SCT 4.0.0 install failed: failed to build wheel for nipy

Dear Julien

Sorry to be the bearer of bad news. I downloaded the latest release (yay!) of SCT as a zip, and then followed the install instructions.

However, the installation fails with the error in the title. Full pastebin here:

I have a working beta 2 version, so this is not urgent, but perhaps I am not the only one with this issue. The beta-2 version works, and sct_check_dependencies returns everything as OK.



Hi Daniel,
Bad news indeed :wink: But thanks for bringing it to our attention! Until now you are the first to have reported it. I’ve opened an issue which we are addressing with the highest priority.

Looks like this is another one of my gremlin errors, like the ME conversion.

Nipy also fails to install outside of the package, so I will ask our local IT. I’ll keep you posted.

what is your output of uname -a?
and gcc --version?

The IT guys have identified this as the likely culprit, but have not yet solved the issue:

libraries mkl_rt not found in [’/Users/dpapp/Downloads/sct/python/envs/venv_sct/lib’, ‘/usr/local/lib’, ‘/usr/lib’, ‘/opt/local/lib’]

gcc --version:
dpapp$ gcc --version

Configured with: --prefix=/Applications/ --with-gxx-include-dir=/Applications/

Apple LLVM version 10.0.1 (clang-1001.0.46.4)

Target: x86_64-apple-darwin18.6.0

Thread model: posix

InstalledDir: /Applications/

uname --a

Darwin 18.6.0 Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64 x86_64

Hi Daniel,

The issue might be fixed in 4.0.1 (dropped dependency to nipy), which you can download here: