understanding the output of brew doctor

[ipatch]

Output of brew config

HOMEBREW_VERSION: 4.4.0-127-g3291ad4
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: 3291ad4fc78f33f8e9bb7ce37745d2a0e697f5fb
Last commit: 3 days ago
Core tap origin: https://github.com/ipatch/homebrew-core.git
Core tap HEAD: ceae918b13e65c6d899ee07b27d6b63587ef7408
Core tap last commit: 2 days ago
Core tap branch: ipatch.asahi.qt@5
HOMEBREW_PREFIX: /home/capin/homebrew
HOMEBREW_REPOSITORY: /home/capin/homebrew
HOMEBREW_CELLAR: /home/capin/homebrew/Cellar
HOMEBREW_CACHE: /home/capin/homebrew/cache
HOMEBREW_CASK_OPTS: []
HOMEBREW_DEVELOPER: set
HOMEBREW_DISPLAY: localhost:10.0
HOMEBREW_EDITOR: nvim
HOMEBREW_MAKE_JOBS: 8
HOMEBREW_NO_ANALYTICS: set
HOMEBREW_NO_AUTOREMOVE: set
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_GITHUB_API: set
HOMEBREW_NO_INSTALL_CLEANUP: set
HOMEBREW_NO_INSTALL_FROM_API: set
HOMEBREW_SORBET_RUNTIME: set
HOMEBREW_TEMP: /opt/tmp/homebrew
Homebrew Ruby: 3.3.5 => /home/capin/homebrew/Cellar/ruby/3.3.5/bin/ruby
CPU: octa-core 64-bit arm
Clang: 19.1.1
Git: 2.47.0 => /bin/git
Curl: 8.6.0 => /bin/curl
Kernel: Linux 6.9.12-401.asahi.fc39.aarch64+16k aarch64 GNU/Linux
OS: Fedora Asahi Remix release 40 (Forty)
Host glibc: 2.39
/usr/bin/gcc: 14.2.1
/usr/bin/ruby: 3.3.5
glibc: N/A
gcc@11: N/A
gcc: 14.2.0
xorg: N/A

Output of brew doctor

xclip: Error: Can't open display: localhost:10.0
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: Suspicious https://github.com/Homebrew/homebrew-core git origin remote found.
The current git origin is:
  https://github.com/ipatch/homebrew-core.git

With a non-standard origin, Homebrew won't update properly.
You can solve this by setting the origin remote:
  git -C "/home/capin/homebrew/Library/Taps/homebrew/homebrew-core" remote set-url origin https://github.com/Homebrew/homebrew-core

