Error: cannot load such file (a Ruby 3.4.8 issue)

[ptsl]

brew doctor output

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/wkhtmltox/*

Verification

• I ran brew update twice and am still able to reproduce my issue.
• My "brew doctor output" above says Your system is ready to brew or a definitely unrelated Tier message.
• This issue's title and/or description do not reference a single formula e.g. brew install wget. If they do, open an issue at https://github.com/Homebrew/homebrew-core/issues/new/choose instead.

brew config output

HOMEBREW_VERSION: 5.0.7
ORIGIN: https://github.com/Homebrew/brew
HEAD: b64029d4f999b8963d0dadb925d3b484207c1cee
Last commit: 3 days ago
Branch: stable
Core tap JSON: 22 Dec 11:37 UTC
HOMEBREW_PREFIX: /home/linuxbrew/.linuxbrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: :1.0
HOMEBREW_DOWNLOAD_CONCURRENCY: 48
HOMEBREW_EDITOR: vim
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_MAKE_JOBS: 24
Homebrew Ruby: 3.4.8 => /home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/bin/ruby
CPU: 24-core 64-bit zen2
Clang: N/A
Git: 2.43.0 => /bin/git
Curl: 8.5.0 => /bin/curl
Kernel: Linux 6.8.0-90-generic x86_64 GNU/Linux
OS: Ubuntu 24.04.3 LTS (noble)
Host glibc: 2.39
Host libstdc++: 6.0.33
/usr/bin/gcc-12: 12.4.0
/usr/bin/ruby: N/A
glibc: N/A
gcc@12: N/A
gcc: N/A
xorg: N/A

What were you trying to do (and why)?

The problem appears when I try to install any package using brew on Linux - Ubuntu 24.04.3 LTS.

More specifically, I tried:

• brew install uv
• brew install ruby
• brew install fresh-editor
  The brew upgrade command seems affected, too.

But this does not seem to matter, the reported errors were identical.

I tried to run brew update twice (as suggested above) - it didn't help. Running it the third time time helped, though, and I was able to install packages.

Unfortunately, a few days have passed and the issue has reappeared.

Regarding the non-empty output of brew doctor: I need wkhtmltopdf for my work and cannot uninstall it. However, its files are grouped in a single directory.

Recently, I had another Ruby-related problem on my computer. Ruby developers decided to move the standard Ruby REXML package (an XML parser) from the gem repos to the core library. I'm not sure if this is or isn't related to the Homebrew issue I'm reporting.

What happened (include all command output)?

==> Upgrading fresh-editor
  0.1.55 -> 0.1.58
==> Pouring fresh-editor--0.1.58.x86_64_linux.bottle.tar.gz
Error: cannot load such file -- /home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/bundle/ruby/3.4.0/gems/bindata-2.5.1/lib/bindata/array.rb
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/gems/3.4.0/gems/bootsnap-1.19.0/lib/bootsnap/load_path_cache/core_ext/kernel_require.rb:30:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/bundle/ruby/3.4.0/gems/bindata-2.5.1/lib/bindata.rb:5:in '<main>'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/gems/3.4.0/gems/bootsnap-1.19.0/lib/bootsnap/load_path_cache/core_ext/kernel_require.rb:30:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/bundle/ruby/3.4.0/gems/elftools-1.3.1/lib/elftools/structs.rb:3:in '<main>'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/gems/3.4.0/gems/bootsnap-1.19.0/lib/bootsnap/load_path_cache/core_ext/kernel_require.rb:30:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/bundle/ruby/3.4.0/gems/elftools-1.3.1/lib/elftools/note.rb:3:in '<main>'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/gems/3.4.0/gems/bootsnap-1.19.0/lib/bootsnap/load_path_cache/core_ext/kernel_require.rb:30:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/bundle/ruby/3.4.0/gems/elftools-1.3.1/lib/elftools/sections/note_section.rb:3:in '<main>'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/gems/3.4.0/gems/bootsnap-1.19.0/lib/bootsnap/load_path_cache/core_ext/kernel_require.rb:30:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/bundle/ruby/3.4.0/gems/elftools-1.3.1/lib/elftools/sections/sections.rb:8:in '<main>'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/gems/3.4.0/gems/bootsnap-1.19.0/lib/bootsnap/load_path_cache/core_ext/kernel_require.rb:30:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/bundle/ruby/3.4.0/gems/elftools-1.3.1/lib/elftools/elf_file.rb:6:in '<main>'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/gems/3.4.0/gems/bootsnap-1.19.0/lib/bootsnap/load_path_cache/core_
ext/kernel_require.rb:30:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/bundle/ruby/3.4.0/gems/patchelf-1.5.2/lib/patchelf/patcher.rb:4:in '<main>'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/gems/3.4.0/gems/bootsnap-1.19.0/lib/bootsnap/load_path_cache/core_ext/kernel_require.rb:30:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/bundle/ruby/3.4.0/gems/patchelf-1.5.2/lib/patchelf.rb:9:in '<main>'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
<internal:/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/3.4.0/rubygems/core_ext/kernel_require.rb>:37:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/lib/ruby/gems/3.4.0/gems/bootsnap-1.19.0/lib/bootsnap/load_path_cache/core_ext/kernel_require.rb:30:in 'Kernel#require'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/os/linux/elf.rb:187:in 'ELFShim::Metadata#initialize'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/os/linux/elf.rb:289:in 'Class#new'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/os/linux/elf.rb:289:in 'ELFShim#metadata'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/os/linux/elf.rb:155:in 'ELFShim#dynamic_elf?'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/extend/os/linux/keg_relocate.rb:32:in 'OS::Linux::Keg#change_rpath!'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/extend/os/linux/keg_relocate.rb:22:in 'block (2 levels) in OS::Linux::Keg#relocate_dynamic_linkage'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/extend/pathname.rb:276:in 'Pathname#ensure_writable'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/extend/os/linux/keg_relocate.rb:21:in 'block in OS::Linux::Keg#relocate_dynamic_linkage'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/extend/os/linux/keg_relocate.rb:20:in 'Array#each'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/extend/os/linux/keg_relocate.rb:20:in 'OS::Linux::Keg#relocate_dynamic_linkage'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/keg_relocate.rb:189:in 'Keg#replace_placeholders_with_locations'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:1535:in 'FormulaInstaller#pour'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:593:in 'FormulaInstaller#install'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/install.rb:493:in 'Homebrew::Install.install_formula'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/upgrade.rb:393:in 'Homebrew::Upgrade.upgrade_formula'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/upgrade.rb:124:in 'block in Homebrew::Upgrade.upgrade_formulae'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/upgrade.rb:123:in 'Array#each'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/upgrade.rb:123:in 'Homebrew::Upgrade.upgrade_formulae'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/cmd/upgrade.rb:267:in 'Homebrew::Cmd::UpgradeCmd#upgrade_outdated_formulae!'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/cmd/upgrade.rb:142:in 'Homebrew::Cmd::UpgradeCmd#run'
/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/brew.rb:102:in '<main>'

What did you expect to happen?

I expected that brew would install the packages.

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

I have already described the steps above.