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Homebrew wants to remove a package, which has not been installed via Homebrew #10988

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HigH-HawK opened this issue Apr 1, 2021 · 11 comments · Fixed by #11237
Closed
1 task

Homebrew wants to remove a package, which has not been installed via Homebrew #10988

HigH-HawK opened this issue Apr 1, 2021 · 11 comments · Fixed by #11237
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@MikeMcQuaid
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bug Reproducible Homebrew/brew bug in progress Maintainers are working on this outdated PR was locked due to age

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@HigH-HawK
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HigH-HawK commented Apr 1, 2021 •
edited

brew config output

HOMEBREW_VERSION: 3.0.10-71-ge265664
ORIGIN: https://github.com/Homebrew/brew
HEAD: e265664518ad8c2b99ff15694f5f8fc13705a56b
Last commit: 14 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: fdee7f4fec8562382dc812729072fe0cc2ee0fdb
Core tap last commit: 21 minutes ago
Core tap branch: master
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_MAKE_JOBS: 8
Homebrew Ruby: 2.6.3 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.6.3_2/bin/ruby
CPU: octa-core 64-bit skylake
Clang: 12.0 build 1200
Git: 2.30.2 => /usr/local/bin/git
Curl: 7.64.1 => /usr/bin/curl
macOS: 10.15.7-x86_64
CLT: 12.0.0.32.29
Xcode: N/A

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!

