Closed meuserj closed 3 years ago
Can you show the output of
brew cleanup --verbose --debug
?
As a workaround, you can set HOMEBREW_NO_INSTALL_CLEANUP
to skip the cleanup step during install/upgrade. You can still do brew cleanup <formulae>
to cleanup things that you did install with brew
(e.g. brew cleanup $(brew ls --formula)
).
Also, what's the output of
ls -la /usr/local/lib/dgagent
?
brew cleanup --verbose --debug
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libtermkey.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/rubberband.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/mosh.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/syncthing.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/imlib2.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/lame.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/pkg-config.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/plantuml.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/libheif.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/vimpager.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/wget.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/ffmpeg.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/pinentry.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/msgpack.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gmime.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libopusenc.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/xorgproto.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/multitail.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/pandoc.rb
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/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/syncthing-inotify.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::FormulaLoader): loading /usr/local/opt/syncthing-inotify/.brew/syncthing-inotify.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/gpgme.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/python@2.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::FormulaLoader): loading /usr/local/opt/python@2/.brew/python@2.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libxau.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/go.rb
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/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/ncurses.rb
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/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/frei0r.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/unibilium.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/nettle.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/pixman.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/clipper.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/libxdmcp.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gnu-getopt.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/opus.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libuv.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/rtmpdump.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libsamplerate.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libvorbis.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/cscope.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/zsh-history-substring-search.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gts.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/sox.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/liblqr.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/pango.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/libyaml.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/xmlto.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/zimg.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/gdk-pixbuf.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/bdw-gc.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/speex.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libogg.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/icu4c.rb
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/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/zeromq.rb
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/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/lua@5.1.rb
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/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/netpbm.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/libxv.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/tokyo-cabinet.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/aom.rb
/usr/local/Homebrew/Library/Homebrew/brew.rb (Formulary::TapLoader): loading /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/utf8proc.rb
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Warning: Skipping aom: most recent version 3.1.2 not installed
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Error: Operation not permitted @ dir_s_rmdir - /usr/local/lib/dgagent
/usr/local/Homebrew/Library/Homebrew/extend/pathname.rb:522:in `rmdir'
/usr/local/Homebrew/Library/Homebrew/extend/pathname.rb:522:in `rmdir'
/usr/local/Homebrew/Library/Homebrew/extend/pathname.rb:522:in `rmdir'
/usr/local/Homebrew/Library/Homebrew/extend/pathname.rb:255:in `rmdir_if_possible'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:476:in `block in prune_prefix_symlinks_and_directories'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:472:in `reverse_each'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:472:in `prune_prefix_symlinks_and_directories'
/usr/local/Homebrew/Library/Homebrew/cleanup.rb:195:in `clean!'
/usr/local/Homebrew/Library/Homebrew/cmd/cleanup.rb:58:in `cleanup'
/usr/local/Homebrew/Library/Homebrew/brew.rb:131:in `<main>'
ls -la /usr/local/lib/dgagent
total 1240
drwxrwxrwt 3 root wheel 96 Feb 19 08:56 .
drwxrwxr-x 2130 meuserj admin 68160 Jul 27 17:41 ..
-rwxrwxrwt 1 root wheel 634784 Jun 16 09:37 libpreload.dylib
I've modified the permissions of the dgagent folder and attempted to delete it manually, but the dylib is loaded in a running process that I cannot kill. I tried this before realizing that the process is the corporate management software required by my company, so I neither can, nor want, to remove it.
Yes, brew
shouldn't be trying to remove that folder. I'm not sure why it's even attempting to, but I'll have a closer look at the backtrace to see what's happening.
brew config
outputbrew doctor
outputbrew update
and am still able to reproduce my issue.brew doctor
and that did not fix my problem.What were you trying to do (and why)?
I was attempting to upgrade all installed packages with
brew upgrade
. Because it has been a while, this required an automaticbrew cleanup
. When it encountered non-Homebrew files in the /usr/local/lib, it attempted to remove them for some reason. The directory in question is/usr/local/lib/dgagent
, which is part of the corporate management software on my machine. I do not have the ability to remove this folder or kill the process which is using the library file within (nor would I want to, since it is required for my employment). Homebrew's assumption that it can remove anything in/usr/local
seems a bit aggressive to say the least.What happened (include all command output)?
