Closed asher-pembroke closed 4 years ago
Thanks Asher.
Since you have the terminal command can’t you invoke that from setup.py?
I believe there is a post-install trigger in setuptools and the package has the paths and such the final code is, or will be, when installed.
On Oct 9, 2019, at 5:25 PM, Asher Pembroke notifications@github.com<mailto:notifications@github.com> wrote:
I ran into problems installing with pip involving the notorious libgfortran rpath bughttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FContinuumIO%2Fanaconda-issues%2Fissues%2F739&data=02%7C01%7Crstoneba%40utdallas.edu%7Ca340e93046f74b7db90808d74d07840f%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C0%7C637062566996679415&sdata=rc%2FB%2FjvgNM5g9Bqqg18SM35sz%2FwZAT9A0%2BnIgCHgO%2B8%3D&reserved=0 on mac.
To reproduce,
ImportError: dlopen(/Users/apembrok/Library/Caches/Python-Eggs/pysatCDF-0.3.0-py2.7-macosx-10.6-x86_64.egg-tmp/pysatCDF/fortran_cdf.so, 2): Library not loaded: @rpath/./libgfortran.3.dylib Referenced from: /Users/apembrok/Library/Caches/Python-Eggs/pysatCDF-0.3.0-py2.7-macosx-10.6-x86_64.egg-tmp/pysatCDF/fortran_cdf.so Reason: image not found
To resolve:
install_name_tool -change @rpath/./libgfortran.3.dylib ${CONDA_PREFIX}/lib/libgfortran.dylib -change @rpath/./libquadmath.0.dylib ${CONDA_PREFIX}/lib/libquadmath.0.dylib fortran_cdf.so ${CONDA_PREFIX}/lib/python2.7/site-packages/pysatCDF/fortran_cdf.so
Conda package installers usually fix the rpath issue automagically. Not sure how to do this with setuptools...
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Hi, I also run into a problem trying to install pysat, pysatCDF, and pysatMagVect with pip. It is not directly relevant but I was hesitant to start a new issue, since it is technically an "installation with pip issue". Please feel free to move/edit as you see fit.
I have the following:
I get a bunch of warnings during installation, all seem to be related with the incompatibility between Apple clang and gfortran versions I installed with Homebrew. To fix I had to define new aliases in my bashrc file to point the gcc and gfortran installed by brew in my /usr/local/bin/.
The problem is similar to https://github.com/pymc-devs/pymc/issues/119
Thanks for the report.
Cheers
A lot of places suggest the delocate tool which makes pip wheels portable. That would at least solve the issue where users aren't able to install with pip.
Also, note that install_name_tool
requires users to have the xcode developer tools installed so putting the command in setup.py may not help: https://stackoverflow.com/a/11598098
The delocate looks like it would be helpful for pip.
I found a lot of issues with clang as well, but gcc seems to work better.
I'm able to install from setup.py using the following environment setup
conda create -n pysatCDF python=2.7
conda install -c anaconda gcc
conda install -c anaconda numpy
pip install pysat (or setup.py after cloning pysat)
Then, from pysatCDF directory:
python setup.py install (or pip install .)
@rstoneback Anything left to do here?
Does it work in python 3? If it’s good then I think we are good.
Cheers, Russell
On Nov 4, 2019, at 11:41 AM, Asher Pembroke notifications@github.com wrote:
I found a lot of issues with clang as well, but gcc seems to work better.
I'm able to install from setup.py using the following environment setup
conda create -n pysatCDF python=2.7 conda install -c anaconda gcc conda install -c anaconda numpy pip install pysat (or setup.py after cloning pysat)
Then, from pysatCDF directory:
python setup.py install (or pip install .)
@rstonebackhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Frstoneback&data=02%7C01%7Crstoneba%40utdallas.edu%7Cb069f242f989454df8a508d7615696cb%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C0%7C637084896840415726&sdata=Bl8QmPA%2Fl4M4J42nXjrokOeJegJzySj2Via2ZNGLtug%3D&reserved=0 Anything left to do here?
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Yep, it works with python3 as well.
I've uploaded delocated versions of pysatCDF to pypi for macosx. python 2 and 3.8 are currently supported.
I was finally able to fix various issues and got pysatCDF to install on my laptop (OSX Mojave) with python 2.7, 3.7, and 3.8.
Great!
I ran into problems installing with pip involving the notorious libgfortran rpath bug on mac.
To reproduce,
import pysatCDF
To resolve:
fortran_cdf.so
:otool -L ${CONDA_PREFIX}/lib/python2.7/site-packages/pysatCDF/fortran_cdf.so
install_name_tool
:Conda package installers usually fix the rpath issue automagically. Not sure how to do this with setuptools...