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/node/android-ifaddrs.h
  /usr/local/include/node/libplatform/libplatform-export.h
  /usr/local/include/node/libplatform/libplatform.h
  /usr/local/include/node/libplatform/v8-tracing.h
  /usr/local/include/node/node.h
  /usr/local/include/node/node_api.h
  /usr/local/include/node/node_api_types.h
  /usr/local/include/node/node_buffer.h
  /usr/local/include/node/node_object_wrap.h
  /usr/local/include/node/node_version.h
  /usr/local/include/node/openssl/aes.h
  /usr/local/include/node/openssl/archs/BSD-x86/opensslconf.h
  /usr/local/include/node/openssl/archs/BSD-x86_64/opensslconf.h
  /usr/local/include/node/openssl/archs/VC-WIN32/opensslconf.h
  /usr/local/include/node/openssl/archs/VC-WIN64A/opensslconf.h
  /usr/local/include/node/openssl/archs/aix-gcc/opensslconf.h
  /usr/local/include/node/openssl/archs/aix64-gcc/opensslconf.h
  /usr/local/include/node/openssl/archs/darwin-i386-cc/opensslconf.h
  /usr/local/include/node/openssl/archs/darwin64-x86_64-cc/opensslconf.h
  /usr/local/include/node/openssl/archs/linux-aarch64/opensslconf.h
  /usr/local/include/node/openssl/archs/linux-armv4/opensslconf.h
  /usr/local/include/node/openssl/archs/linux-elf/opensslconf.h
  /usr/local/include/node/openssl/archs/linux-ppc/opensslconf.h
  /usr/local/include/node/openssl/archs/linux-ppc64/opensslconf.h
  /usr/local/include/node/openssl/archs/linux-x32/opensslconf.h
  /usr/local/include/node/openssl/archs/linux-x86_64/opensslconf.h
  /usr/local/include/node/openssl/archs/linux32-s390x/opensslconf.h
  /usr/local/include/node/openssl/archs/linux64-s390x/opensslconf.h
  /usr/local/include/node/openssl/archs/solaris-x86-gcc/opensslconf.h
  /usr/local/include/node/openssl/archs/solaris64-x86_64-gcc/opensslconf.h
  /usr/local/include/node/openssl/asn1.h
  /usr/local/include/node/openssl/asn1_mac.h
  /usr/local/include/node/openssl/asn1t.h
  /usr/local/include/node/openssl/bio.h
  /usr/local/include/node/openssl/blowfish.h
  /usr/local/include/node/openssl/bn.h
  /usr/local/include/node/openssl/buffer.h
  /usr/local/include/node/openssl/camellia.h
  /usr/local/include/node/openssl/cast.h
  /usr/local/include/node/openssl/cmac.h
  /usr/local/include/node/openssl/cms.h
  /usr/local/include/node/openssl/comp.h
  /usr/local/include/node/openssl/conf.h
  /usr/local/include/node/openssl/conf_api.h
  /usr/local/include/node/openssl/crypto.h
  /usr/local/include/node/openssl/des.h
  /usr/local/include/node/openssl/des_old.h
  /usr/local/include/node/openssl/dh.h
  /usr/local/include/node/openssl/dsa.h
  /usr/local/include/node/openssl/dso.h
  /usr/local/include/node/openssl/dtls1.h
  /usr/local/include/node/openssl/e_os2.h
  /usr/local/include/node/openssl/ebcdic.h
  /usr/local/include/node/openssl/ec.h
  /usr/local/include/node/openssl/ecdh.h
  /usr/local/include/node/openssl/ecdsa.h
  /usr/local/include/node/openssl/engine.h
  /usr/local/include/node/openssl/err.h
  /usr/local/include/node/openssl/evp.h
  /usr/local/include/node/openssl/hmac.h
  /usr/local/include/node/openssl/idea.h
  /usr/local/include/node/openssl/krb5_asn.h
  /usr/local/include/node/openssl/kssl.h
  /usr/local/include/node/openssl/lhash.h
  /usr/local/include/node/openssl/md4.h
  /usr/local/include/node/openssl/md5.h
  /usr/local/include/node/openssl/mdc2.h
  /usr/local/include/node/openssl/modes.h
  /usr/local/include/node/openssl/obj_mac.h
  /usr/local/include/node/openssl/objects.h
  /usr/local/include/node/openssl/ocsp.h
  /usr/local/include/node/openssl/opensslconf.h
  /usr/local/include/node/openssl/opensslv.h
  /usr/local/include/node/openssl/ossl_typ.h
  /usr/local/include/node/openssl/pem.h
  /usr/local/include/node/openssl/pem2.h
  /usr/local/include/node/openssl/pkcs12.h
  /usr/local/include/node/openssl/pkcs7.h
  /usr/local/include/node/openssl/pqueue.h
  /usr/local/include/node/openssl/rand.h
  /usr/local/include/node/openssl/rc2.h
  /usr/local/include/node/openssl/rc4.h
  /usr/local/include/node/openssl/ripemd.h
  /usr/local/include/node/openssl/rsa.h
  /usr/local/include/node/openssl/safestack.h
  /usr/local/include/node/openssl/seed.h
  /usr/local/include/node/openssl/sha.h
  /usr/local/include/node/openssl/srp.h
  /usr/local/include/node/openssl/srtp.h
  /usr/local/include/node/openssl/ssl.h
  /usr/local/include/node/openssl/ssl2.h
  /usr/local/include/node/openssl/ssl23.h
  /usr/local/include/node/openssl/ssl3.h
  /usr/local/include/node/openssl/stack.h
  /usr/local/include/node/openssl/symhacks.h
  /usr/local/include/node/openssl/tls1.h
  /usr/local/include/node/openssl/ts.h
  /usr/local/include/node/openssl/txt_db.h
  /usr/local/include/node/openssl/ui.h
  /usr/local/include/node/openssl/ui_compat.h
  /usr/local/include/node/openssl/whrlpool.h
  /usr/local/include/node/openssl/x509.h
  /usr/local/include/node/openssl/x509_vfy.h
  /usr/local/include/node/openssl/x509v3.h
  /usr/local/include/node/pthread-barrier.h
  /usr/local/include/node/stdint-msvc2008.h
  /usr/local/include/node/tree.h
  /usr/local/include/node/uv-aix.h
  /usr/local/include/node/uv-bsd.h
  /usr/local/include/node/uv-darwin.h
  /usr/local/include/node/uv-errno.h
  /usr/local/include/node/uv-linux.h
  /usr/local/include/node/uv-os390.h
  /usr/local/include/node/uv-posix.h
  /usr/local/include/node/uv-sunos.h
  /usr/local/include/node/uv-threadpool.h
  /usr/local/include/node/uv-unix.h
  /usr/local/include/node/uv-version.h
  /usr/local/include/node/uv-win.h
  /usr/local/include/node/uv.h
  /usr/local/include/node/v8-debug.h
  /usr/local/include/node/v8-inspector-protocol.h
  /usr/local/include/node/v8-inspector.h
  /usr/local/include/node/v8-platform.h
  /usr/local/include/node/v8-profiler.h
  /usr/local/include/node/v8-testing.h
  /usr/local/include/node/v8-util.h
  /usr/local/include/node/v8-value-serializer-version.h
  /usr/local/include/node/v8-version-string.h
  /usr/local/include/node/v8-version.h
  /usr/local/include/node/v8.h
  /usr/local/include/node/v8config.h
  /usr/local/include/node/zconf.h
  /usr/local/include/node/zlib.h

  • The brew doctor above contains no "Warning" lines.

