfpw0000gn/T/pip-build-_3jNCO/guiqwt/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /var/folders/pf/kc8qz5m12gb2w3c0dmt5mfpw0000gn/T/pip-lOdeej-record/install-record.txt --single-version-externally-managed --compile:
wire152019015140:~ gstuber$