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/libspl/assert.h
  /usr/local/include/libspl/atomic.h
  /usr/local/include/libspl/libgen.h
  /usr/local/include/libspl/libshare.h
  /usr/local/include/libspl/rpc/xdr.h
  /usr/local/include/libspl/statcommon.h
  /usr/local/include/libspl/stdlib.h
  /usr/local/include/libspl/string.h
  /usr/local/include/libspl/sys/acl.h
  /usr/local/include/libspl/sys/acl_impl.h
  /usr/local/include/libspl/sys/asm_linkage.h
  /usr/local/include/libspl/sys/byteorder.h
  /usr/local/include/libspl/sys/callb.h
  /usr/local/include/libspl/sys/cmn_err.h
  /usr/local/include/libspl/sys/cred.h
  /usr/local/include/libspl/sys/debug.h
  /usr/local/include/libspl/sys/dkio.h
  /usr/local/include/libspl/sys/dklabel.h
  /usr/local/include/libspl/sys/dktp/fdisk.h
  /usr/local/include/libspl/sys/errno.h
  /usr/local/include/libspl/sys/feature_tests.h
  /usr/local/include/libspl/sys/ia32/asm_linkage.h
  /usr/local/include/libspl/sys/inttypes.h
  /usr/local/include/libspl/sys/isa_defs.h
  /usr/local/include/libspl/sys/kmem.h
  /usr/local/include/libspl/sys/kstat.h
  /usr/local/include/libspl/sys/list.h
  /usr/local/include/libspl/sys/list_impl.h
  /usr/local/include/libspl/sys/mhd.h
  /usr/local/include/libspl/sys/mkdev.h
  /usr/local/include/libspl/sys/mnttab.h
  /usr/local/include/libspl/sys/mount.h
  /usr/local/include/libspl/sys/param.h
  /usr/local/include/libspl/sys/policy.h
  /usr/local/include/libspl/sys/poll.h
  /usr/local/include/libspl/sys/priv.h
  /usr/local/include/libspl/sys/processor.h
  /usr/local/include/libspl/sys/simd.h
  /usr/local/include/libspl/sys/stack.h
  /usr/local/include/libspl/sys/stat.h
  /usr/local/include/libspl/sys/stdtypes.h
  /usr/local/include/libspl/sys/string.h
  /usr/local/include/libspl/sys/sunddi.h
  /usr/local/include/libspl/sys/sysmacros.h
  /usr/local/include/libspl/sys/systeminfo.h
  /usr/local/include/libspl/sys/time.h
  /usr/local/include/libspl/sys/trace_spl.h
  /usr/local/include/libspl/sys/trace_zfs.h
  /usr/local/include/libspl/sys/types.h
  /usr/local/include/libspl/sys/types32.h
  /usr/local/include/libspl/sys/uio.h
  /usr/local/include/libspl/sys/vnode.h
  /usr/local/include/libspl/sys/wmsum.h
  /usr/local/include/libspl/sys/zfs_context_os.h
  /usr/local/include/libspl/sys/zone.h
  /usr/local/include/libspl/umem.h
  /usr/local/include/libspl/unistd.h
  /usr/local/include/libspl/zone.h
  /usr/local/include/libzfs/cityhash.h
  /usr/local/include/libzfs/libnvpair.h
  /usr/local/include/libzfs/libuutil.h
  /usr/local/include/libzfs/libuutil_common.h
  /usr/local/include/libzfs/libuutil_impl.h
  /usr/local/include/libzfs/libzfs.h
  /usr/local/include/libzfs/libzfs_core.h
  /usr/local/include/libzfs/libzfsbootenv.h
  /usr/local/include/libzfs/libzutil.h
  /usr/local/include/libzfs/sys/abd.h
  /usr/local/include/libzfs/sys/abd_impl.h
  /usr/local/include/libzfs/sys/aggsum.h
  /usr/local/include/libzfs/sys/arc.h
  /usr/local/include/libzfs/sys/arc_impl.h
  /usr/local/include/libzfs/sys/asm_linkage.h
  /usr/local/include/libzfs/sys/avl.h
  /usr/local/include/libzfs/sys/avl_impl.h
  /usr/local/include/libzfs/sys/bitmap.h
  /usr/local/include/libzfs/sys/bitops.h