What were you trying to do (and why)?

I ran brew update and brew upgrade where Homebrew noticed that the cleanup hasn't been run in the last 30 days, so it started the cleanup and quits with the error message:

Error: Permission denied @ apply2files - /usr/local/lib/prey/versions/1.9.9/.DS_Store

What happened (include all command output)?

I ran brew update and brew upgrade, when brew started a cleanup, which stops with an error (see above)

What did you expect to happen?

I expected the cleanup to run through without any errors, especially because Prey has not been installed via Homebrew but via a macOS package. I guess both use the same path, hence Homebrew claims it and wants to clean it.

Step-by-step reproduction instructions (by running brew commands)

brew cleanup
@HigH-HawK HigH-HawK added the bug Reproducible Homebrew/brew bug label Apr 1, 2021
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This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

@github-actions github-actions bot added the stale No recent activity label Apr 23, 2021
@MikeMcQuaid
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I ran brew update and brew upgrade where Homebrew noticed that the cleanup hasn't been run in the last 30 days, so it started the cleanup and quits with the error message:

Can you supply the full output of brew cleanup? Thanks!

@HigH-HawK
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I did run brew update and updated to the latest Homebrew (3.1.3-85-gdcd9bf1) version and ran the cleanup command again.

#: brew cleanup
Warning: Skipping autoconf: most recent version 2.71 not installed
Warning: Skipping automake: most recent version 1.16.3_1 not installed
Warning: Skipping cmake: most recent version 3.20.1 not installed
Warning: Skipping composer: most recent version 2.0.12 not installed
Warning: Skipping curl: most recent version 7.76.1 not installed
Warning: Skipping freetds: most recent version 1.2.20 not installed
Warning: Skipping git: most recent version 2.31.1 not installed
Warning: Skipping glib: most recent version 2.68.1 not installed
Warning: Skipping highlight: most recent version 4.0 not installed
Warning: Skipping imagemagick@6: most recent version 6.9.12-7 not installed
Warning: Skipping lua: most recent version 5.4.3 not installed
Warning: Skipping oniguruma: most recent version 6.9.7.1 not installed
Warning: Skipping php-cs-fixer: most recent version 2.18.6 not installed
Warning: Skipping python@3.9: most recent version 3.9.4 not installed
Warning: Skipping sqlite: most recent version 3.35.4 not installed
Warning: Skipping zstd: most recent version 1.4.9_1 not installed
Error: Permission denied @ apply2files - /usr/local/lib/prey/versions/1.9.9/.DS_Store

The skipping is happening because it doesn't let me upgrade those, due to the cleanup error

@MikeMcQuaid
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@HigH-HawK Can I see the output of brew cleanup --debug? Thanks!

@HigH-HawK
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HigH-HawK commented Apr 23, 2021 •
edited

Sure, I may have misunderstood your first request:

