Permissions errors are silently swallowed in `bundle clean`

[maxfelsher-cgi]

Describe the problem as clearly as you can

If some gems cannot be deleted during bundle clean due to permissions issues, the errors are left unreported. The output and exit code are the same as when all unneeded gems are removed successfully.

Did you try upgrading rubygems & bundler?

Yes.

Post steps to reproduce the problem

Set your Bundler path to an explicit directory (this step can be skipped, but then you may have to use the --force option for bundle clean).

$ bundle config set path '.bundle'

Make sure you have at least one gem installed in the relevant directory that is no longer listed in your Gemfile.lock, and make sure that the file permissions are set such that you don't have the ability to delete that gem's files/directories. Because of #9395, this can happen easily if you have multiple users doing deployments for a project.

For these steps, I set things up so that my Gemfile.lock listed thor 1.5.0, but I also had thor 1.4.0 installed. I manually changed the owner of the thor-1.4.0 directory to root as a simulation, but the more typical situation would be that it's some non-root user other than yourself.

$ ls -l .bundle/ruby/4.0.0/gems
total 8
drwxr-xr-x. 4 root     rvm 4096 Mar 13 16:08 thor-1.4.0
drwxr-xr-x. 4 mfelsher rvm 4096 Mar 13 16:12 thor-1.5.0

Which command did you run?

bundle clean

What were you expecting to happen?

If there are permissions errors that stop a directory from being removed during bundle clean, I would expect an error or warning message to be output. I'd probably expect the command to return with an error status as well.

What happened instead?

The command says it's removing thor 1.4.0 without any warnings/errors and returns with a success status, even though the directory and its contents still exist.

$ bundle clean
Removing thor (1.4.0)
$ echo $?
0
$ ls -l .bundle/ruby/4.0.0/gems
total 8
drwxr-xr-x. 4 root     rvm 4096 Mar 13 16:08 thor-1.4.0
drwxr-xr-x. 4 mfelsher rvm 4096 Mar 13 16:12 thor-1.5.0
$ ls -l .bundle/ruby/4.0.0/gems/thor-1.4.0/
total 24
drwxrwxr-x. 2 root root 4096 Mar 13 16:08 bin
-rw-r--r--. 1 root root 1030 Mar 13 16:08 CONTRIBUTING.md
drwxrwxr-x. 3 root root 4096 Mar 13 16:08 lib
-rw-r--r--. 1 root root 1075 Mar 13 16:08 LICENSE.md
-rw-r--r--. 1 root root 1410 Mar 13 16:08 README.md
-rw-r--r--. 1 root root 1210 Mar 13 16:08 thor.gemspec

Additional detail

I'm guessing that this is occurring because of the use of FileUtils.rm_rf here, swallowing any permissions errors:

rubygems/bundler/lib/bundler/runtime.rb

Lines 306 to 307 in bcc4469

	Bundler.ui.info "Removing #{output}"
	FileUtils.rm_rf(dir)

If not included with the output of your command, run bundle env and paste the output below

Environment

Bundler             4.0.8
  Platforms         ruby, x86_64-linux
Ruby                4.0.1p0 (2026-01-13 revision e04267a14b1a5dea2d2c368e48d41bd3db441f4f) [x86_64-linux]
  Full Path         /usr/local/rvm/rubies/ruby-4.0.1/bin/ruby
  Config Dir        /usr/local/rvm/rubies/ruby-4.0.1/etc
RubyGems            4.0.8
  Gem Home          /usr/local/rvm/gems/ruby-4.0.1
  Gem Path          /usr/local/rvm/gems/ruby-4.0.1:/usr/local/rvm/rubies/ruby-4.0.1/lib/ruby/gems/4.0.0
  User Home         /home/mfelsher
  User Path         /home/mfelsher/.local/share/gem/ruby/4.0.0
  Bin Dir           /usr/local/rvm/gems/ruby-4.0.1/bin
Tools               
  Git               2.43.7
  RVM               1.29.12 (latest)
  rbenv             not installed
  chruby            not installed
  rubygems-bundler  (1.4.5)

Bundler Build Metadata

Timestamp  2026-03-11
Git SHA    1a32b76b73

Bundler settings

path
  Set for your local app (/home/mfelsher/bundler_permissions_issue/.bundle/config): ".bundle"

Gemfile

Gemfile

# frozen_string_literal: true

source "https://rubygems.org"

gem 'thor'

Gemfile.lock

GEM
  remote: https://rubygems.org/
  specs:
    thor (1.5.0)

PLATFORMS
  ruby
  x86_64-linux

DEPENDENCIES
  thor

CHECKSUMS
  thor (1.5.0) sha256=e3a9e55fe857e44859ce104a84675ab6e8cd59c650a49106a05f55f136425e73

BUNDLED WITH
  4.0.8