  /usr/local/include/libzfs/sys/blake3.h
  /usr/local/include/libzfs/sys/blkptr.h
  /usr/local/include/libzfs/sys/bplist.h
  /usr/local/include/libzfs/sys/bpobj.h
  /usr/local/include/libzfs/sys/bptree.h
  /usr/local/include/libzfs/sys/bqueue.h
  /usr/local/include/libzfs/sys/brt.h
  /usr/local/include/libzfs/sys/brt_impl.h
  /usr/local/include/libzfs/sys/btree.h
  /usr/local/include/libzfs/sys/crypto/api.h
  /usr/local/include/libzfs/sys/crypto/common.h
  /usr/local/include/libzfs/sys/crypto/icp.h
  /usr/local/include/libzfs/sys/dataset_kstats.h
  /usr/local/include/libzfs/sys/dbuf.h
  /usr/local/include/libzfs/sys/ddt.h
  /usr/local/include/libzfs/sys/dmu.h
  /usr/local/include/libzfs/sys/dmu_impl.h
  /usr/local/include/libzfs/sys/dmu_objset.h
  /usr/local/include/libzfs/sys/dmu_recv.h
  /usr/local/include/libzfs/sys/dmu_redact.h
  /usr/local/include/libzfs/sys/dmu_send.h
  /usr/local/include/libzfs/sys/dmu_traverse.h
  /usr/local/include/libzfs/sys/dmu_tx.h
  /usr/local/include/libzfs/sys/dmu_zfetch.h
  /usr/local/include/libzfs/sys/dnode.h
  /usr/local/include/libzfs/sys/dsl_bookmark.h
  /usr/local/include/libzfs/sys/dsl_crypt.h
  /usr/local/include/libzfs/sys/dsl_dataset.h
  /usr/local/include/libzfs/sys/dsl_deadlist.h
  /usr/local/include/libzfs/sys/dsl_deleg.h
  /usr/local/include/libzfs/sys/dsl_destroy.h
  /usr/local/include/libzfs/sys/dsl_dir.h
  /usr/local/include/libzfs/sys/dsl_pool.h
  /usr/local/include/libzfs/sys/dsl_prop.h
  /usr/local/include/libzfs/sys/dsl_scan.h
  /usr/local/include/libzfs/sys/dsl_synctask.h
  /usr/local/include/libzfs/sys/dsl_userhold.h
  /usr/local/include/libzfs/sys/edonr.h
  /usr/local/include/libzfs/sys/efi_partition.h
  /usr/local/include/libzfs/sys/fm/fs/zfs.h
  /usr/local/include/libzfs/sys/fm/protocol.h
  /usr/local/include/libzfs/sys/fm/util.h
  /usr/local/include/libzfs/sys/frame.h
  /usr/local/include/libzfs/sys/fs/zfs.h
  /usr/local/include/libzfs/sys/hkdf.h
  /usr/local/include/libzfs/sys/lua/lauxlib.h
  /usr/local/include/libzfs/sys/lua/lua.h
  /usr/local/include/libzfs/sys/lua/luaconf.h
  /usr/local/include/libzfs/sys/lua/lualib.h
  /usr/local/include/libzfs/sys/metaslab.h
  /usr/local/include/libzfs/sys/metaslab_impl.h
  /usr/local/include/libzfs/sys/mmp.h
  /usr/local/include/libzfs/sys/mntent.h
  /usr/local/include/libzfs/sys/mod.h
  /usr/local/include/libzfs/sys/multilist.h
  /usr/local/include/libzfs/sys/nvpair.h
  /usr/local/include/libzfs/sys/nvpair_impl.h
  /usr/local/include/libzfs/sys/objlist.h
  /usr/local/include/libzfs/sys/pathname.h
  /usr/local/include/libzfs/sys/qat.h
  /usr/local/include/libzfs/sys/range_tree.h
  /usr/local/include/libzfs/sys/rrwlock.h
  /usr/local/include/libzfs/sys/sa.h
  /usr/local/include/libzfs/sys/sa_impl.h
  /usr/local/include/libzfs/sys/sha2.h
  /usr/local/include/libzfs/sys/skein.h
  /usr/local/include/libzfs/sys/spa.h
  /usr/local/include/libzfs/sys/spa_checkpoint.h
  /usr/local/include/libzfs/sys/spa_checksum.h
  /usr/local/include/libzfs/sys/spa_impl.h
  /usr/local/include/libzfs/sys/spa_log_spacemap.h
  /usr/local/include/libzfs/sys/space_map.h
  /usr/local/include/libzfs/sys/space_reftree.h
  /usr/local/include/libzfs/sys/sysevent.h
  /usr/local/include/libzfs/sys/sysevent/dev.h
