brew upgrade uninstalled a bunch of things including ksh93 which I depend on #5395

wfiveash · 2024-05-23T16:11:52Z

wfiveash
May 23, 2024

Output of `brew config`

HOMEBREW_VERSION: 4.3.1
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: e0bc557e7b991cb23583679e1cf1c8a92b793aeb
Last commit: 3 days ago
Core tap JSON: 23 May 15:38 UTC
Core cask tap JSON: 23 May 15:39 UTC
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.cVno4WsPjL/org.macosforge.xquartz:0
HOMEBREW_EDITOR: vim
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_MAKE_JOBS: 10
HOMEBREW_NO_ENV_HINTS: set
Homebrew Ruby: 3.3.1 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/3.3.1/bin/ruby
CPU: 10-core 64-bit westmere
Clang: 15.0.0 build 1500
Git: 2.45.1 => /usr/local/bin/git
Curl: 8.6.0 => /usr/bin/curl
macOS: 14.5-x86_64
CLT: 12.0.0.32.21
Xcode: 15.4
Rosetta 2: true

Output of `brew doctor`

$ 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Warning: Your Command Line Tools are too outdated.
Update them from Software Update in System Settings.

If that doesn't show you any updates, run:
  sudo rm -rf /Library/Developer/CommandLineTools
  sudo xcode-select --install

Alternatively, manually download them from:
  https://developer.apple.com/download/all/.
You should download the Command Line Tools for Xcode 15.1.


Warning: A newer Command Line Tools release is available.
Update them from Software Update in System Settings.

If that doesn't show you any updates, run:
  sudo rm -rf /Library/Developer/CommandLineTools
  sudo xcode-select --install

Alternatively, manually download them from:
  https://developer.apple.com/download/all/.
You should download the Command Line Tools for Xcode 15.1.


Warning: Some installed kegs have no formulae!
This means they were either deleted or installed manually.
You should find replacements for the following formulae:
  python-jinja
  python-click
  python-markupsafe

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  [email protected]
  [email protected]
  python-charset-normalizer
  python-dateutil
  python-idna
  python-requests
  python-urllib3
  [email protected]

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:
  gnupg
  wireshark

Description of issue

Today I ran "brew upgrade" on my Mac (which I have done many times before without problem) and after it ran I was unable to start a new session of iTerm because the startup shell, /usr/local/bin/ksh, was deleted during the upgrade. This seems like a major bug. Here is the output of the "brew upgrade" I ran:
$ brew outdated
==> Auto-updating Homebrew...
==> Auto-updated Homebrew!
Updated 2 taps (homebrew/core and homebrew/cask).
==> New Formulae
podlet
==> New Casks
phocus screaming-frog-log-file-analyser ugg
quicktune semeru-jdk-open@21

You have 8 outdated formulae installed.
Error: Unexpected method 'appcast' called on Cask transmission-remote-gui.
Follow the instructions here:
https://github.com/Homebrew/homebrew-cask#reporting-bugs
Error: Unexpected method 'appcast' called on Cask transmission-remote-gui.
Follow the instructions here:
https://github.com/Homebrew/homebrew-cask#reporting-bugs

