"bundle list" can not find an installed gem after running "bundle install --standalone"

[junaruga]

Describe the problem as clearly as you can

I am using the ruby at the ruby/ruby master branch relatively latest commit ed18a212abe2d92feb441db2b6f084c0c77a65e4, and the bundle command in it.

After running, bundle install, gem uninstall gem2rpm, bundle install --standalone, then bundle list fails.

Did you try upgrading rubygems & bundler?

I tried to run the gem update --system. However, the gem update --system was stucking. So, I couldn't run the command.

Post steps to reproduce the problem

OS: Fedora Linux 42
Ruby: ruby/ruby master branch commit compiled from the source.

$ which ruby
~/.local/ruby-4.0.0dev-debug-ed18a212ab/bin/ruby
$ ruby -v
ruby 4.0.0dev (2025-12-10T16:08:55Z master ed18a212ab) +PRISM [x86_64-linux]
$ which gem
~/.local/ruby-4.0.0dev-debug-ed18a212ab/bin/gem
$ gem -v
4.0.1
$ which bundle
~/.local/ruby-4.0.0dev-debug-ed18a212ab/bin/bundle
$ bundle -v
4.0.1

$ gem env
RubyGems Environment:
  - RUBYGEMS VERSION: 4.0.1
  - RUBY VERSION: 4.0.0 (2025-12-11 patchlevel -1) [x86_64-linux]
  - INSTALLATION DIRECTORY: /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/lib/ruby/gems/4.0.0+0
  - USER INSTALLATION DIRECTORY: /home/jaruga/.local/share/gem/ruby/4.0.0+0
  - CREDENTIALS FILE: /home/jaruga/.local/share/gem/credentials
  - RUBY EXECUTABLE: /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/bin/ruby
  - GIT EXECUTABLE: /bin/git
  - EXECUTABLE DIRECTORY: /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/bin
  - SPEC CACHE DIRECTORY: /home/jaruga/.cache/gem/specs
  - SYSTEM CONFIGURATION DIRECTORY: /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/etc
  - RUBYGEMS PLATFORMS:
     - ruby
     - x86_64-linux
  - GEM PATHS:
     - /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/lib/ruby/gems/4.0.0+0
     - /home/jaruga/.local/share/gem/ruby/4.0.0+0
  - GEM CONFIGURATION:
     - :update_sources => true
     - :verbose => true
     - :backtrace => true
     - :bulk_threshold => 1000
  - REMOTE SOURCES:
     - https://rubygems.org/
  - SHELL PATH:
     - /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/bin
     - /usr/local/wasmtime-1.0.1/bin
     - /home/jaruga/.go/bin
     - /home/jaruga/git/gem2rpm/bin
     - /home/jaruga/git/rpmlint/dist/usr/bin
     - /bin
     - /usr/bin
     - /usr/sbin
     - /usr/local/bin
     - /usr/local/sbin
     - /home/jaruga/bin
     - /home/jaruga/.local/bin
     - /home/jaruga/.local/FASTK-f18a4e6/bin
     - /home/jaruga/.local/GENESCOPE.FK-380815c/bin
     - /home/jaruga/.local/MERQURY.FK-8f3ab70/bin
     - /var/lib/snapd/snap/bin
     - /usr/local/powercap/bin
     - /usr/local/mongodb-linux-x86_64-rhel80-4.4.1/bin
     - /home/jaruga/.npm-global/bin

Steps:

$ cat Gemfile
source 'https://rubygems.org'

gem 'gem2rpm'

$ bundle install
Fetching gem metadata from https://rubygems.org/.
Resolving dependencies...
Fetching gem2rpm 1.0.2
Installing gem2rpm 1.0.2
Bundle complete! 1 Gemfile dependency, 2 gems now installed.
Use `bundle info [gemname]` to see where a bundled gem is installed.

$ bundle list
Gems included by the bundle:
  * gem2rpm (1.0.2)
Use `bundle info` to print more detailed information about a gem

$ gem uninstall gem2rpm
Remove executables:
	gem2rpm

in addition to the gem? [Yn]  Y
Removing gem2rpm
Successfully uninstalled gem2rpm-1.0.2

