Skip to content

Error installing brewsci/bio/kat #1615

@RSLow25

Description

@RSLow25

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?

To help us debug your issue please explain:

  • What you were trying to do (and why)
    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.
  • 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, python@3.11 and scipy
    ==> Installing brewsci/bio/kat dependency: brewsci/bio/matplotlib
    ==> /opt/homebrew/opt/python@3.9/bin/python3 -c import setuptools... --no-user-c
    Last 15 lines from /Users/Ross/Library/Logs/Homebrew/matplotlib/01.python3:

/opt/homebrew/opt/python@3.9/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

  • What you expected to happen
    I was expecting the package to install correctly and be ready to use.
  • Step-by-step reproduction instructions (by running 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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type
    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions