advice in dealing with clang bug: use non-default prefix?

[jaysachs]

Output of brew config

HOMEBREW_VERSION: 4.3.24
ORIGIN: https://github.com/Homebrew/brew
HEAD: 916044581862c32fc2365e8e9ff0b1507a98925e
Last commit: 6 days ago
Core tap JSON: 24 Sep 22:07 UTC
Core cask tap JSON: 24 Sep 22:07 UTC
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_MAKE_JOBS: 16
Homebrew Ruby: 3.3.4 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/3.3.4_1/bin/ruby
CPU: 16-core 64-bit kabylake
Clang: 16.0.0 build 1600
Git: 2.39.5 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 14.6.1-x86_64
CLT: 15.3.0.0.1.1708646388
Xcode: 16.0

Output of brew doctor

Warning: Some installed casks are deprecated or disabled.
You should find replacements for the following casks:
  wkhtmltopdf

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  [email protected]

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected dylibs:
  /usr/local/lib/libdvdcss.2.dylib
  /usr/local/lib/libwkhtmltox.0.12.6.dylib

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected header files:
  /usr/local/include/wkhtmltox/image.h
  /usr/local/include/wkhtmltox/pdf.h

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:
  [email protected]

Warning: Homebrew's "sbin" was not found in your PATH but you have installed
formulae that put executables in /usr/local/sbin.
Consider setting your PATH for example like so:
  echo 'export PATH="/usr/local/sbin:$PATH"' >> ~/.zshrc

Description of issue

TLDR: how weight-bearing are the fairly dire warnings about installing Homebrew outside of the default prefix?

Background: to the best of my understanding, it looks like /usr/bin/clang in XCode 16 (and possibly others) has a bug, in that -isystem directories are not prepended to the system search list, but instead added after /usr/local/include. This is a problem for some builds depending on e.g. boringssl (under bazel) where the openssl headers installed by homebrew in /usr/local/include are found before the boringssl headers (whose location is added via -isystem). (I reported the /usr/bin/clang bug here).

If someone has another suggestion on how to approach working around this, I'm all ears.

[carlocab]

You can brew unlink openssl@3 to remove the OpenSSL headers from /usr/local before building boringssl.

[jaysachs]

Interesting. And the consequences of that would be restricted to dealing with non-homebrew builds that I want to depend on the brew-installed openssl? (in which case I'd simply need to ensure /usr/local/Cellar/openssl@3/3.3.1/include is in the search path for those compilations) In particular, unlinking would not affect any homebrew-managed libraries/binaries depending on openssl? Or might it affect things that brew needs to build as well?

[carlocab]

It could affect things that brew needs to build. I suggest doing brew link openssl@3 when you're done.

[carlocab]

(in which case I'd simply need to ensure /usr/local/Cellar/openssl@3/3.3.1/include is in the search path for those compilations)

I also suggest treating */Cellar/* paths as implementation details that don't exist. Instead, use "$(brew --prefix openssl@3)" or /usr/local/opt/openssl@3.

[jaysachs]

Thanks -- after brew unlink for openssl, snappy, and leveldb, I can get my bazel build to succeed (or at least past the homebrew-related issues).

Maybe for a workaround I'll write a wrapper for brew that re-links those libraries, does the brew stuff, and then unlinks them ... or, I write a bazel wrapper which unlinks them, runs bazel, and then re-links. Neither is particularly satisfactory, but I run brew much less frequently.