  /usr/local/include/libzfs/sys/sysevent/eventdefs.h
  /usr/local/include/libzfs/sys/txg.h
  /usr/local/include/libzfs/sys/txg_impl.h
  /usr/local/include/libzfs/sys/u8_textprep.h
  /usr/local/include/libzfs/sys/u8_textprep_data.h
  /usr/local/include/libzfs/sys/uberblock.h
  /usr/local/include/libzfs/sys/uberblock_impl.h
  /usr/local/include/libzfs/sys/uio_impl.h
  /usr/local/include/libzfs/sys/unique.h
  /usr/local/include/libzfs/sys/uuid.h
  /usr/local/include/libzfs/sys/vdev.h
  /usr/local/include/libzfs/sys/vdev_disk.h
  /usr/local/include/libzfs/sys/vdev_draid.h
  /usr/local/include/libzfs/sys/vdev_file.h
  /usr/local/include/libzfs/sys/vdev_impl.h
  /usr/local/include/libzfs/sys/vdev_indirect_births.h
  /usr/local/include/libzfs/sys/vdev_indirect_mapping.h
  /usr/local/include/libzfs/sys/vdev_initialize.h
  /usr/local/include/libzfs/sys/vdev_raidz.h
  /usr/local/include/libzfs/sys/vdev_raidz_impl.h
  /usr/local/include/libzfs/sys/vdev_rebuild.h
  /usr/local/include/libzfs/sys/vdev_removal.h
  /usr/local/include/libzfs/sys/vdev_trim.h
  /usr/local/include/libzfs/sys/xvattr.h
  /usr/local/include/libzfs/sys/zap.h
  /usr/local/include/libzfs/sys/zap_impl.h
  /usr/local/include/libzfs/sys/zap_leaf.h
  /usr/local/include/libzfs/sys/zcp.h
  /usr/local/include/libzfs/sys/zcp_global.h
  /usr/local/include/libzfs/sys/zcp_iter.h
  /usr/local/include/libzfs/sys/zcp_prop.h
  /usr/local/include/libzfs/sys/zcp_set.h
  /usr/local/include/libzfs/sys/zfeature.h
  /usr/local/include/libzfs/sys/zfs_acl.h
  /usr/local/include/libzfs/sys/zfs_bootenv.h
  /usr/local/include/libzfs/sys/zfs_chksum.h
  /usr/local/include/libzfs/sys/zfs_context.h
  /usr/local/include/libzfs/sys/zfs_debug.h
  /usr/local/include/libzfs/sys/zfs_delay.h
  /usr/local/include/libzfs/sys/zfs_file.h
  /usr/local/include/libzfs/sys/zfs_fuid.h
  /usr/local/include/libzfs/sys/zfs_impl.h
  /usr/local/include/libzfs/sys/zfs_project.h
  /usr/local/include/libzfs/sys/zfs_quota.h
  /usr/local/include/libzfs/sys/zfs_racct.h
  /usr/local/include/libzfs/sys/zfs_ratelimit.h
  /usr/local/include/libzfs/sys/zfs_refcount.h
  /usr/local/include/libzfs/sys/zfs_rlock.h
  /usr/local/include/libzfs/sys/zfs_sa.h
  /usr/local/include/libzfs/sys/zfs_stat.h
  /usr/local/include/libzfs/sys/zfs_sysfs.h
  /usr/local/include/libzfs/sys/zfs_vfsops.h
  /usr/local/include/libzfs/sys/zfs_vnops.h
  /usr/local/include/libzfs/sys/zfs_znode.h
  /usr/local/include/libzfs/sys/zil.h
  /usr/local/include/libzfs/sys/zil_impl.h
  /usr/local/include/libzfs/sys/zio.h
  /usr/local/include/libzfs/sys/zio_checksum.h
  /usr/local/include/libzfs/sys/zio_compress.h
  /usr/local/include/libzfs/sys/zio_crypt.h
  /usr/local/include/libzfs/sys/zio_impl.h
  /usr/local/include/libzfs/sys/zio_priority.h
  /usr/local/include/libzfs/sys/zrlock.h
  /usr/local/include/libzfs/sys/zstd/zstd.h
  /usr/local/include/libzfs/sys/zthr.h
  /usr/local/include/libzfs/thread_pool.h
  /usr/local/include/libzfs/zfeature_common.h
  /usr/local/include/libzfs/zfs_comutil.h
  /usr/local/include/libzfs/zfs_deleg.h
  /usr/local/include/libzfs/zfs_fletcher.h
  /usr/local/include/libzfs/zfs_namecheck.h
  /usr/local/include/libzfs/zfs_prop.h