cookiecutter (2.6.0_2) < 2.6.0_3
emacs (29.3) < 29.3_1
gdk-pixbuf (2.42.11) < 2.42.12
libass (0.17.1_1) < 0.17.2
openldap (2.6.7) < 2.6.8
snappy (1.2.0) < 1.2.1
sphinx-doc (7.3.7_1) < 7.3.7_2
wireshark (4.2.4) < 4.2.5
/Users/willf/bin
$ /Users/willf/bin/mybrewupgrade
==> Upgrading 8 outdated packages:
gdk-pixbuf 2.42.11 -> 2.42.12
cookiecutter 2.6.0_2 -> 2.6.0_3
emacs 29.3 -> 29.3_1
snappy 1.2.0 -> 1.2.1
sphinx-doc 7.3.7_1 -> 7.3.7_2
openldap 2.6.7 -> 2.6.8
libass 0.17.1_1 -> 0.17.2
wireshark 4.2.5
==> Downloading https://ghcr.io/v2/homebrew/core/sphinx-doc/manifests/7.3.7_2
==> Fetching sphinx-doc
==> Downloading https://ghcr.io/v2/homebrew/core/sphinx-doc/blobs/sha256:8bd577657867a31fe01d80d0c042a83de54022da4892060d1bd0cfd7589045e2
==> Downloading https://ghcr.io/v2/homebrew/core/openldap/manifests/2.6.8
==> Fetching openldap
==> Downloading https://ghcr.io/v2/homebrew/core/openldap/blobs/sha256:6ce29ea406a5839bab5071a1844b49d4df905cfa88a9868673b03290d43f263b
==> Downloading https://ghcr.io/v2/homebrew/core/emacs/manifests/29.3_1
==> Fetching emacs
==> Downloading https://ghcr.io/v2/homebrew/core/emacs/blobs/sha256:f955eb0981734a52a9ef168d6d2a3946ed406f2eec177caba985743427335f5d
==> Downloading https://ghcr.io/v2/homebrew/core/snappy/manifests/1.2.1
==> Fetching snappy
==> Downloading https://ghcr.io/v2/homebrew/core/snappy/blobs/sha256:4a39b310e4c5a726de262265e14cb0ee219f89c0da0afd19328007d965dba7f8
==> Downloading https://ghcr.io/v2/homebrew/core/libass/manifests/0.17.2
==> Fetching libass
==> Downloading https://ghcr.io/v2/homebrew/core/libass/blobs/sha256:5b9b9dc3754f07eff37a4a09d9139e1671ab7107f586b861330d6aa47919e87f
==> Downloading https://ghcr.io/v2/homebrew/core/gdk-pixbuf/manifests/2.42.12
==> Fetching gdk-pixbuf
==> Downloading https://ghcr.io/v2/homebrew/core/gdk-pixbuf/blobs/sha256:3e7266d92df1d8a3afde5e67030878a610ede9d9dfa75572e54dcb74d5779cdc
==> Downloading https://ghcr.io/v2/homebrew/core/wireshark/manifests/4.2.5
==> Fetching wireshark
==> Downloading https://ghcr.io/v2/homebrew/core/wireshark/blobs/sha256:cdf2576b63904b56bbcb563b681455e6f0c247afd3011b56e1f0552937c5619b
==> Downloading https://ghcr.io/v2/homebrew/core/cookiecutter/manifests/2.6.0_3
==> Fetching cookiecutter
==> Downloading https://ghcr.io/v2/homebrew/core/cookiecutter/blobs/sha256:a9f720a2fdc287a9f06a3223ea54ddfc6ef0269156a1824c9df9a72c75179d21
==> Upgrading sphinx-doc
7.3.7_1 -> 7.3.7_2
==> Pouring sphinx-doc--7.3.7_2.sonoma.bottle.tar.gz
🍺 /usr/local/Cellar/sphinx-doc/7.3.7_2: 3,070 files, 49.9MB
==> Running brew cleanup sphinx-doc...
Removing: /usr/local/Cellar/sphinx-doc/7.3.7_1... (3,070 files, 49.9MB)
Removing: /Users/willf/Library/Caches/Homebrew/sphinx-doc_bottle_manifest--7.3.7_1... (19.9KB)
Removing: /Users/willf/Library/Caches/Homebrew/sphinx-doc--7.3.7_1... (13.9MB)
==> Upgrading openldap
2.6.7 -> 2.6.8
==> Pouring openldap--2.6.8.sonoma.bottle.tar.gz
🍺 /usr/local/Cellar/openldap/2.6.8: 342 files, 7.2MB
==> Running brew cleanup openldap...
Removing: /usr/local/Cellar/openldap/2.6.7... (340 files, 7.5MB)
Removing: /Users/willf/Library/Caches/Homebrew/openldap_bottle_manifest--2.6.7... (24.4KB)
Removing: /Users/willf/Library/Caches/Homebrew/openldap--2.6.7... (2.9MB)
==> Upgrading emacs
29.3 -> 29.3_1
==> Pouring emacs--29.3_1.sonoma.bottle.tar.gz
==> Caveats
To start emacs now and restart at login:
brew services start emacs
Or, if you don't want/need a background service you can just run:
/usr/local/opt/emacs/bin/emacs --fg-daemon
==> Summary
🍺 /usr/local/Cellar/emacs/29.3_1: 4,227 files, 119MB
==> Running brew cleanup emacs...
Removing: /usr/local/Cellar/emacs/29.3... (4,226 files, 119MB)
Removing: /Users/willf/Library/Caches/Homebrew/emacs_bottle_manifest--29.3... (22.3KB)
Removing: /Users/willf/Library/Caches/Homebrew/emacs--29.3... (52.1MB)
==> Upgrading snappy
1.2.0 -> 1.2.1
==> Pouring snappy--1.2.1.sonoma.bottle.tar.gz
🍺 /usr/local/Cellar/snappy/1.2.1: 19 files, 141.6KB
==> Running brew cleanup snappy...
Removing: /usr/local/Cellar/snappy/1.2.0... (18 files, 136.7KB)
Removing: /Users/willf/Library/Caches/Homebrew/snappy_bottle_manifest--1.2.0... (7.3KB)
Removing: /Users/willf/Library/Caches/Homebrew/snappy--1.2.0... (47.0KB)
==> Upgrading libass
0.17.1_1 -> 0.17.2
==> Pouring libass--0.17.2.sonoma.bottle.tar.gz
🍺 /usr/local/Cellar/libass/0.17.2: 12 files, 669.2KB
==> Running brew cleanup libass...
Removing: /usr/local/Cellar/libass/0.17.1_1... (11 files, 628.1KB)
Removing: /Users/willf/Library/Caches/Homebrew/libass_bottle_manifest--0.17.1_1... (27.0KB)
Removing: /Users/willf/Library/Caches/Homebrew/libass--0.17.1_1... (233.1KB)
==> Upgrading gdk-pixbuf
2.42.11 -> 2.42.12
==> Pouring gdk-pixbuf--2.42.12.sonoma.bottle.tar.gz
==> /usr/local/Cellar/gdk-pixbuf/2.42.12/bin/gdk-pixbuf-query-loaders --update-c
🍺 /usr/local/Cellar/gdk-pixbuf/2.42.12: 152 files, 3.3MB
==> Running brew cleanup gdk-pixbuf...
Removing: /usr/local/Cellar/gdk-pixbuf/2.42.11... (142 files, 3MB)
Removing: /Users/willf/Library/Caches/Homebrew/gdk-pixbuf_bottle_manifest--2.42.11... (22.1KB)
Removing: /Users/willf/Library/Caches/Homebrew/gdk-pixbuf--2.42.11... (703.7KB)
==> Upgrading wireshark
-> 4.2.5
==> Pouring wireshark--4.2.5.sonoma.bottle.tar.gz
==> wireshark cask is installed, skipping link.
==> Caveats
This formula only installs the command-line utilities by default.

