Tier 3 gcc@16 issue: Patch file must be within the formula repository.

[mathomp4]

Output of brew config

HOMEBREW_VERSION: 6.0.2-61-g8208306
ORIGIN: https://github.com/Homebrew/brew
HEAD: 8208306216edfa69b161deb91a199904a6086c4f
Last commit: 3 hours ago
Branch: main
Core tap HEAD: bb2d1102701a959fc844eff3d9dcca0ba24a3d47
Core tap last commit: 5 hours ago
Core tap JSON: 18 Jun 16:30 UTC
Core cask tap: N/A
HOMEBREW_PREFIX: /Users/mathomp4/.homebrew/brew
HOMEBREW_REPOSITORY: /Users/mathomp4/.homebrew/brew
HOMEBREW_CELLAR: /Users/mathomp4/.homebrew/brew/Cellar
HOMEBREW_CASK_OPTS: ["--appdir=/Users/mathomp4/Applications"]
HOMEBREW_DISPLAY: /var/run/com.apple.launchd.qcSptTFECU/org.xquartz:0
HOMEBREW_DOWNLOAD_CONCURRENCY: 24
HOMEBREW_EDITOR: /Users/mathomp4/.homebrew/brew/bin/vim
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_MAKE_JOBS: 12
HOMEBREW_NO_ENV_HINTS: set
HOMEBREW_REQUIRE_TAP_TRUST: set
Homebrew Ruby: 4.0.5 => /Users/mathomp4/.homebrew/brew/Library/Homebrew/vendor/portable-ruby/4.0.5_1/bin/ruby
CPU: dodeca-core 64-bit arm_blizzard_avalanche
Clang: 21.0.0 build 2100
Git: 2.54.0 => /Users/mathomp4/.homebrew/brew/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 26.5-arm64
CLT: 26.5.0.0.1777544298
Xcode: 26.5
Metal Toolchain: 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: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  pcre

Warning: Your Homebrew's prefix is not /opt/homebrew.

Most of Homebrew's bottles (binary packages) can only be used with the default prefix.
Consider uninstalling Homebrew and reinstalling into the default prefix.

This is a Tier 3 configuration:
  https://docs.brew.sh/Support-Tiers#tier-3
You can report issues with Tier 3 configurations to Homebrew/* repositories!
Read the above document before opening any issues or PRs.

Description of issue

As the above bits show, my Homebrew is not in /opt/homebrew because I don't have admin rights to my work laptop. So, yes, this means I have to do quite a bit of building from source, etc., but I'm used to that (queue grumble about frequent llvm releases).

But today I saw that gcc@16 is now available (thanks to @fxcoudert !). But when I tried to upgrade:

❯ brew upgrade gcc
==> Would upgrade 1 outdated package
gcc 15.2.0_1 -> 16.1.0
==> 1 homebrew/core formula that would build from source
gcc
==> Fetching downloads for: gcc
✔︎ API Source gcc.rb                                                                                                                                               Verified     11.2KB/ 11.2KB
Warning: Building gcc from source as the bottle needs:
- `HOMEBREW_CELLAR=/opt/homebrew/Cellar` (yours is /Users/mathomp4/.homebrew/brew/Cellar)
- `HOMEBREW_PREFIX=/opt/homebrew` (yours is /Users/mathomp4/.homebrew/brew)
==> Downloading https://raw.githubusercontent.com/Homebrew/homebrew-core/3046186df791842d30b7018d4ee1bcde2f2fa75a/Patches/gcc/gcc-16.1.0.diff
###################################################################################################################################################################################### 100.0%
Warning: Cannot verify integrity of 'fe34ebb263f1e1c027c8804a14b0252ce7a691438884be7926931de9ef645885--gcc-16.1.0.diff'.
No checksum was provided.
For your reference, the checksum is:
  sha256 "1593153257db78c270282742088ffe961b44d793f7bbaa458895357094d6f7fc"
✔︎ Formula gcc (16.1.0)                                                                                                                                            Verified    102.5MB/102.5MB
==> Upgrading gcc
  15.2.0_1 -> 16.1.0
==> Patching
Error: An exception occurred within a child process:
  ArgumentError: Patch file must be within the formula repository.

Now, ye olde ChatGPT said to do:

HOMEBREW_NO_INSTALL_FROM_API=1 brew upgrade gcc

and, well, that did get to configure (and is now building, I hope):

❯ HOMEBREW_NO_INSTALL_FROM_API=1 brew upgrade gcc
==> Auto-updating Homebrew...
==> You have `$HOMEBREW_NO_INSTALL_FROM_API` set
Homebrew >=4.1.0 is dramatically faster and less error-prone when installing
from the JSON API. Please consider unsetting `$HOMEBREW_NO_INSTALL_FROM_API`.
This message will only be printed once.