Warning: Unbrewed '.la' files 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 '.la' files:
  /usr/local/lib/libnvpair.la
  /usr/local/lib/libuutil.la
  /usr/local/lib/libzfs.la
  /usr/local/lib/libzfs_core.la
  /usr/local/lib/libzfsbootenv.la
  /usr/local/lib/libzpool.la

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

Unexpected '.pc' files:
  /usr/local/lib/pkgconfig/libzfs.pc
  /usr/local/lib/pkgconfig/libzfs_core.pc
  /usr/local/lib/pkgconfig/libzfsbootenv.pc

Warning: Unbrewed static libraries 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 static libraries:
  /usr/local/lib/libnvpair.a
  /usr/local/lib/libuutil.a
  /usr/local/lib/libzfs.a
  /usr/local/lib/libzfs_core.a
  /usr/local/lib/libzfsbootenv.a
  /usr/local/lib/libzpool.a

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:
  gcc@13

Warning: Your Homebrew's prefix is not /home/linuxbrew/.linuxbrew.

Many of Homebrew's bottles (binary packages) can only be used with the default prefix.
Consider uninstalling Homebrew and reinstalling into the default prefix.
It is expected behaviour that some formulae will fail to build in this unsupported configuration.
It is expected behaviour that Homebrew will be buggy and slow.
Do not create any issues about this on Homebrew's GitHub repositories.
Do not create any issues even if you think this message is unrelated.
Any opened issues will be immediately closed without response.
Do not ask for help from Homebrew or its maintainers on social media.
You may ask for help in Homebrew's discussions but are unlikely to receive a response.
Try to figure out the problem yourself and submit a fix as a pull request.
We will review it but may or may not accept it.


Warning: Your CPU architecture (arm64) is not supported. We only support
x86_64 CPU architectures. You will be unable to use binary packages (bottles).
It is expected behaviour that some formulae will fail to build in this unsupported configuration.
It is expected behaviour that Homebrew will be buggy and slow.
Do not create any issues about this on Homebrew's GitHub repositories.
Do not create any issues even if you think this message is unrelated.
Any opened issues will be immediately closed without response.
Do not ask for help from Homebrew or its maintainers on social media.
You may ask for help in Homebrew's discussions but are unlikely to receive a response.
Try to figure out the problem yourself and submit a fix as a pull request.
We will review it but may or may not accept it.


Warning: Some taps are not on the default git origin branch and may not receive
updates. If this is a surprise to you, check out the default branch with:
  git -C $(brew --repo homebrew/core) checkout master

Description of issue

running homebrew on asahi linux here, and using one of the older kernels ie. 6.6.x 6.9.x so i get zfs support going on this box for various backup reasons. homebrew seems to work reasonable well on this setup, but something i am noticing and have noticed in the past is the warnings with brew doctor output.

for this particular homebrew setup i have homebrew setup in the below dir.

brew --prefix

output

/home/capin/homebrew

does it make sense for brew doctor to warn about files in /usr/local when that isn't even my prefix for my homebrew installation?

[ZhongRuoyu]

does it make sense for brew doctor to warn about files in /usr/local when that isn't even my prefix for my homebrew installation?

What brew doctor suggests is "they could cause problems when building Homebrew formulae". That is true. /usr/local/include, for example, is meant to be where C compilers look for local header files (see man 7 hier):

$ echo | gcc -xc -E -v -
[...]
 /usr/lib/gcc/x86_64-linux-gnu/11/cc1 -E -quiet -v -imultiarch x86_64-linux-gnu - -mtune=generic -march=x86-64 -fasynchronous-unwind-tables -fstack-protector-strong -Wformat -Wformat-security -fstack-clash-protection -fcf-protection -dumpbase -
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/11/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
 /usr/lib/gcc/x86_64-linux-gnu/11/include
 /usr/local/include
 /usr/include/x86_64-linux-gnu
 /usr/include
[...]

Notice that /usr/local/include is indeed in the list of header search paths.

So, to answer your question: it makes sense for brew doctor to warn about files in /usr/local, because they can affect formula builds. But you don't need to worry about this if it's not creating troubles for you, because, from the first part of your brew doctor output:

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!

[ipatch]

thanks for the thorough answer reply. 👍️

[ipatch]

well i guess you could say the plot thickens here. i just ran your above command, echo | gcc -xc -E -v - on my local arch linux install with homebrew, and i get the below output.

Using built-in specs.
COLLECT_GCC=gcc
Target: x86_64-pc-linux-gnu
Configured with: /build/gcc/src/gcc/configure --enable-languages=ada,c,c++,d,fortran,go,lto,m2,objc,obj-c++,rust --enable-bootstrap --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://gitlab.archlinux.org/archlinux/packaging/packages/gcc/-/issues --with-build-config=bootstrap-lto --with-linker-hash-style=gnu --with-system-zlib --enable-__cxa_atexit --enable-cet=auto --enable-checking=release --enable-clocale=gnu --enable-default-pie --enable-default-ssp --enable-gnu-indirect-function --enable-gnu-unique-object --enable-libstdcxx-backtrace --enable-link-serialization=1 --enable-linker-build-id --enable-lto --enable-multilib --enable-plugin --enable-shared --enable-threads=posix --disable-libssp --disable-libstdcxx-pch --disable-werror
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.1 20240910 (GCC)
COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'
 /usr/lib/gcc/x86_64-pc-linux-gnu/14.2.1/cc1 -E -quiet -v - -mtune=generic -march=x86-64 -dumpbase -
ignoring nonexistent directory "/usr/lib/gcc/x86_64-pc-linux-gnu/14.2.1/../../../../x86_64-pc-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
 /usr/lib/gcc/x86_64-pc-linux-gnu/14.2.1/include
 /usr/local/include
 /usr/lib/gcc/x86_64-pc-linux-gnu/14.2.1/include-fixed
 /usr/include
End of search list.
# 0 "<stdin>"
# 0 "<built-in>"
# 0 "<command-line>"
# 1 "/usr/include/stdc-predef.h" 1 3 4
# 0 "<command-line>" 2
# 1 "<stdin>"
COMPILER_PATH=/usr/lib/gcc/x86_64-pc-linux-gnu/14.2.1/:/usr/lib/gcc/x86_64-pc-linux-gnu/14.2.1/:/usr/lib/gcc/x86_64-pc-linux-gnu/:/usr/lib/gcc/x86_64-pc-linux-gnu/14.2.1/:/usr/lib/gcc/x86_64-pc-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-pc-linux-gnu/14.2.1/:/usr/lib/gcc/x86_64-pc-linux-gnu/14.2.1/../../../../lib/:/lib/../lib/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-pc-linux-gnu/14.2.1/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'