==> Upgrading 76 outdated packages: rubberband 1.9.1 -> 1.9.2 mosh 1.3.2_15 -> 1.3.2_16 syncthing 1.15.1 -> 1.18.0 plantuml 1.2021.4 -> 1.2021.9 libheif 1.11.0_2 -> 1.12.0 libtiff 4.2.0 -> 4.3.0 libtool 2.4.6_3 -> 2.4.6_4 ffmpeg 4.4 -> 4.4_2 xorgproto 2021.3 -> 2021.4 pandoc 2.13 -> 2.14.1 pssh 2.3.1_3 -> 2.3.1_4 libksba 1.5.1 -> 1.6.0 gpgme 1.15.1 -> 1.16.0 go 1.16.3 -> 1.16.6 ghostscript 9.53.3_1 -> 9.54.0 nettle 3.7.2 -> 3.7.3 cmake 3.20.1 -> 3.21.0 libuv 1.41.0 -> 1.42.0 freetype 2.10.4 -> 2.11.0 boost 1.75.0_2 -> 1.76.0 pango 1.48.4 -> 1.48.7 zimg 3.0.1 -> 3.0.2 libogg 1.3.4 -> 1.3.5 icu4c 68.2 -> 69.1 harfbuzz 2.8.0 -> 2.8.2 duck 7.8.5.34493 -> 7.9.3.35019 glib 2.68.1 -> 2.68.3 zsh-completions 0.32.0 -> 0.33.0_1 netpbm 10.86.21 -> 10.86.23 aom 3.0.0 -> 3.1.2 awscli 2.1.38 -> 2.2.22 srt 1.4.2 -> 1.4.3 gobject-introspection 1.68.0 -> 1.68.0_1 sshfs 2.10_2 -> 3.7.2 bash 5.1.4 -> 5.1.8 openexr 2.5.5 -> 3.0.5_1 libgcrypt 1.9.2 -> 1.9.3_1 wfxr/code-minimap/code-minimap 0.5.1 -> 0.6.0 libxfixes 5.0.3 -> 6.0.0 libmaxminddb 1.5.2 -> 1.6.0 macvim 8.2-171 -> 8.2-171_1 snappy 1.1.8 -> 1.1.9 librsvg 2.50.4 -> 2.50.7 graphviz 2.47.0 -> 2.48.0 dav1d 0.8.2 -> 0.9.0 tmux 3.2 -> 3.2a libtasn1 4.16.0_1 -> 4.17.0 pcre2 10.36 -> 10.37_1 eslint 7.24.0 -> 7.31.0 notmuch 0.31.4_1 -> 0.32.2 nnn 4.0 -> 4.2 leptonica 1.80.0 -> 1.81.1 pcre 8.44 -> 8.45 x264 r3049 -> r3060 libidn 1.36 -> 1.38 node 15.14.0 -> 16.5.0 libomp 12.0.0 -> 12.0.1 neovim 0.4.4_2 -> 0.5.0 talloc 2.3.2 -> 2.3.3 ripgrep 12.1.1 -> 13.0.0 libass 0.15.0 -> 0.15.1 you-get 0.4.1520 -> 0.4.1536 imagemagick 7.0.11-8 -> 7.1.0-4_1 guile 3.0.5 -> 3.0.7 gnupg 2.2.27 -> 2.3.1_1 jasper 2.0.31 -> 2.0.32 clementtsang/bottom/bottom 0.5.7 -> 0.6.3 p11-kit 0.23.22 -> 0.24.0 libx11 1.7.0 -> 1.7.2 luv 1.41.0-0 -> 1.41.1-0 protobuf 3.15.8 -> 3.17.3 wireshark 3.4.4 -> 3.4.7 automake 1.16.3_1 -> 1.16.4 git 2.31.1 -> 2.32.0_1 python@3.9 3.9.4 -> 3.9.6 gnutls 3.6.15 -> 3.6.16 ==> Upgrading icu4c 68.2 -> 69.1 ==> Downloading https://ghcr.io/v2/homebrew/core/icu4c/manifests/69.1 ==> Downloading https://ghcr.io/v2/homebrew/core/icu4c/blobs/sha256:3f75c907dadc6e7e647920506e740a312e56279369f3c9708cac54b018410120 ==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sha256:3f75c907dadc6e7e647920506e740a312e56279369f3c9708cac54b018410120?se=2021-07-27T21%3A00%3A00Z&sig=BaoiU80loY6gnPftUNwH1uWE2FIbAgTVmSHK6DpGeIY%3D&sp=r&spr=https&sr=b&sv=2019-12-12 ==> Pouring icu4c--69.1.catalina.bottle.tar.gz 🍺 /usr/local/Cellar/icu4c/69.1: 259 files, 72.8MB ==>
brew cleanup
has not been run in 30 days, running now... Removing: /usr/local/Cellar/icu4c/68.2... (259 files, 72.5MB) Error: Operation not permitted @ dir_s_rmdir - /usr/local/lib/dgagentWhat did you expect to happen?
I expected Homebrew to clean and upgrade files associated with it and not remove unrelated files necessary to my use of the system.
Step-by-step reproduction instructions (by running
brew
commands)