==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> New Formulae
ip2location: C library and CLI to geolocate IP addresses
liquidsoap: Audio and video streaming language
tirith: Detect terminal injection, homograph, and pipe-to-shell attacks

You have 1 outdated formula installed.

==> Would upgrade 1 outdated package
gcc 15.2.0_1 -> 16.1.0
==> 1 homebrew/core formula that would build from source
gcc
==> Fetching downloads for: gcc
Warning: Building gcc from source as the bottle needs:
- `HOMEBREW_CELLAR=/opt/homebrew/Cellar` (yours is /Users/mathomp4/.homebrew/brew/Cellar)
- `HOMEBREW_PREFIX=/opt/homebrew` (yours is /Users/mathomp4/.homebrew/brew)
✔︎ Formula gcc (16.1.0)                                                                                                                                            Verified    102.5MB/102.5MB
==> Upgrading gcc
  15.2.0_1 -> 16.1.0
==> Patching
Warning: Calling MacOS.sdk_path_if_needed is deprecated! Use MacOS.sdk_path instead.
Please report this issue to the Homebrew/homebrew-core tap, or even better, submit a PR to fix it:
  /Users/mathomp4/.homebrew/brew/Library/Taps/homebrew/homebrew-core/Formula/g/gcc.rb:110

==> ../configure --prefix=/Users/mathomp4/.homebrew/brew/opt/gcc --libdir=/Users/mathomp4/.homebrew/brew/opt/gcc/lib/gcc/current --disable-nls --enable-checking=release --with-gcc-major-ver
...

I guess my question is: is this now the right thing to do? Or is my non-standard brew setup broken in some way? (I've had it for years, so maybe the new JSON brew needs a fresh install?)

NOTE: The patch does seem to be there:

❯ ls -l "$(brew --repository homebrew/core)/Patches/gcc"
Permissions Size User     Group Date Modified Name
.rw-r--r--@ 1.8M mathomp4 staff 29 Oct  2025   gcc-11.5.0.diff
.rw-r--r--@ 667k mathomp4 staff 20 Mar 13:15   gcc-12.4.0.diff
.rw-r--r--@ 590k mathomp4 staff 29 Oct  2025   gcc-13.4.0.diff
.rw-r--r--@ 204k mathomp4 staff 29 Oct  2025   gcc-14.3.0.diff
.rw-r--r--@ 202k mathomp4 staff 29 Oct  2025   gcc-15.1.0.diff
.rw-r--r--@ 228k mathomp4 staff 18 Jun 08:58   gcc-15.3.0.diff
.rw-r--r--@ 202k mathomp4 staff 18 Jun 08:58   gcc-16.1.0.diff

but it's like brew doesn't see it? 🤷🏼

[mathomp4]

Update. I'm...not sure if it built or not.

I get an error but yet it says success.

==> gmake BOOT_LDFLAGS=-Wl,-headerpad_max_install_names
==> gmake install DESTDIR=/private/tmp/gcc-20260618-63256-s5y6bc/gcc-16.1.0/build/../instdir
Error: Failed changing dylib ID of /Users/mathomp4/.homebrew/brew/Cellar/gcc/16.1.0/lib/gcc/current/libatomic.1.dylib
  from @rpath/libatomic.1.dylib
    to /Users/mathomp4/.homebrew/brew/opt/gcc/lib/gcc/current/libatomic.1.dylib
Error: Failed to fix install linkage
Updated load commands do not fit in the header of /Users/mathomp4/.homebrew/brew/Cellar/gcc/16.1.0/lib/gcc/current/libatomic.1.dylib. /Users/mathomp4/.homebrew/brew/Cellar/gcc/16.1.0/lib/gcc/current/libatomic.1.dylib needs to be relinked, possibly with -headerpad or -headerpad_max_install_names
The formula built, but you may encounter issues using it or linking other
formulae against it.
==> Summary
🍺  /Users/mathomp4/.homebrew/brew/Cellar/gcc/16.1.0: 1,704 files, 498.8MB, built in 31 minutes 40 seconds
==> Running `brew cleanup gcc`...
Removing: /Users/mathomp4/.homebrew/brew/Cellar/gcc/15.2.0_1... (1,602 files, 462.4MB)
==> Upgraded 1 outdated package
gcc 15.2.0_1 -> 16.1.0
==> 1 homebrew/core formula built from source
gcc

[mathomp4]

Ahh. Update update. I think I am hitting Homebrew/homebrew-core#266996 as reported/fixed by @RazerM.