Install Wireshark.app with Homebrew Cask:
brew install --cask wireshark

If your list of available capture interfaces is empty
(default macOS behavior), install ChmodBPF:
brew install --cask wireshark-chmodbpf
==> Summary
🍺 /usr/local/Cellar/wireshark/4.2.5: 977 files, 104.9MB
==> Running brew cleanup wireshark...
Removing: /usr/local/Cellar/wireshark/4.2.4... (976 files, 104.8MB)
Removing: /Users/willf/Library/Caches/Homebrew/wireshark_bottle_manifest--4.2.4... (33KB)
Removing: /Users/willf/Library/Caches/Homebrew/wireshark--4.2.4... (24.9MB)
==> Upgrading cookiecutter
2.6.0_2 -> 2.6.0_3
==> Pouring cookiecutter--2.6.0_3.sonoma.bottle.tar.gz
==> Caveats
zsh completions have been installed to:
/usr/local/share/zsh/site-functions
==> Summary
🍺 /usr/local/Cellar/cookiecutter/2.6.0_3: 901 files, 10MB
==> Running brew cleanup cookiecutter...
Removing: /usr/local/Cellar/cookiecutter/2.6.0_2... (901 files, 10MB)
Removing: /Users/willf/Library/Caches/Homebrew/cookiecutter_bottle_manifest--2.6.0_2... (17.9KB)
Removing: /Users/willf/Library/Caches/Homebrew/cookiecutter--2.6.0_2... (2.4MB)
==> brew cleanup has not been run in the last 30 days, running now...
Removing: /Users/willf/Library/Caches/Homebrew/autoconf_bottle_manifest--2.72... (10.5KB)
Removing: /Users/willf/Library/Caches/Homebrew/autoconf--2.72... (1MB)
Removing: /Users/willf/Library/Caches/Homebrew/bash_bottle_manifest--5.2.26... (8.4KB)
Removing: /Users/willf/Library/Caches/Homebrew/bash--5.2.26... (3.2MB)
Removing: /Users/willf/Library/Caches/Homebrew/ffmpeg_bottle_manifest--7.0_1... (99.2KB)
Removing: /Users/willf/Library/Caches/Homebrew/ffmpeg--7.0_1... (20.5MB)
Removing: /Users/willf/Library/Caches/Homebrew/fontconfig_bottle_manifest--2.15.0... (10.2KB)
Removing: /Users/willf/Library/Caches/Homebrew/fontconfig--2.15.0... (627.5KB)
Removing: /Users/willf/Library/Caches/Homebrew/jpeg_bottle_manifest--9f... (7.4KB)
Removing: /Users/willf/Library/Caches/Homebrew/jpeg--9f... (316.7KB)
Removing: /Users/willf/Library/Caches/Homebrew/leptonica_bottle_manifest--1.84.1... (15.8KB)
Removing: /Users/willf/Library/Caches/Homebrew/leptonica--1.84.1... (2.4MB)
Removing: /Users/willf/Library/Caches/Homebrew/libmaxminddb_bottle_manifest--1.9.1... (7.5KB)
Removing: /Users/willf/Library/Caches/Homebrew/libmaxminddb--1.9.1... (60.2KB)
Removing: /Users/willf/Library/Caches/Homebrew/libssh_bottle_manifest--0.10.6... (9.3KB)
Removing: /Users/willf/Library/Caches/Homebrew/libssh--0.10.6... (454.0KB)
Removing: /Users/willf/Library/Caches/Homebrew/libvmaf_bottle_manifest--3.0.0... (7.5KB)
Removing: /Users/willf/Library/Caches/Homebrew/libvmaf--3.0.0... (1.1MB)
Removing: /Users/willf/Library/Caches/Homebrew/little-cms2_bottle_manifest--2.16... (11.5KB)
Removing: /Users/willf/Library/Caches/Homebrew/little-cms2--2.16... (418.5KB)
Removing: /Users/willf/Library/Caches/Homebrew/mpdecimal_bottle_manifest--4.0.0-1... (7.7KB)
Removing: /Users/willf/Library/Caches/Homebrew/mpdecimal--4.0.0... (181.5KB)
Removing: /Users/willf/Library/Caches/Homebrew/openssl@3_bottle_manifest--3.3.0... (9.2KB)
Removing: /Users/willf/Library/Caches/Homebrew/[email protected]... (8.8MB)
Removing: /Users/willf/Library/Caches/Homebrew/python-jinja--3.1.3... (255.5KB)
Removing: /Users/willf/Library/Caches/Homebrew/rav1e_bottle_manifest--0.7.1... (7.4KB)
Removing: /Users/willf/Library/Caches/Homebrew/rav1e--0.7.1... (12.8MB)
Removing: /Users/willf/Library/Caches/Homebrew/ripgrep_bottle_manifest--14.1.0... (8.3KB)
Removing: /Users/willf/Library/Caches/Homebrew/ripgrep--14.1.0... (2MB)
Removing: /Users/willf/Library/Caches/Homebrew/rust_bottle_manifest--1.78.0... (22KB)
Removing: /Users/willf/Library/Caches/Homebrew/rust--1.78.0... (159.9MB)
Removing: /Users/willf/Library/Caches/Homebrew/tmux_bottle_manifest--3.4_1... (11.6KB)
Removing: /Users/willf/Library/Caches/Homebrew/tmux--3.4_1... (477.3KB)
==> Autoremoving 71 unneeded formulae:
adns
assimp
bdw-gc
cmake
cmocka
cscope
dbus
docbook
docbook-xsl
docutils
double-conversion
duktape
gdbm
gnu-getopt
gnupg
gobject-introspection
gpgme
guile
hunspell
jasper
jemalloc
jpeg
ksh93
libassuan
libcroco
libev
libffi
[email protected]
libiconv
libksba
libmng
libproxy
libpthread-stubs
libusb
libvo-aacenc
llvm@16
luajit
md4c
mutt
nghttp2
npth
openldap
pcre
pinentry
protobuf@21
pygments
python-charset-normalizer
python-click
python-dateutil
python-idna
python-jinja
python-markupsafe
python-requests
python-setuptools
python-tabulate
python-urllib3
[email protected]
[email protected]
[email protected]
[email protected]
pyyaml
qt
rtmpdump
shared-mime-info
six
sphinx-doc
swig
texi2html
tokyo-cabinet
xmlto
yasm
Uninstalling /usr/local/Cellar/python-jinja/3.1.3... (75 files, 1006.2KB)
Uninstalling /usr/local/Cellar/libproxy/0.5.6... (16 files, 141KB)
Uninstalling /usr/local/Cellar/yasm/1.3.0_2... (45 files, 3MB)
Uninstalling /usr/local/Cellar/libiconv/1.17... (31 files, 2.7MB)
Uninstalling /usr/local/Cellar/nghttp2/1.61.0... (17 files, 2.2MB)
Uninstalling /usr/local/Cellar/python-click/8.1.7_1... (80 files, 1MB)
Uninstalling /usr/local/Cellar/swig/4.2.1... (829 files, 5.7MB)
Uninstalling /usr/local/Cellar/pygments/2.18.0... (347 files, 4.3MB)
Uninstalling /usr/local/Cellar/python-setuptools/69.5.1... (274 files, 3.2MB)
Uninstalling /usr/local/Cellar/llvm@16/16.0.6_1... (6,767 files, 1.4GB)
Uninstalling /usr/local/Cellar/cmake/3.29.3... (3,385 files, 59.3MB)
Uninstalling /usr/local/Cellar/python-dateutil/2.9.0.post0... (62 files, 929.3KB)
Uninstalling /usr/local/Cellar/docutils/0.21.2... (239 files, 2.1MB)
Uninstalling /usr/local/Cellar/rtmpdump/2.4-20151223_3... (20 files, 542.0KB)
Uninstalling /usr/local/Cellar/cmocka/1.1.7... (17 files, 176.5KB)
Uninstalling /usr/local/Cellar/python-requests/2.31.0... (58 files, 457.3KB)
Uninstalling /usr/local/Cellar/cscope/15.9... (11 files, 711.6KB)
Uninstalling /usr/local/Cellar/texi2html/5.0... (278 files, 6.2MB)
Uninstalling /usr/local/Cellar/libvo-aacenc/0.1.3... (16 files, 300.3KB)
Uninstalling /usr/local/Cellar/xmlto/0.0.28... (46 files, 142.0KB)
Uninstalling /usr/local/Cellar/shared-mime-info/2.4... (88 files, 4.7MB)
Uninstalling /usr/local/Cellar/ksh93/2020.0.0... (8 files, 3.7MB)
Uninstalling /usr/local/Cellar/qt/6.7.0_1... (15,057 files, 675.2MB)
Uninstalling /usr/local/Cellar/gobject-introspection/1.80.1... (541 files, 5.6MB)
Uninstalling /usr/local/Cellar/protobuf@21/21.12... (288 files, 19.6MB)
Uninstalling /usr/local/Cellar/python-tabulate/0.9.0_1... (40 files, 428.0KB)
Uninstalling /usr/local/Cellar/libpthread-stubs/0.5... (5 files, 6.8KB)
Uninstalling /usr/local/Cellar/libcroco/0.6.13_1... (80 files, 1.7MB)
Uninstalling /usr/local/Cellar/sphinx-doc/7.3.7_2... (3,070 files, 49.9MB)
Uninstalling /usr/local/Cellar/pyyaml/6.0.1_1... (86 files, 1.6MB)
Uninstalling /usr/local/Cellar/[email protected]/3.10.14... (3,096 files, 53.8MB)
Uninstalling /usr/local/Cellar/[email protected]/1.6.5... (104 files, 4.4MB)
Uninstalling /usr/local/Cellar/luajit/2.1.1713773202... (55 files, 1.9MB)
Uninstalling /usr/local/Cellar/mutt/2.2.13... (126 files, 10MB)
Uninstalling /usr/local/Cellar/jpeg/9f... (21 files, 871.0KB)
Uninstalling /usr/local/Cellar/[email protected]/3.11.9... (3,326 files, 59.4MB)
Uninstalling /usr/local/Cellar/[email protected]/3.8.19... (5,089 files, 75.8MB)
Uninstalling /usr/local/Cellar/guile/3.0.9_1... (848 files, 59.4MB)
Uninstalling /usr/local/Cellar/[email protected]/3.9.19... (3,066 files, 53.5MB)
Uninstalling /usr/local/Cellar/adns/1.6.1... (14 files, 660.1KB)
Uninstalling /usr/local/Cellar/python-idna/3.6... (36 files, 566.5KB)
Uninstalling /usr/local/Cellar/gpgme/1.23.2_1... (107 files, 4.4MB)
Uninstalling /usr/local/Cellar/gdbm/1.23... (24 files, 956.7KB)
Warning: The following may be dbus configuration files and have not been removed!
If desired, remove them manually with rm -rf:
/usr/local/etc/dbus-1
Warning: The following gnupg configuration files have not been removed!
If desired, remove them manually with rm -rf:
/usr/local/etc/gnupg
/usr/local/etc/gnupg/scdaemon.conf
Uninstalling /usr/local/Cellar/gnu-getopt/2.40.1... (12 files, 196.3KB)
Uninstalling /usr/local/Cellar/assimp/5.4.1... (104 files, 11.1MB)
Uninstalling /usr/local/Cellar/md4c/0.5.2... (19 files, 262.2KB)
Uninstalling /usr/local/Cellar/jemalloc/5.3.0... (16 files, 2.7MB)
Uninstalling /usr/local/Cellar/bdw-gc/8.2.6... (73 files, 1.6MB)
Uninstalling /usr/local/Cellar/python-urllib3/2.2.1... (91 files, 841.3KB)
Uninstalling /usr/local/Cellar/tokyo-cabinet/1.4.48... (79 files, 4.2MB)
Uninstalling /usr/local/Cellar/hunspell/1.7.2... (86 files, 2.6MB)
Uninstalling /usr/local/Cellar/dbus/1.14.10... (77 files, 2.4MB)

