Build issue for wheel for scipy OS X Catalina

[Jack Wimberley]

Hello all,

I installed sage via homebrew on OS X 10.15.7 (Macbook Pro laptop) with python3 version 3.8.5. (I'm not sure if I got python3 through homebrew, as I also seem to have more copies of python lying about than I thought.) My first issue was that a Jupyter page could not load due to being unable to import the _ssl module, and the log suggested that I run "sage -f python." Upon doing so, this eventually failed while compiling the wheel for scipy:

[scipy-1.5.2] ********************************************************************************

[scipy-1.5.2] Error building a wheel for scipy-1.5.2

[scipy-1.5.2] ********************************************************************************

[scipy-1.5.2]

[scipy-1.5.2] real 2m19.074s

[scipy-1.5.2] user 3m40.041s

[scipy-1.5.2] sys 0m34.633s

[scipy-1.5.2] ************************************************************************

[scipy-1.5.2] Error installing package scipy-1.5.2

[scipy-1.5.2] ************************************************************************

[scipy-1.5.2] Please email sage-devel (http://groups.google.com/group/sage-devel)

[scipy-1.5.2] explaining the problem and including the log file

I attempt to open the subshell

cd '/Applications/SageMath-9.2.app/Contents/Resources/sage/local/var/tmp/sage/build/scipy-1.5.2' && '/Applications/SageMath-9.2.app/Contents/Resources/sage/sage' --buildsh

and run "MACOSX_DEPLOYMENT_TARGET=11.0 make scipy", as I saw mentioned in a recent thread titled "MACOSX_DEPLOYMENT_TARGET problems", but I think I was mixing and matching wrong suggestions as this just told me there was no rule to make scipy.

I have attached the logfile from the failed "sage -f python" build here:

/Applications/SageMath-9.2.app/Contents/Resources/sage/logs/pkgs/scipy-1.5.2.log

Best,

Jack

[Zachary Scherr]

Maybe somebody with more experience can answer, but the problem is likely caused by the fact that you used a prebuilt binary of sage and then tried to remake it on your own computer.  What tends to happen in this situation is that the prebuilt binary was built with a specific version of Xcode but then in the meantime Xcode is updated and when you try to remake sage it breaks because it's retained paths to libraries that have been changed by Xcode updates.

There are a few different options for installing Sage on Mac and getting it to work.

1.  Install it through homebrew cask and then apply the fix for ssl at https://github.com/3-manifolds/fix_mac_sage.  I have not personally tried this but I've seen others in this forum have success.

2.  Install it through anaconda.  This is currently my favorite approach since it is simple, fast, and everything just seems to work.  Directions are at https://doc.sagemath.org/html/en/installation/conda.html

3.  Install from source.  You can get directions from https://doc.sagemath.org/html/en/installation/source.html.  The basic workflow after you've extracted the archive would be to run:

>>> source .homebrew-build-env

>>> ./configure

>>> make -jNUM

   where NUM is the number of parallel processes you want to use in your build process.

[Masoud Soroush]

Jack,

I had the same problem. Suggested by Nathan Dunfield, I followed the steps in https://github.com/3-manifolds/fix_mac_sage, and Sage is now working in the Jupyter environment on my mac. I believe this solution is the same as the first option of Zachary's response.

Masoud

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[Jack Wimberley]

Hi Zach and Masoud,

Thanks for the suggestions! I tried fix_mac_sage and this worked perfectly.

Best,

Jack