Closed zhemingfan closed 2 years ago
This looks like a compiler error. OSX uses a different compiler by default than linux distributions. Could you post the version of that? gcc --version
Did you update setuptools and pip before installing? Newer versions of those install pre-compiled binaries where possible which often allows you to bypass compilation problems
pip install --upgrade pip setuptools
prior to installation
setuptools version: 54.0.0
pip version: pip 21.0.1
Gcc version output:
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/c++/4.2.1 Apple clang version 12.0.0 (clang-1200.0.32.27) Target: x86_64-apple-darwin19.6.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin
MAVIS is primarily developed for linux, although I have tested it on some OSX environments. The issue here appears to be happening during installing pysam. It doesn't have a pre-compiled binary for your OS and so it attempts to compile it from scratch, but b/c OSX uses a non-standard compiler (clang instead of gcc) it is running into issues
Python 3.9 is super new so it might not have all the pre-compiled verisons yet, could you try with a lower python version? perhaps 3.8 or 3.7?
Ok I have been able to reproduce a similar error on ubuntu with python3.9 + pysam so it may not be a OS issue. We will look into this further. @calchoo we froze pysam at 0.15.1 because of breaking changes in 0.15.2, do you remember what those were? have they been fixed?
Okay great thanks!
Describe the bug
To Reproduce Steps to reproduce the behavior:
blat
and create a separate python virtual environment:Expected behavior Complete installation of MAVIS with expected output.
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