but that gcc reference in my path points to the non homebrew install of gcc. ie.

╰─λ type -a gcc
gcc is /usr/bin/gcc
gcc is /bin/gcc

and the homebrew gcc compilers i have installed are

╰─λ l $bp/bin/gcc-*
lrwxrwxrwx 1 capin users 34 Sep 24 18:49 /home/capin/homebrew/bin/gcc-13 -> '../Cellar/gcc@13/13.3.0/bin/gcc-13'*
lrwxrwxrwx 1 capin users 31 Sep 24 21:06 /home/capin/homebrew/bin/gcc-14 -> ../Cellar/gcc/14.2.0/bin/gcc-14*
lrwxrwxrwx 1 capin users 37 Sep 24 18:49 /home/capin/homebrew/bin/gcc-ar-13 -> '../Cellar/gcc@13/13.3.0/bin/gcc-ar-13'*
lrwxrwxrwx 1 capin users 34 Sep 24 21:06 /home/capin/homebrew/bin/gcc-ar-14 -> ../Cellar/gcc/14.2.0/bin/gcc-ar-14*
lrwxrwxrwx 1 capin users 37 Sep 24 18:49 /home/capin/homebrew/bin/gcc-nm-13 -> '../Cellar/gcc@13/13.3.0/bin/gcc-nm-13'*
lrwxrwxrwx 1 capin users 34 Sep 24 21:06 /home/capin/homebrew/bin/gcc-nm-14 -> ../Cellar/gcc/14.2.0/bin/gcc-nm-14*
lrwxrwxrwx 1 capin users 41 Sep 24 18:49 /home/capin/homebrew/bin/gcc-ranlib-13 -> '../Cellar/gcc@13/13.3.0/bin/gcc-ranlib-13'*
lrwxrwxrwx 1 capin users 38 Sep 24 21:06 /home/capin/homebrew/bin/gcc-ranlib-14 -> ../Cellar/gcc/14.2.0/bin/gcc-ranlib-14*

