Linkage broken with wrong HOMEBREW_PREFIX on Apple Silicon #5605

emmercm · 2024-09-15T07:42:07Z

emmercm
Sep 15, 2024
Sponsor

Output of `brew config`

HOMEBREW_VERSION: 4.3.21-18-g1f306b4
ORIGIN: https://github.com/Homebrew/brew
HEAD: 1f306b4d150cf1c72791786d6180a6ab83aea03d
Last commit: 29 hours ago
Core tap JSON: 15 Sep 07:28 UTC
Core cask tap JSON: 15 Sep 07:28 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_EDITOR: /usr/bin/nano
HOMEBREW_MAKE_JOBS: 8
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 3.3.4 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.3.4_1/bin/ruby
CPU: octa-core 64-bit arm_blizzard_avalanche
Clang: 15.0.0 build 1500
Git: 2.39.3 => /Library/Developer/CommandLineTools/usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 14.6.1-arm64
CLT: 15.3.0.0.1.1708646388
Xcode: N/A
Rosetta 2: false

Output of `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:
  igir

Warning: Broken symlinks were found. Remove them with `brew cleanup`:
  /opt/homebrew/bin/rar
  /opt/homebrew/bin/unrar
  /opt/homebrew/opt/igir
  /opt/homebrew/opt/python@3

Description of issue

I cannot for the life of me figure out why the formula in my tap has broken linkages.

I have a formula (permalink) that depends_on libdeflate, libuv, lz4, node@20, and sdl2. When I install it via typical commands on my M2 MacBook:

brew tap emmercm/igir
brew install igir

I get a broken linkage:

$ brew linkage --test igir
Missing libraries:
  /usr/local/opt/libuv/lib/libuv.1.dylib
  /usr/local/opt/lz4/lib/liblz4.1.dylib
  /usr/local/opt/sdl2/lib/libSDL2-2.0.0.dylib

My understanding is that /usr/local was replaced with /opt/homebrew on Apple silicon. If so, why is Homebrew looking for these libraries in the old prefix? The libraries do get installed correctly in the new prefix:

$ ls -al /opt/homebrew/opt/*               
lrwxr-xr-x  1 cemmer  admin  22 Sep 15 00:27 /opt/homebrew/opt/brotli -> ../Cellar/brotli/1.1.0
lrwxr-xr-x  1 cemmer  admin  23 Sep 15 00:27 /opt/homebrew/opt/c-ares -> ../Cellar/c-ares/1.33.1
lrwxr-xr-x  1 cemmer  admin  36 Sep 15 00:27 /opt/homebrew/opt/ca-certificates -> ../Cellar/ca-certificates/2024-07-02
lrwxr-xr-x  1 cemmer  admin  20 Sep 15 00:27 /opt/homebrew/opt/icu4c -> ../Cellar/icu4c/74.2
lrwxr-xr-x  1 cemmer  admin  20 Sep 15 00:28 /opt/homebrew/opt/igir -> ../Cellar/igir/3.0.0
lrwxr-xr-x  1 cemmer  admin  25 Sep 15 00:27 /opt/homebrew/opt/libdeflate -> ../Cellar/libdeflate/1.21
lrwxr-xr-x  1 cemmer  admin  27 Sep 15 00:27 /opt/homebrew/opt/libnghttp2 -> ../Cellar/libnghttp2/1.63.0
lrwxr-xr-x  1 cemmer  admin  22 Sep 15 00:27 /opt/homebrew/opt/libuv -> ../Cellar/libuv/1.48.0
lrwxr-xr-x  1 cemmer  admin  20 Sep 15 00:27 /opt/homebrew/opt/lz4 -> ../Cellar/lz4/1.10.0
lrwxr-xr-x  1 cemmer  admin  25 Sep 15 00:27 /opt/homebrew/opt/node@20 -> ../Cellar/node@20/20.17.0
lrwxr-xr-x  1 cemmer  admin  25 Sep 15 00:27 /opt/homebrew/opt/openssl -> ../Cellar/openssl@3/3.3.2
lrwxr-xr-x  1 cemmer  admin  25 Sep 15 00:27 /opt/homebrew/opt/openssl@3 -> ../Cellar/openssl@3/3.3.2
lrwxr-xr-x  1 cemmer  admin  25 Sep 15 00:27 /opt/homebrew/opt/openssl@3.3 -> ../Cellar/openssl@3/3.3.2
lrwxr-xr-x@ 1 cemmer  admin  28 Sep  2 14:40 /opt/homebrew/opt/python@3 -> ../Cellar/python@3.12/3.12.5
lrwxr-xr-x  1 cemmer  admin  21 Sep 15 00:27 /opt/homebrew/opt/sdl2 -> ../Cellar/sdl2/2.30.7

