Libraries were compiled with a flat namespace?

[mrjbq7]

Output of brew config

HOMEBREW_VERSION: 3.6.17-68-g106af03-dirty
ORIGIN: https://github.com/Homebrew/brew
HEAD: 106af035578d5f8716ae9510c1f9ad8c19f73a79
Last commit: 4 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 2c9e9e99ad98ea4826a3c035d266e8fd86218953
Core tap last commit: 86 minutes ago
Core tap branch: master
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DEVELOPER: set
HOMEBREW_EDITOR: /usr/bin/vim
HOMEBREW_MAKE_JOBS: 10
HOMEBREW_NO_ANALYTICS: set
Homebrew Ruby: 2.6.10 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: 10-core 64-bit arm_firestorm_icestorm
Clang: 14.0.0 build 1400
Git: 2.37.1 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 7.85.0 => /usr/bin/curl
macOS: 13.1-arm64
CLT: 14.2.0.0.1.1668646533
Xcode: 14.2
Rosetta 2: false

Output of brew doctor

brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause formulae that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  pygments
  docutils
  python-tabulate
  numpy
  six
  protobuf

Warning: You have uncommitted modifications to Homebrew/brew.
If this is a surprise to you, then you should stash these modifications.
Stashing returns Homebrew to a pristine state but can be undone
should you later need to do so for some reason.
  cd /opt/homebrew && git stash -u && git clean -d -f

Uncommitted files:
   M CHANGELOG.md
   M README.md

You have uncommitted modifications to Homebrew/homebrew-core.
If this is a surprise to you, then you should stash these modifications.
Stashing returns Homebrew to a pristine state but can be undone
should you later need to do so for some reason.
  cd /opt/homebrew/Library/Taps/homebrew/homebrew-core && git stash -u && git clean -d -f

Uncommitted files:
  ?? Formula/bzip3.rb

Description of issue

I am writing a formula for the bzip3 project:

class Bzip3 < Formula
  desc "Better and stronger spiritual successor to BZip2"
  homepage "https://github.com/kspalaiologos/bzip3"
  url "https://github.com/kspalaiologos/bzip3/releases/download/1.2.1/bzip3-1.2.1.tar.gz"
  sha256 "bba90d867f53efa4291de1df9c22da1578e1a93ca819e0fc68881da6fcc4149d"
  license "LGPL-3.0-only"

  def install
    system "./configure", *std_configure_args, "--disable-silent-rules", "--disable-arch-native"
    system "make", "install"
  end

  test do
    testfilepath = testpath + "sample_in.txt"
    zipfilepath = testpath + "sample_in.txt.bz3"

    testfilepath.write "TEST CONTENT"

    system "#{bin}/bzip3", testfilepath
    system "#{bin}/bunzip3", "-f", zipfilepath

    assert_equal "TEST CONTENT", testfilepath.read
  end
end

And I get an audit error for flat namespace:

$ brew audit bzip3
bzip3:
  * Libraries were compiled with a flat namespace.
    This can cause linker errors due to name collisions, and
    is often due to a bug in detecting the macOS version.
      /opt/homebrew/Cellar/bzip3/1.2.1/lib/libbzip3.0.dylib
Error: 1 problem in 1 formula detected

I'm not sure how to resolve this, or understand exactly what is causing this issue -- could you assist?

[SMillerDev]

The configure script is using outdated settings for macOS and should be reconfigured using a new autoconf to prevent flat namespaces.

[mrjbq7]

In talking to the upstream project, they are already using the latest autoconf version 2.71.

iczelia/bzip3#81 (comment)

[mrjbq7]

Using this patch makes it work:

  # Fix -flat_namespace being used on Big Sur and later.
  patch do
    url "https://raw.githubusercontent.com/Homebrew/formula-patches/03cf8088210822aa2c1ab544ed58ea04c897d9c4/libtool/configure-big_sur.diff"
    sha256 "35acd6aebc19843f1a2b3a63e880baceb0f5278ab1ace661e57a502d9d78c93c"
  end

[mrjbq7]

Further investigation shows this is an issue in the current stable release of libtool 2.4.6, which is standard in ubuntu 22.04 LTS.

The patch is required unless you are able to use the development release of libtool 2.4.7 or newer, which is available from ubuntu 22.10.