Uninstalling /usr/local/Cellar/double-conversion/3.3.0... (26 files, 245.3KB)
Uninstalling /usr/local/Cellar/docbook-xsl/1.79.2_1... (4,910 files, 94.0MB)
Uninstalling /usr/local/Cellar/pcre/8.45... (204 files, 5.8MB)
Uninstalling /usr/local/Cellar/six/1.16.0_4... (20 files, 122.4KB)
Uninstalling /usr/local/Cellar/python-charset-normalizer/3.3.2... (50 files, 364.2KB)
Uninstalling /usr/local/Cellar/libmng/2.0.3_1... (16 files, 1.1MB)
Uninstalling /usr/local/Cellar/jasper/4.2.4... (44 files, 1.4MB)
Uninstalling /usr/local/Cellar/libev/4.33... (12 files, 454.7KB)
Uninstalling /usr/local/Cellar/libffi/3.4.6... (17 files, 688KB)
Uninstalling /usr/local/Cellar/python-markupsafe/2.1.5... (33 files, 161.2KB)
Uninstalling /usr/local/Cellar/duktape/2.7.0... (15 files, 1.2MB)
Uninstalling /usr/local/Cellar/docbook/5.1_1... (199 files, 8.9MB)
Uninstalling /usr/local/Cellar/gnupg/2.4.5... (140 files, 13.9MB)