$ ls -al /opt/homebrew/opt/libuv/lib/
total 1024
drwxr-xr-x   6 cemmer  admin     192 Sep 15 00:27 .
drwxr-xr-x  14 cemmer  admin     448 Sep 15 00:27 ..
-r--r--r--   1 cemmer  admin  229392 Sep 15 00:27 libuv.1.dylib
-r--r--r--   1 cemmer  admin  288280 Feb  7  2024 libuv.a
lrwxr-xr-x   1 cemmer  admin      13 Feb  7  2024 libuv.dylib -> libuv.1.dylib
drwxr-xr-x   3 cemmer  admin      96 Sep 15 00:27 pkgconfig

$ ls -al /opt/homebrew/opt/lz4/lib   
total 648
drwxr-xr-x   7 cemmer  admin     224 Sep 15 00:27 .
drwxr-xr-x  12 cemmer  admin     384 Sep 15 00:27 ..
-rw-r--r--   1 cemmer  admin  176960 Sep 15 00:27 liblz4.1.10.0.dylib
lrwxr-xr-x   1 cemmer  admin      19 Jul 21 10:29 liblz4.1.dylib -> liblz4.1.10.0.dylib
-r--r--r--   1 cemmer  admin  150632 Jul 21 10:29 liblz4.a
lrwxr-xr-x   1 cemmer  admin      19 Jul 21 10:29 liblz4.dylib -> liblz4.1.10.0.dylib
drwxr-xr-x   3 cemmer  admin      96 Sep 15 00:27 pkgconfig

$ ls -al /opt/homebrew/opt/sdl2/lib/
total 8504
drwxr-xr-x   9 cemmer  admin      288 Sep 15 00:27 .
drwxr-xr-x  12 cemmer  admin      384 Sep 15 00:27 ..
drwxr-xr-x   3 cemmer  admin       96 Sep  1 08:21 cmake
-rw-r--r--   1 cemmer  admin  1561776 Sep 15 00:27 libSDL2-2.0.0.dylib
-r--r--r--   1 cemmer  admin  2522120 Sep  1 08:21 libSDL2.a
lrwxr-xr-x   1 cemmer  admin       19 Sep  1 08:21 libSDL2.dylib -> libSDL2-2.0.0.dylib
-r--r--r--   1 cemmer  admin   260608 Sep  1 08:21 libSDL2_test.a
-r--r--r--   1 cemmer  admin      736 Sep  1 08:21 libSDL2main.a
drwxr-xr-x   3 cemmer  admin       96 Sep 15 00:27 pkgconfig

I get the same issue when I try to test the formula in CI, with the caveat that I have to force HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 because otherwise the update-after-install will unlink my binary because of the broken linkage:

$ HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 brew install --debug --verbose --formula --build-from-source "$(pwd)/Formula/igir.rb"

$ brew linkage --test igir
Missing libraries:
  /usr/local/opt/libuv/lib/libuv.1.dylib
  /usr/local/opt/lz4/lib/liblz4.1.dylib
  /usr/local/opt/sdl2/lib/libSDL2-2.0.0.dylib

carlocab · 2024-09-15T08:03:00Z

carlocab
Sep 15, 2024

Your call to npm install probably installs pre-built binaries (which npm is notorious for), which is why they link to libraries installed in /usr/local. You need to install those prebuilt binaries from source in order to link to libraries in /opt/homebrew.

3 replies

emmercm Sep 15, 2024
Author Sponsor

Do you mean they need to be linked there because the prebuilt binaries would expect them there?

But you're absolutely right, there is a prebuilt binary:

 ==> Finishing up
/opt/homebrew/Library/Homebrew/brew.rb (Cask::CaskLoader::NullLoader): loading igir
ln -s ../Cellar/igir/3.0.0/bin/igir igir
==> Changing dylib ID of /opt/homebrew/Cellar/igir/3.0.0/libexec/lib/node_modules/igir/node_modules/@node-rs/crc32-darwin-arm64/crc32.darwin-arm64.node
  from /Users/runner/work/node-rs/node-rs/target/aarch64-apple-darwin/release/deps/libnode_rs_crc32.dylib
    to /opt/homebrew/opt/igir/libexec/lib/node_modules/igir/node_modules/@node-rs/crc32-darwin-arm64/libnode_rs_crc32.dylib
==> Codesigning /opt/homebrew/Cellar/igir/3.0.0/libexec/lib/node_modules/igir/node_modules/@node-rs/crc32-darwin-arm64/crc32.darwin-arm64.node
/usr/bin/env codesign --display --file-list - /opt/homebrew/Cellar/igir/3.0.0/libexec/lib/node_modules/igir/node_modules/@node-rs/crc32-darwin-arm64/crc32.darwin-arm64.node

except it's also written to /opt/homebrew.

I'm mostly confused about the behavior of why Homebrew is installing packages in one directory but then immediately expecting them to be in another.

carlocab Sep 15, 2024

I'm mostly confused about the behavior of why Homebrew is installing packages in one directory but then immediately expecting them to be in another.

It's not Homebrew that expects them to be in a given location -- it's the prebuilt binary that does. Homebrew is just complaining because it knows that the prebuilt binaries were built to look in the wrong locations.