[alvinthomas]

I'm having the same issue and agree that this might be solved by @RazerM's approach.

[mathomp4]

Well, partially solved. So, it seems to work for brew install gcc. But Homebrew/homebrew-core#266996 only fixed the gcc formula. Running brew install gcc@15 still fails:

==> Patching
==> ../configure --prefix=/Users/mathomp4/.homebrew/brew/opt/gcc@15 --libdir=/Users/mathomp4/.homebrew/brew/opt/gcc@15/lib/gcc/15 --disable-nls --enable-checking=release --with-gcc-major-ve
==> gmake BOOT_LDFLAGS=-Wl,-headerpad_max_install_names
==> gmake install DESTDIR=/private/tmp/gccA15-20260622-15280-jeaqwj/gcc-15.3.0/build/../instdir
Error: Failed changing dylib ID of /Users/mathomp4/.homebrew/brew/Cellar/gcc@15/15.3.0/lib/gcc/15/libatomic.1.dylib
  from @rpath/libatomic.1.dylib
    to /Users/mathomp4/.homebrew/brew/opt/gcc@15/lib/gcc/15/libatomic.1.dylib
Error: Failed to fix install linkage
Updated load commands do not fit in the header of /Users/mathomp4/.homebrew/brew/Cellar/gcc@15/15.3.0/lib/gcc/15/libatomic.1.dylib. /Users/mathomp4/.homebrew/brew/Cellar/gcc@15/15.3.0/lib/gcc/15/libatomic.1.dylib needs to be relinked, possibly with -headerpad or -headerpad_max_install_names
The formula built, but you may encounter issues using it or linking other
formulae against it.
Warning: The post-install step did not complete successfully
You can try again using:
  brew postinstall gcc@15
==> Summary
🍺  /Users/mathomp4/.homebrew/brew/Cellar/gcc@15/15.3.0: 1,574 files, 463.7MB, built in 29 minutes 3 seconds
==> Running `brew cleanup gcc@15`...

Ugh. Query for @RazerM and @fxcoudert : I can submit a PR to fix this (though I'll need to remember my "How do I make PRs by hand to brew" steps), but how far back should I go? It looks like gcc@12 to gcc@15 would have the issue since they have the make_args line similar to gcc@16. Is there a compelling reason to try and fix up older gcc? I mean, I don't use gcc@12 even, but I know it's still popular. But is gcc@11 and older still in use on macOS?

[mathomp4]

And I guess one more change to make as well:

Warning: Calling MacOS.sdk_path_if_needed is deprecated! Use MacOS.sdk_path instead.
Please report this issue to the Homebrew/homebrew-core tap, or even better, submit a PR to fix it:
  /Users/mathomp4/.homebrew/brew/Library/Taps/homebrew/homebrew-core/Formula/g/gcc.rb:111

PR time today for me!

[fxcoudert]

==> Patching
Error: An exception occurred within a child process:
  ArgumentError: Patch file must be within the formula repository.

This I think is a brew bug, and should be reported there.

Warning: Calling MacOS.sdk_path_if_needed is deprecated! Use MacOS.sdk_path instead.

This is just a warning, can be safely ignored.

I guess my question is: is this now the right thing to do?

HOMEBREW_NO_INSTALL_FROM_API is a workaround but I think the root cause is a bug in the new "local file patch" feature in brew.

Error: Failed changing dylib ID of /Users/mathomp4/.homebrew/brew/Cellar/gcc/16.1.0/lib/gcc/current/libatomic.1.dylib
  from @rpath/libatomic.1.dylib
    to /Users/mathomp4/.homebrew/brew/opt/gcc/lib/gcc/current/libatomic.1.dylib

Yes, this might be fixed by Homebrew/homebrew-core#266996 with emphasis on might. The solution works sometimes but not always, we don't have a foolproof solution for that problem.

[mathomp4]

==> Patching
Error: An exception occurred within a child process:
  ArgumentError: Patch file must be within the formula repository.

This I think is a brew bug, and should be reported there.

@fxcoudert Okay. I'll make sure I can duplicate and report there (I just wasn't sure if I was allowed to report Tier 3 bugs on the main repos (hence, discussions).

Also...which brew repo? homebrew-core or brew?

[fxcoudert]

Please report on the brew repo, and mention me in the report. I'll try to have a look.

[branchv]

This was reported and fixed in Homebrew/brew#22802

[mathomp4]

So, good news. Homebrew/brew#22802 does fix the patch thing.

Bad news, I can't build gcc@15 because of the other issue talked about above. But getting close!