Uninstalling /usr/local/Cellar/pinentry/1.3.0... (12 files, 343.4KB)
Uninstalling /usr/local/Cellar/libksba/1.6.6... (18 files, 499.2KB)
Warning: The following openldap configuration files have not been removed!
If desired, remove them manually with rm -rf:
/usr/local/etc/openldap
/usr/local/etc/openldap/ldap.conf
/usr/local/etc/openldap/ldap.conf.default
/usr/local/etc/openldap/schema
/usr/local/etc/openldap/schema/README
/usr/local/etc/openldap/schema/README.default
/usr/local/etc/openldap/schema/collective.ldif
/usr/local/etc/openldap/schema/collective.ldif.default
/usr/local/etc/openldap/schema/collective.schema
/usr/local/etc/openldap/schema/collective.schema.default
/usr/local/etc/openldap/schema/corba.ldif
/usr/local/etc/openldap/schema/corba.ldif.default
/usr/local/etc/openldap/schema/corba.schema
/usr/local/etc/openldap/schema/corba.schema.default
/usr/local/etc/openldap/schema/core.ldif
/usr/local/etc/openldap/schema/core.ldif.default
/usr/local/etc/openldap/schema/core.schema
/usr/local/etc/openldap/schema/core.schema.default
/usr/local/etc/openldap/schema/cosine.ldif
/usr/local/etc/openldap/schema/cosine.ldif.default
/usr/local/etc/openldap/schema/cosine.schema
/usr/local/etc/openldap/schema/cosine.schema.default
/usr/local/etc/openldap/schema/dsee.ldif
/usr/local/etc/openldap/schema/dsee.ldif.default
/usr/local/etc/openldap/schema/dsee.schema
/usr/local/etc/openldap/schema/dsee.schema.default
/usr/local/etc/openldap/schema/duaconf.ldif
/usr/local/etc/openldap/schema/duaconf.ldif.default
/usr/local/etc/openldap/schema/duaconf.schema
/usr/local/etc/openldap/schema/duaconf.schema.default
/usr/local/etc/openldap/schema/dyngroup.ldif
/usr/local/etc/openldap/schema/dyngroup.ldif.default
/usr/local/etc/openldap/schema/dyngroup.schema
/usr/local/etc/openldap/schema/dyngroup.schema.default
/usr/local/etc/openldap/schema/inetorgperson.ldif
/usr/local/etc/openldap/schema/inetorgperson.ldif.default
/usr/local/etc/openldap/schema/inetorgperson.schema
/usr/local/etc/openldap/schema/inetorgperson.schema.default
/usr/local/etc/openldap/schema/java.ldif
/usr/local/etc/openldap/schema/java.ldif.default
/usr/local/etc/openldap/schema/java.schema
/usr/local/etc/openldap/schema/java.schema.default
/usr/local/etc/openldap/schema/misc.ldif
/usr/local/etc/openldap/schema/misc.ldif.default
/usr/local/etc/openldap/schema/misc.schema
/usr/local/etc/openldap/schema/misc.schema.default
/usr/local/etc/openldap/schema/msuser.ldif
/usr/local/etc/openldap/schema/msuser.ldif.default
/usr/local/etc/openldap/schema/msuser.schema
/usr/local/etc/openldap/schema/msuser.schema.default
/usr/local/etc/openldap/schema/namedobject.ldif
/usr/local/etc/openldap/schema/namedobject.ldif.default
/usr/local/etc/openldap/schema/namedobject.schema
/usr/local/etc/openldap/schema/namedobject.schema.default
/usr/local/etc/openldap/schema/nis.ldif
/usr/local/etc/openldap/schema/nis.ldif.default
/usr/local/etc/openldap/schema/nis.schema
/usr/local/etc/openldap/schema/nis.schema.default
/usr/local/etc/openldap/schema/openldap.ldif
/usr/local/etc/openldap/schema/openldap.ldif.default
/usr/local/etc/openldap/schema/openldap.schema
/usr/local/etc/openldap/schema/openldap.schema.default
/usr/local/etc/openldap/schema/pmi.ldif
/usr/local/etc/openldap/schema/pmi.ldif.default
/usr/local/etc/openldap/schema/pmi.schema
/usr/local/etc/openldap/schema/pmi.schema.default
/usr/local/etc/openldap/slapd.conf
/usr/local/etc/openldap/slapd.conf.default
/usr/local/etc/openldap/slapd.conf.default.default
/usr/local/etc/openldap/slapd.ldif
/usr/local/etc/openldap/slapd.ldif.default
/usr/local/etc/openldap/slapd.ldif.default.default
Uninstalling /usr/local/Cellar/openldap/2.6.8... (342 files, 7.2MB)

Uninstalling /usr/local/Cellar/libusb/1.0.27... (22 files, 568.8KB)
Uninstalling /usr/local/Cellar/npth/1.7... (12 files, 143.9KB)
Uninstalling /usr/local/Cellar/libassuan/2.5.7... (17 files, 507.9KB)
Removing: /Users/willf/Library/Caches/Homebrew/Cask/unison--2.53.4.tar.gz... (1.6MB)
Removing: /Users/willf/Library/Caches/Homebrew/api-source/Homebrew/homebrew-cask/0e3b5fc1a173e076840d3e92448491d23dc15807/Cask/unison.rb... (1.2KB)
Removing: /Users/willf/Library/Logs/Homebrew/gdk-pixbuf... (205B)
Removing: /Users/willf/Library/Logs/Homebrew/[email protected]... (2 files, 2KB)
Removing: /Users/willf/Library/Logs/Homebrew/glib... (64B)
Removing: /Users/willf/Library/Logs/Homebrew/rust... (64B)
Removing: /Users/willf/Library/Logs/Homebrew/openssl@3... (64B)
Removing: /Users/willf/Library/Logs/Homebrew/clamav... (64B)
Removing: /Users/willf/Library/Logs/Homebrew/gnutls... (64B)
Removing: /usr/local/lib/python3.12/site-packages/_distutils_hack/pycache/init.cpython-312.pyc... (9.7KB)
Pruned 0 symbolic links and 12 directories from /usr/local
==> Caveats
==> emacs
To start emacs now and restart at login:
brew services start emacs
Or, if you don't want/need a background service you can just run:
/usr/local/opt/emacs/bin/emacs --fg-daemon
==> wireshark
This formula only installs the command-line utilities by default.