#: brew cleanup --debug
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/cowsay.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/php-cs-fixer.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/tree.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libtiff.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libtool.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/coreutils.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/jansson.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gmp.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/postgresql.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/wget.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libidn2.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/imagemagick@6.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libxml2.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/nghttp2.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/little-cms2.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libpng.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/ncurses.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/ghostscript.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gdbm.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/mpdecimal.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/cmake.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/freetype.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/mpfr.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/argon2.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/rtmpdump.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/highlight.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/boost.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/mhash.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libunistring.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/openjpeg.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/apr-util.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/jemalloc.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/brotli.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/icu4c.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/mtr.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/composer.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/glib.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/readline.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/glog.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/lz4.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/tbb.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/webp.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/sqlite.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/c-ares.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/php.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/xz.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/unixodbc.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/hhvm/homebrew-hhvm/Formula/hhvm-4.84.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/lua.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/fontconfig.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/double-conversion.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/htop.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/memcached.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gflags.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/curl.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/krb5.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/freetds.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gawk.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libelf.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gettext.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libssh2.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/dwarfutils.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/zstd.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/tcl-tk.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/mcrypt.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libsodium.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/apr.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/autoconf.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libpq.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/aspell.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/tidy-html5.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/m4.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/oniguruma.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gd.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/pcre2.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libevent.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/openssl@1.1.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/pcre.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libmemcached.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/jpeg.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libzip.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libmetalink.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/openldap.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libev.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/automake.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/git.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libffi.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/telnet.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/python@3.9.rb
Warning: Skipping autoconf: most recent version 2.71 not installed
Warning: Skipping automake: most recent version 1.16.3_1 not installed
Warning: Skipping cmake: most recent version 3.20.1 not installed
Warning: Skipping composer: most recent version 2.0.12 not installed
Warning: Skipping curl: most recent version 7.76.1 not installed
Warning: Skipping freetds: most recent version 1.2.20 not installed
Warning: Skipping git: most recent version 2.31.1 not installed
Warning: Skipping glib: most recent version 2.68.1 not installed
Warning: Skipping highlight: most recent version 4.0 not installed
Warning: Skipping imagemagick@6: most recent version 6.9.12-7 not installed
Warning: Skipping lua: most recent version 5.4.3 not installed
Warning: Skipping oniguruma: most recent version 6.9.7.1 not installed
Warning: Skipping php-cs-fixer: most recent version 2.18.6 not installed
Warning: Skipping python@3.9: most recent version 3.9.4 not installed
Warning: Skipping sqlite: most recent version 3.35.4 not installed
Warning: Skipping zstd: most recent version 1.4.9_1 not installed
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::FormulaLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/md5sha1sum.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::FormulaLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/pkg-config.rb
Error: Permission denied @ apply2files - /usr/local/lib/prey/versions/1.9.9/.DS_Store
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:438:in `unlink'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:438:in `unlink'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:438:in `each'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:438:in `rm_ds_store'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:199:in `clean!'
/usr/local/Homebrew/Library/Homebrew/cmd/cleanup.rb:58:in `cleanup'
/usr/local/Homebrew/Library/Homebrew/brew.rb:122:in `<main>'

@MikeMcQuaid MikeMcQuaid added in progress Maintainers are working on this and removed stale No recent activity labels Apr 23, 2021
@MikeMcQuaid MikeMcQuaid self-assigned this Apr 23, 2021
@MikeMcQuaid MikeMcQuaid mentioned this issue Apr 23, 2021
Merged
@redbar0n
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redbar0n commented Apr 26, 2021 •
edited

also getting Error: Permission denied @ apply2files - /usr/local/lib/prey/versions/1.9.9/.DS_Store during brew install and brew cleanup.

brew cleanup --debug gives:

...
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::FormulaLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/rtmpdump.rb
Error: Permission denied @ apply2files - /usr/local/lib/prey/versions/1.9.9/.DS_Store
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:438:in `unlink'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:438:in `unlink'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:438:in `each'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:438:in `rm_ds_store'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:199:in `clean!'
/usr/local/Homebrew/Library/Homebrew/cmd/cleanup.rb:58:in `cleanup'
/usr/local/Homebrew/Library/Homebrew/brew.rb:122:in `<main>'

What to do?

@HigH-HawK
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HigH-HawK commented Apr 26, 2021 •
edited

Try updating your Homebrew - The update from Friday last week, fixed the issue for me.

#: brew update && brew cleanup

@redbar0n
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I actually just did, before receiving that error.

@HigH-HawK
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Can you please run the following command and post the output?

#: brew config

@redbar0n
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Sure!

› brew config
HOMEBREW_VERSION: 3.1.3
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: d89eda09abbeae907eb88bd6d01dc9cde7ff0e19
Last commit: 7 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 1da7ce26f5cfa33eec131571755152680a5321b7
Core tap last commit: 14 hours ago
Core tap branch: master
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.wDbdRHUH8x/org.macosforge.xquartz:0
HOMEBREW_EDITOR: subl
HOMEBREW_MAKE_JOBS: 12
Homebrew Ruby: 2.6.3 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.6.3_2/bin/ruby
CPU: dodeca-core 64-bit kabylake
Clang: 12.0 build 1200
Git: 2.28.0 => /usr/local/bin/git
Curl: 7.64.1 => /usr/bin/curl
macOS: 10.15.7-x86_64
CLT: 12.4.0.0.1.1610135815
Xcode: N/A
XQuartz: 2.7.7 => /opt/X11

@Bo98
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Bo98 commented Apr 27, 2021

The fix will be released with Homebrew 3.1.4.

@github-actions github-actions bot added the outdated PR was locked due to age label May 28, 2021
@github-actions github-actions bot locked as resolved and limited conversation to collaborators May 28, 2021
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cleanup: ignore DS_Store access failures. MikeMcQuaid/brew
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@MikeMcQuaid @redbar0n @Bo98 @HigH-HawK