To see this, try doing otool -L on the prebuilt binaries that were installed by emmercm/igir/igir, e.g.

otool -L /opt/homebrew/Cellar/igir/3.0.0/libexec/lib/node_modules/igir/node_modules/@node-rs/crc32-darwin-arm64/crc32.darwin-arm64.node

and then do otool -L on the prebuilt binaries that were installed by doing npm install outside of Homebrew.

This should hopefully make clear that the fact that emmercm/igir/igir looks for libraries in /usr/local does not have anything to do with Homebrew, and instead has everything to do with how the prebuilt binaries you installed were built.

emmercm Sep 15, 2024
Author Sponsor

Understood on the prebuilt binaries, that makes sense.

I think the log message I provided is a red herring, I have two npm packages that provide binaries for both ARM and x64. Does Homebrew run otool -L against all npm-installed executables and change its behavior accordingly?

ARM binary that depends on sdl2:

$ otool -L /opt/homebrew/Cellar/igir/3.0.0.reinstall/libexec/lib/node_modules/igir/node_modules/chdman/bin/darwin/arm64/chdman 
/opt/homebrew/Cellar/igir/3.0.0.reinstall/libexec/lib/node_modules/igir/node_modules/chdman/bin/darwin/arm64/chdman:
	/System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore (compatibility version 1.2.0, current version 1.11.0, weak)
	/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)
	/System/Library/Frameworks/IOKit.framework/Versions/A/IOKit (compatibility version 1.0.0, current version 275.0.0)
	/System/Library/Frameworks/Metal.framework/Versions/A/Metal (compatibility version 1.0.0, current version 341.16.0, weak)
	/System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio (compatibility version 1.0.0, current version 1.0.0)
	/System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox (compatibility version 1.0.0, current version 1000.0.0)
	/System/Library/Frameworks/CoreHaptics.framework/Versions/A/CoreHaptics (compatibility version 1.0.0, current version 1.0.0, weak)
	/System/Library/Frameworks/GameController.framework/Versions/A/GameController (compatibility version 1.0.0, current version 11.0.24, weak)
	/System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback (compatibility version 1.0.0, current version 1.0.2)
	/System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo (compatibility version 1.2.0, current version 1.5.0)
	/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa (compatibility version 1.0.0, current version 24.0.0)
	/System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 170.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1336.0.0)
	/opt/homebrew/opt/sdl2/lib/libSDL2-2.0.0.dylib (compatibility version 3001.0.0, current version 3001.5.0)
	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 1600.151.0)
	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 64.0.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 2048.1.255)
	/System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 1226.0.0)

x64 binary:

$ otool -L /opt/homebrew/Cellar/igir/3.0.0.reinstall/libexec/lib/node_modules/igir/node_modules/chdman/bin/darwin/x64/chdman  
/opt/homebrew/Cellar/igir/3.0.0.reinstall/libexec/lib/node_modules/igir/node_modules/chdman/bin/darwin/x64/chdman:
	/System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore (compatibility version 1.2.0, current version 1.11.0, weak)
	/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)
	/System/Library/Frameworks/IOKit.framework/Versions/A/IOKit (compatibility version 1.0.0, current version 275.0.0)
	/System/Library/Frameworks/Metal.framework/Versions/A/Metal (compatibility version 1.0.0, current version 341.35.0, weak)
	/System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio (compatibility version 1.0.0, current version 1.0.0)
	/System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox (compatibility version 1.0.0, current version 1000.0.0)
	/System/Library/Frameworks/CoreHaptics.framework/Versions/A/CoreHaptics (compatibility version 1.0.0, current version 1.0.0, weak)
	/System/Library/Frameworks/GameController.framework/Versions/A/GameController (compatibility version 1.0.0, current version 11.2.3, weak)
	/System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback (compatibility version 1.0.0, current version 1.0.2)
	/System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo (compatibility version 1.2.0, current version 1.5.0)
	/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa (compatibility version 1.0.0, current version 24.0.0)
	/System/Library/Frameworks/Carbon.framework/Versions/A/Carbon (compatibility version 2.0.0, current version 170.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1336.61.1)
	/usr/local/opt/sdl2/lib/libSDL2-2.0.0.dylib (compatibility version 3001.0.0, current version 3001.5.0)
	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 1600.157.0)
	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 64.0.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 2202.0.0)
	/System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 1226.0.0)

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Homebrew

Linkage broken with wrong HOMEBREW_PREFIX on Apple Silicon #5605

emmercm Sep 15, 2024 Sponsor

Output of brew config

Output of brew doctor

Description of issue

Replies: 1 comment · 3 replies

carlocab Sep 15, 2024

emmercm Sep 15, 2024 Author Sponsor

carlocab Sep 15, 2024

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emmercm
Sep 15, 2024
Sponsor

Output of `brew config`

Output of `brew doctor`

Replies: 1 comment 3 replies

carlocab
Sep 15, 2024

emmercm Sep 15, 2024
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emmercm Sep 15, 2024
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