Install Wireshark.app with Homebrew Cask:
brew install --cask wireshark

If your list of available capture interfaces is empty
(default macOS behavior), install ChmodBPF:
brew install --cask wireshark-chmodbpf
==> cookiecutter
zsh completions have been installed to:
/usr/local/share/zsh/site-functions

wfiveash · 2024-05-23T16:13:02Z

wfiveash
May 23, 2024
Author

Note, /usr/local/bin/ksh is supplied by the ksh93 homebrew formula.

0 replies

wfiveash · 2024-05-23T17:26:45Z

wfiveash
May 23, 2024
Author

I thought I'd try to uninstall cookiecutter formula since the upgrade of that appears to delete a bunch of other formula. Here is the result:
$ brew uninstall cookiecutter
Uninstalling /usr/local/Cellar/cookiecutter/2.6.0_2... (901 files, 10MB)
==> Autoremoving 72 unneeded formulae:
adns
assimp
bdw-gc
certifi
cmake
cmocka
cscope
dbus
docbook
docbook-xsl
docutils
double-conversion
duktape
gdbm
gnu-getopt
gnupg
gobject-introspection
gpgme
guile
hunspell
jasper
jemalloc
jpeg
ksh93
libassuan
libcroco
libev
libffi
[email protected]
libiconv
libksba
libmng
libproxy
libpthread-stubs
libusb
libvo-aacenc
llvm@16
luajit
md4c
mutt
nghttp2
npth
openldap
pcre
pinentry
protobuf@21
pygments
python-charset-normalizer
python-click
python-dateutil
python-idna
python-jinja
python-markupsafe
python-requests
python-setuptools
python-tabulate
python-urllib3
[email protected]
[email protected]
[email protected]
[email protected]
pyyaml
qt
rtmpdump
shared-mime-info
six
sphinx-doc
swig
texi2html
tokyo-cabinet
xmlto
yasm
Uninstalling /usr/local/Cellar/python-jinja/3.1.3... (75 files, 1006.2KB)
Uninstalling /usr/local/Cellar/libproxy/0.5.6... (16 files, 141KB)
Uninstalling /usr/local/Cellar/yasm/1.3.0_2... (45 files, 3MB)
Uninstalling /usr/local/Cellar/libiconv/1.17... (31 files, 2.7MB)
Uninstalling /usr/local/Cellar/nghttp2/1.61.0... (17 files, 2.2MB)
Uninstalling /usr/local/Cellar/python-click/8.1.7_1... (80 files, 1MB)
Uninstalling /usr/local/Cellar/swig/4.2.1... (829 files, 5.7MB)
Uninstalling /usr/local/Cellar/pygments/2.18.0... (347 files, 4.3MB)
Uninstalling /usr/local/Cellar/python-setuptools/69.5.1... (274 files, 3.2MB)
Uninstalling /usr/local/Cellar/llvm@16/16.0.6_1... (6,767 files, 1.4GB)
Uninstalling /usr/local/Cellar/cmake/3.29.3... (3,385 files, 59.3MB)
Uninstalling /usr/local/Cellar/python-dateutil/2.9.0.post0... (62 files, 929.3KB)
Uninstalling /usr/local/Cellar/docutils/0.21.2... (239 files, 2.1MB)
Uninstalling /usr/local/Cellar/rtmpdump/2.4-20151223_3... (20 files, 542.0KB)
Uninstalling /usr/local/Cellar/cmocka/1.1.7... (17 files, 176.5KB)
Uninstalling /usr/local/Cellar/python-requests/2.31.0... (58 files, 457.3KB)
Uninstalling /usr/local/Cellar/cscope/15.9... (11 files, 711.6KB)
Uninstalling /usr/local/Cellar/texi2html/5.0... (278 files, 6.2MB)
Uninstalling /usr/local/Cellar/libvo-aacenc/0.1.3... (16 files, 300.3KB)
Uninstalling /usr/local/Cellar/xmlto/0.0.28... (46 files, 142.0KB)
Uninstalling /usr/local/Cellar/shared-mime-info/2.4... (88 files, 4.7MB)
Uninstalling /usr/local/Cellar/ksh93/2020.0.0... (8 files, 3.7MB)
Uninstalling /usr/local/Cellar/qt/6.7.0_1... (15,057 files, 675.2MB)
Uninstalling /usr/local/Cellar/gobject-introspection/1.80.1... (541 files, 5.6MB)
Uninstalling /usr/local/Cellar/protobuf@21/21.12... (288 files, 19.6MB)
Uninstalling /usr/local/Cellar/python-tabulate/0.9.0_1... (40 files, 428.0KB)
Uninstalling /usr/local/Cellar/libpthread-stubs/0.5... (5 files, 6.8KB)
Uninstalling /usr/local/Cellar/libcroco/0.6.13_1... (80 files, 1.7MB)
Uninstalling /usr/local/Cellar/sphinx-doc/7.3.7_1... (3,070 files, 49.9MB)
Uninstalling /usr/local/Cellar/pyyaml/6.0.1_1... (86 files, 1.6MB)
Uninstalling /usr/local/Cellar/[email protected]/3.10.14... (3,096 files, 53.8MB)
Uninstalling /usr/local/Cellar/[email protected]/1.6.5... (104 files, 4.4MB)
Uninstalling /usr/local/Cellar/luajit/2.1.1713773202... (55 files, 1.9MB)
Uninstalling /usr/local/Cellar/mutt/2.2.13... (126 files, 10MB)
Uninstalling /usr/local/Cellar/jpeg/9f... (21 files, 871.0KB)
Uninstalling /usr/local/Cellar/[email protected]/3.11.9... (3,326 files, 59.4MB)
Uninstalling /usr/local/Cellar/[email protected]/3.8.19... (5,089 files, 75.8MB)
Uninstalling /usr/local/Cellar/guile/3.0.9_1... (848 files, 59.4MB)
Uninstalling /usr/local/Cellar/[email protected]/3.9.19... (3,066 files, 53.5MB)
Uninstalling /usr/local/Cellar/adns/1.6.1... (14 files, 660.1KB)
Uninstalling /usr/local/Cellar/python-idna/3.6... (36 files, 566.5KB)
Uninstalling /usr/local/Cellar/gpgme/1.23.2_1... (107 files, 4.4MB)
Uninstalling /usr/local/Cellar/gdbm/1.23... (24 files, 956.7KB)
Uninstalling /usr/local/Cellar/gnu-getopt/2.40.1... (12 files, 196.3KB)
Uninstalling /usr/local/Cellar/assimp/5.4.1... (104 files, 11.1MB)
Uninstalling /usr/local/Cellar/md4c/0.5.2... (19 files, 262.2KB)
Uninstalling /usr/local/Cellar/jemalloc/5.3.0... (16 files, 2.7MB)
Uninstalling /usr/local/Cellar/bdw-gc/8.2.6... (73 files, 1.6MB)
Uninstalling /usr/local/Cellar/python-urllib3/2.2.1... (91 files, 841.3KB)
Uninstalling /usr/local/Cellar/tokyo-cabinet/1.4.48... (79 files, 4.2MB)
Uninstalling /usr/local/Cellar/hunspell/1.7.2... (86 files, 2.6MB)
Uninstalling /usr/local/Cellar/dbus/1.14.10... (77 files, 2.4MB)