so when i use something like gcc-14 with your above example i get,

Reading specs from /home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/x86_64-pc-linux-gnu/14/specs
COLLECT_GCC=gcc-14
Target: x86_64-pc-linux-gnu
Configured with: ../configure --prefix=/home/capin/homebrew/opt/gcc --libdir=/home/capin/homebrew/opt/gcc/lib/gcc/current --disable-nls --enable-checking=release --with-gcc-major-version-only --enable-languages=c,c++,objc,obj-c++,fortran,m2 --program-suffix=-14 --with-gmp=/home/capin/homebrew/opt/gmp --with-mpfr=/home/capin/homebrew/opt/mpfr --with-mpc=/home/capin/homebrew/opt/libmpc --with-isl=/home/capin/homebrew/opt/isl --with-zstd=/home/capin/homebrew/opt/zstd --with-pkgversion='Homebrew GCC 14.2.0' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --with-system-zlib --with-boot-ldflags='-static-libstdc++ -static-libgcc ' --disable-multilib --enable-default-pie
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Homebrew GCC 14.2.0)
COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'
 /home/capin/homebrew/Cellar/gcc/14.2.0/bin/../libexec/gcc/x86_64-pc-linux-gnu/14/cc1 -E -quiet -v -iprefix /home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/x86_64-pc-linux-gnu/14/ - -isysroot /home/capin/homebrew/nonexistent -idirafter /home/capin/homebrew/include -idirafter /usr/include/ -idirafter /usr/include -mtune=generic -march=x86-64 -dumpbase -
ignoring nonexistent directory "/home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/x86_64-pc-linux-gnu/14/../../../../../../x86_64-pc-linux-gnu/include"
ignoring duplicate directory "/home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/../../../../lib/gcc/current/gcc/x86_64-pc-linux-gnu/14/include"
ignoring nonexistent directory "/home/capin/homebrew/nonexistent/usr/local/include"
ignoring duplicate directory "/home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/../../../../lib/gcc/current/gcc/x86_64-pc-linux-gnu/14/include-fixed"
ignoring nonexistent directory "/home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/../../../../lib/gcc/current/gcc/x86_64-pc-linux-gnu/14/../../../../../../x86_64-pc-linux-gnu/include"
ignoring nonexistent directory "/home/capin/homebrew/nonexistent/usr/include"
ignoring duplicate directory "/usr/include"
#include "..." search starts here:
#include <...> search starts here:
 /home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/x86_64-pc-linux-gnu/14/include
 /home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/x86_64-pc-linux-gnu/14/include-fixed
 /home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/../../../../include
 /home/capin/homebrew/include
 /usr/include/
End of search list.
# 0 "<stdin>"
# 0 "<built-in>"
# 0 "<command-line>"
# 1 "/usr/include/stdc-predef.h" 1 3 4
# 0 "<command-line>" 2
# 1 "<stdin>"
COMPILER_PATH=/home/capin/homebrew/Cellar/gcc/14.2.0/bin/../libexec/gcc/x86_64-pc-linux-gnu/14/:/home/capin/homebrew/Cellar/gcc/14.2.0/bin/../libexec/gcc/
LIBRARY_PATH=/home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/x86_64-pc-linux-gnu/14/:/home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/:/home/capin/homebrew/Cellar/gcc/14.2.0/bin/../lib/gcc/current/gcc/x86_64-pc-linux-gnu/14/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'

which greping through output i do not see any mention of /usr/local/include

i guess what i'm saying is the brew doctor command is kindof throwing a false positive here.

[ZhongRuoyu]

which greping through output i do not see any mention of /usr/local/include

Homebrew's GCC does not look at /usr/local/include by design.

Actually, I was referring to the system GCC, because Homebrew uses that by default unless you installed a new enough Homebrew GCC or it can't (e.g., when it's not new enough, or when the formula requires a specific compiler).

Also, if it helps to explain: your Asahi is aarch64 Linux so nothing is prebuilt by Homebrew, not even Homebrew GCC. A pre-existing compiler (usually system GCC) has to be used to at least install Homebrew GCC.

(EDIT: Underline text was added.)

[ipatch]

on both my asahi box and my archlinux box with ~/homebrew being the brew --prefix homebrew uses gcc-14 to compile all programs that require gcc. if llvm is required then homebrew uses clang clang++ provided by the llvm homebrew formula depending on the version of llvm required by the formula.

i guess what i'm trying to say is if somebody who has homebrew setup in a non standard install location, and the homebrew gcc compiler does not look for header files in /usr/local/include then i do not see why there should be a warning in the output. (but that's just like my opinion)

and i guess i could see why to include the above output, for sake of be "overly verbose" in case something is over looked. but i do think the brew doctor logic could be improved upon to say the least. (but that's just like my opinion)

[ZhongRuoyu]

on both my asahi box and my archlinux box with ~/homebrew being the brew --prefix homebrew uses gcc-14 to compile all programs that require gcc

This gcc-14 is the Homebrew GCC because a new enough Homebrew GCC is installed, but it is the system GCC if you didn't install the Homebrew one. (Updated my previous comment to clarify what I meant by "default".) My previous point regarding Asahi was: which compiler was used to build your Homebrew GCC locally from source on Asahi? That has to be an pre-existing compiler from your system.

That aside, there are other toolchains that rely on /usr/local. I believe that on many Linux setups /usr/local/lib is in the search paths of the default linker and the GNU ld from Homebrew Binutils.

The /usr/local warnings are really just there for diagnostic purposes. Not because they are 100% useful in every case, but because they could sometimes be useful when you report an issue. Perhaps for the sake of being "overly verbose", as you said. Just like the warning that your Homebrew prefix is not the default one -- you still have been living with that without problems.