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Please fill out the issue checklist below, and provide all of the requested information.
Please always follow these steps:
[ x] Confirmed this is a problem with brew installing one, specific formula and not every time you run brew? If it's a general brew problem please file this issue at https://github.com/Homebrew/brew/issues/new.
[ x] Ran brew update and retried your prior step?
[ x] Ran brew doctor, fixed all issues and retried your prior step?
[ x] Ran brew gist-logs <formula> (where <formula> is the name of the formula that failed) and included the output link?
[ x] If brew gist-logs didn't work: ran brew config and brew doctor and included their output with your issue?
What happened (include command output)
The command (brew install brewsci/bio/kat) terminates unexpectedly and gives the following error message:
==> Installing kat from brewsci/bio
==> Installing dependencies for brewsci/bio/kat: brewsci/bio/matplotlib, pybind11, [email protected] and scipy
==> Installing brewsci/bio/kat dependency: brewsci/bio/matplotlib
==> /opt/homebrew/opt/[email protected]/bin/python3 -c import setuptools... --no-user-c
Last 15 lines from /Users/Ross/Library/Logs/Homebrew/matplotlib/01.python3:
Please fill out the issue checklist below, and provide all of the requested information.
Please always follow these steps:
brew install
ing one, specific formula and not every time you runbrew
? If it's a generalbrew
problem please file this issue at https://github.com/Homebrew/brew/issues/new.brew update
and retried your prior step?brew doctor
, fixed all issues and retried your prior step?brew gist-logs <formula>
(where<formula>
is the name of the formula that failed) and included the output link?brew gist-logs
didn't work: ranbrew config
andbrew doctor
and included their output with your issue?To help us debug your issue please explain:
I am trying to install KAT (Kmer analysis toolkit) as per the documentation (https://kat.readthedocs.io/en/latest/installation.html) on a new MacBook running Ventura 13.3.1.
The command (brew install brewsci/bio/kat) terminates unexpectedly and gives the following error message:
==> Installing kat from brewsci/bio
==> Installing dependencies for brewsci/bio/kat: brewsci/bio/matplotlib, pybind11, [email protected] and scipy
==> Installing brewsci/bio/kat dependency: brewsci/bio/matplotlib
==> /opt/homebrew/opt/[email protected]/bin/python3 -c import setuptools... --no-user-c
Last 15 lines from /Users/Ross/Library/Logs/Homebrew/matplotlib/01.python3:
/opt/homebrew/opt/[email protected]/bin/python3
-c
import setuptools, tokenize
file = 'setup.py'
exec(compile(getattr(tokenize, 'open', open)(file).read()
.replace('\r\n', '\n'), file, 'exec'))
--no-user-cfg
install
--prefix=/opt/homebrew/Cellar/matplotlib/3.3.4
--install-scripts=/opt/homebrew/Cellar/matplotlib/3.3.4/bin
--install-lib=/opt/homebrew/Cellar/matplotlib/3.3.4/lib/python3.9/site-packages
--single-version-externally-managed
--record=installed.txt
If reporting this issue please do so at (not Homebrew/brew or Homebrew/homebrew-core):
https://github.com/brewsci/homebrew-bio/issues
These open issues may also help:
matplotlib 3.5.1 #1497
I was expecting the package to install correctly and be ready to use.
brew install
commands)% brew config
HOMEBREW_VERSION: 4.0.17
ORIGIN: https://github.com/Homebrew/brew
HEAD: c0f8068573bbf886fdc78d3f9daca54d53e7e49e
Last commit: 2 days ago
Core tap JSON: 09 May 20:23 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_MAKE_JOBS: 12
Homebrew Ruby: 2.6.10 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: dodeca-core 64-bit arm_blizzard_avalanche
Clang: 14.0.3 build 1403
Git: 2.39.2 => /Library/Developer/CommandLineTools/usr/bin/git
Curl: 7.87.0 => /usr/bin/curl
macOS: 13.3.1-arm64
CLT: 14.3.0.0.1.1679647830
Xcode: N/A
Rosetta 2: false
% brew doctor
Your system is ready to brew.
Formula additions or changes
To get formulae added or changed in Brewsci/bio please file a Pull Request.
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