Warning: The following may be dbus configuration files and have not been removed!
If desired, remove them manually with rm -rf:
/usr/local/etc/dbus-1
Uninstalling /usr/local/Cellar/double-conversion/3.3.0... (26 files, 245.3KB)
Uninstalling /usr/local/Cellar/docbook-xsl/1.79.2_1... (4,910 files, 94.0MB)
Uninstalling /usr/local/Cellar/certifi/2024.2.2... (30 files, 24.6KB)

Warning: The following may be certifi configuration files and have not been removed!
If desired, remove them manually with rm -rf:
/usr/local/etc/ca-certificates
Uninstalling /usr/local/Cellar/pcre/8.45... (204 files, 5.8MB)
Uninstalling /usr/local/Cellar/six/1.16.0_4... (20 files, 122.4KB)
Uninstalling /usr/local/Cellar/python-charset-normalizer/3.3.2... (50 files, 364.2KB)
Uninstalling /usr/local/Cellar/libmng/2.0.3_1... (16 files, 1.1MB)
Uninstalling /usr/local/Cellar/jasper/4.2.4... (44 files, 1.4MB)
Uninstalling /usr/local/Cellar/libev/4.33... (12 files, 454.7KB)
Uninstalling /usr/local/Cellar/libffi/3.4.6... (17 files, 688KB)
Uninstalling /usr/local/Cellar/python-markupsafe/2.1.5... (33 files, 161.2KB)
Uninstalling /usr/local/Cellar/duktape/2.7.0... (15 files, 1.2MB)
Uninstalling /usr/local/Cellar/docbook/5.1_1... (199 files, 8.9MB)
Uninstalling /usr/local/Cellar/gnupg/2.4.5... (140 files, 13.9MB)

Warning: The following gnupg configuration files have not been removed!
If desired, remove them manually with rm -rf:
/usr/local/etc/gnupg
/usr/local/etc/gnupg/scdaemon.conf
Uninstalling /usr/local/Cellar/pinentry/1.3.0... (12 files, 343.4KB)
Uninstalling /usr/local/Cellar/libksba/1.6.6... (18 files, 499.2KB)
Uninstalling /usr/local/Cellar/openldap/2.6.7... (340 files, 7.5MB)

Warning: The following openldap configuration files have not been removed!
If desired, remove them manually with rm -rf:
/usr/local/etc/openldap
/usr/local/etc/openldap/ldap.conf
/usr/local/etc/openldap/ldap.conf.default
/usr/local/etc/openldap/schema
/usr/local/etc/openldap/schema/README
/usr/local/etc/openldap/schema/collective.ldif
/usr/local/etc/openldap/schema/collective.schema
/usr/local/etc/openldap/schema/corba.ldif
/usr/local/etc/openldap/schema/corba.schema
/usr/local/etc/openldap/schema/core.ldif
/usr/local/etc/openldap/schema/core.schema
/usr/local/etc/openldap/schema/cosine.ldif
/usr/local/etc/openldap/schema/cosine.schema
/usr/local/etc/openldap/schema/dsee.ldif
/usr/local/etc/openldap/schema/dsee.schema
/usr/local/etc/openldap/schema/duaconf.ldif
/usr/local/etc/openldap/schema/duaconf.schema
/usr/local/etc/openldap/schema/dyngroup.ldif
/usr/local/etc/openldap/schema/dyngroup.schema
/usr/local/etc/openldap/schema/inetorgperson.ldif
/usr/local/etc/openldap/schema/inetorgperson.schema
/usr/local/etc/openldap/schema/java.ldif
/usr/local/etc/openldap/schema/java.schema
/usr/local/etc/openldap/schema/misc.ldif
/usr/local/etc/openldap/schema/misc.schema
/usr/local/etc/openldap/schema/msuser.ldif
/usr/local/etc/openldap/schema/msuser.schema
/usr/local/etc/openldap/schema/namedobject.ldif
/usr/local/etc/openldap/schema/namedobject.schema
/usr/local/etc/openldap/schema/nis.ldif
/usr/local/etc/openldap/schema/nis.schema
/usr/local/etc/openldap/schema/openldap.ldif
/usr/local/etc/openldap/schema/openldap.schema
/usr/local/etc/openldap/schema/pmi.ldif
/usr/local/etc/openldap/schema/pmi.schema
/usr/local/etc/openldap/slapd.conf
/usr/local/etc/openldap/slapd.conf.default
/usr/local/etc/openldap/slapd.conf.default.default
/usr/local/etc/openldap/slapd.ldif
/usr/local/etc/openldap/slapd.ldif.default
/usr/local/etc/openldap/slapd.ldif.default.default
Uninstalling /usr/local/Cellar/libusb/1.0.27... (22 files, 568.8KB)
Uninstalling /usr/local/Cellar/npth/1.7... (12 files, 143.9KB)
Uninstalling /usr/local/Cellar/libassuan/2.5.7... (17 files, 507.9KB)

Note, I ran "brew uninstall cookiecutter" after I had restored everything in /usr/local from a Time Machine backup at a point prior to my running "brew upgrade" which caused ksh93 to be uninstalled.

12 replies

gromgit May 29, 2024

That odd version number is key: you originally installed the old ksh formula, which was replaced by ksh93 back in 2022:

commit 7a7e18de3fb8cfa63e9657555e7606b948fc1118
Author: Jeffrey H. Johnson <[email protected]>
Date:   Sun Jul 17 21:36:42 2022 -0400

    ksh93 1.0.0 (new formula)
    
    Update ksh93 2020.0.0 (2019-10-19) to ksh93u+m 1.0.0-beta.2 (2021-12-17)
    
    Update for ksh93u+m 1.0.0
    
    Adjust desc; remove automatic installed files
    
    Restore ksh.rb
    
    Add ksh93u+m 1.0.0
    
    deprecate ksh
    
    ksh is abandoned, unmaintained, no releases since 2020; consider ksh93 instead
    
    Simplify doc.install
    
    Revert to original
    
    Add `rksh93` link, and also correspondig man page.
    
    Update Formula/ksh93.rb
    
    Closes #106033.
    
    Co-authored-by: Carlo Cabrera <[email protected]>
    Signed-off-by: Carlo Cabrera <[email protected]>
    Signed-off-by: BrewTestBot <[email protected]>

It also hints at why the JSON says you installed it twice with the same version. What's the output of:

ls -l /usr/local/opt/ksh* /usr/local/Cellar/ksh*/*

?

@carlocab, could this be a migration corner case, where users install an old formula that gets swapped out with a migration to a different formula name?

wfiveash May 29, 2024
Author

$ ls -l /usr/local/opt/ksh* /usr/local/Cellar/ksh*/*
lrwxr-xr-x 1 willf admin 24 Oct 24 2022 /usr/local/opt/ksh@ -> ../Cellar/ksh93/2020.0.0
lrwxr-xr-x 1 willf admin 24 Oct 24 2022 /usr/local/opt/ksh93@ -> ../Cellar/ksh93/2020.0.0

/usr/local/Cellar/ksh/2020.0.0:
total 80
-rw-r--r-- 1 willf staff 14228 Oct 10 2019 CHANGELOG.md
-rw-r--r-- 1 willf staff 751 May 24 09:59 INSTALL_RECEIPT.json
-rw-r--r-- 1 willf staff 11249 Oct 10 2019 LICENSE
-rw-r--r-- 1 willf staff 6593 Oct 10 2019 README.md
drwxr-xr-x 4 willf staff 128 Oct 10 2019 bin/
drwxr-xr-x 3 willf staff 96 Oct 10 2019 share/

/usr/local/Cellar/ksh93/2020.0.0:
total 80
-rw-r--r-- 1 willf staff 14228 Oct 10 2019 CHANGELOG.md
-rw-r--r-- 1 willf staff 751 May 24 09:59 INSTALL_RECEIPT.json
-rw-r--r-- 1 willf staff 11249 Oct 10 2019 LICENSE
-rw-r--r-- 1 willf staff 6593 Oct 10 2019 README.md
drwxr-xr-x 4 willf staff 128 Oct 10 2019 bin/
drwxr-xr-x 3 willf staff 96 Oct 10 2019 share/

carlocab May 29, 2024

@carlocab, could this be a migration corner case, where users install an old formula that gets swapped out with a migration to a different formula name?

Sounds plausible. It even seems like autoremove is trying to get rid of ksh without realising it's now the same thing as ksh93, which it knows to keep.

MikeMcQuaid May 29, 2024
Maintainer

Sounds plausible. It even seems like autoremove is trying to get rid of ksh without realising it's now the same thing as ksh93, which it knows to keep.

Good catch. This is definitely a 🐛 with autoremove that should be filed and fixed 👍🏻

gromgit May 29, 2024

There's another wrinkle to this: @wfiveash's current ksh/ksh93 state is completely wrong, as shown by his ls and JSON output. With a version number that's strictly greater than anything the current ksh93 could ever attain, would brew upgrade ksh93 even work. or would he have to brew rm ksh93; brew install ksh93?

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brew upgrade uninstalled a bunch of things including ksh93 which I depend on #5395

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Homebrew

brew upgrade uninstalled a bunch of things including ksh93 which I depend on #5395

wfiveash May 23, 2024

Output of brew config

Output of brew doctor

Description of issue

Replies: 2 comments · 12 replies

wfiveash May 23, 2024 Author

wfiveash May 23, 2024 Author

gromgit May 29, 2024

wfiveash May 29, 2024 Author

carlocab May 29, 2024

MikeMcQuaid May 29, 2024 Maintainer

gromgit May 29, 2024

wfiveash
May 23, 2024

Output of `brew config`

Output of `brew doctor`

Replies: 2 comments 12 replies

wfiveash
May 23, 2024
Author

wfiveash
May 23, 2024
Author

wfiveash May 29, 2024
Author

MikeMcQuaid May 29, 2024
Maintainer