$ rm Gemfile.lock

$ bundle install --verbose --standalone
Running `bundle install --standalone  --verbose` with bundler 4.0.1
Resolving dependencies because there's no lockfile
HTTP GET https://index.rubygems.org/versions
HTTP 206 Partial Content https://index.rubygems.org/versions
Fetching gem metadata from https://rubygems.org/
Looking up gems ["gem2rpm"]
Resolving dependencies...
Using bundler 4.0.1
0:  bundler (4.0.1) from /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/lib/ruby/gems/4.0.0+0/specifications/default/bundler-4.0.1.gemspec
Fetching gem2rpm 1.0.2
Downloaded gem2rpm in: 0.119s
Installing gem2rpm 1.0.2
Installed gem2rpm in: 0.007s
1:  gem2rpm (1.0.2) from /home/jaruga/doc/memo/20251212_bundler_test/bundle/ruby/4.0.0+0/specifications/gem2rpm-1.0.2.gemspec
Bundle complete! 1 Gemfile dependency, 2 gems now installed.
Bundled gems are installed into `./bundle`

$ bundle list
Could not find gem2rpm-1.0.2 in locally installed gems
Install missing gems with `bundle install`.

$ ls
bundle/  Gemfile  Gemfile.lock

$ ls bundle/ruby/4.0.0+0/gems/gem2rpm-1.0.2/
AUTHORS  bin/  lib/  LICENSE  README.md  templates/

But it seems the gem2rpm gem was installed in the bundle/ruby/4.0.0+0/gems/gem2rpm-1.0.2/ regardless the message Could not find gem2rpm-1.0.2 in locally installed gems.

Which command did you run?

bundle install, bundle list

What were you expecting to happen?

The bundle list shows a list of the gems without error.

What happened instead?

$ bundle list
Could not find gem2rpm-1.0.2 in locally installed gems
Install missing gems with `bundle install`.

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

$ bundle env

Environment

Bundler       4.0.1
  Platforms   ruby, x86_64-linux
Ruby          4.0.0p-1 (2025-12-11 revision ed18a212abe2d92feb441db2b6f084c0c77a65e4) [x86_64-linux]
  Full Path   /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/bin/ruby
  Config Dir  /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/etc
RubyGems      4.0.1
  Gem Home    /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/lib/ruby/gems/4.0.0+0
  Gem Path    /home/jaruga/.local/share/gem/ruby/4.0.0+0:/home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/lib/ruby/gems/4.0.0+0
  User Home   /home/jaruga
  User Path   /home/jaruga/.local/share/gem/ruby/4.0.0+0
  Bin Dir     /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/bin
Tools
  Git         2.51.0
  RVM         not installed
  rbenv       not installed
  chruby      not installed

Bundler Build Metadata

Timestamp  2025-12-12
Git SHA    unknown

Gemfile

Gemfile

source 'https://rubygems.org'

gem 'gem2rpm'

Gemfile.lock

GEM
  remote: https://rubygems.org/
  specs:
    gem2rpm (1.0.2)

PLATFORMS
  ruby
  x86_64-linux

DEPENDENCIES
  gem2rpm

CHECKSUMS
  gem2rpm (1.0.2) sha256=21695912765a469cdde0d2ace690b8485ae43ec195866c3a51eed3584975eafd

BUNDLED WITH
  4.0.1

[junaruga]

This issue just happens on the following simple steps without the pre-executed bundle install.

$ cat Gemfile
source 'https://rubygems.org'

gem 'rake-compiler'

$ bundle install --verbose --standalone
Running `bundle install --standalone  --verbose` with bundler 4.0.1
Resolving dependencies because there's no lockfile
HTTP GET https://index.rubygems.org/versions
HTTP 206 Partial Content https://index.rubygems.org/versions
Fetching gem metadata from https://rubygems.org/
Looking up gems ["rake-compiler"]
Looking up gems ["rake"]
HTTP GET https://index.rubygems.org/info/rake
HTTP 206 Partial Content https://index.rubygems.org/info/rake
Resolving dependencies...
Fetching rake 13.3.1
Downloaded rake in: 0.174s
Installing rake 13.3.1
Installed rake in: 0.013s
0:  rake (13.3.1) from /home/jaruga/doc/memo/20251212_bundler_test_2/bundle/ruby/4.0.0+0/specifications/rake-13.3.1.gemspec
Using bundler 4.0.1
0:  bundler (4.0.1) from /home/jaruga/.local/ruby-4.0.0dev-debug-ed18a212ab/lib/ruby/gems/4.0.0+0/specifications/default/bundler-4.0.1.gemspec
Fetching rake-compiler 1.3.0
Downloaded rake-compiler in: 0.124s
Installing rake-compiler 1.3.0
Installed rake-compiler in: 0.015s
1:  rake-compiler (1.3.0) from /home/jaruga/doc/memo/20251212_bundler_test_2/bundle/ruby/4.0.0+0/specifications/rake-compiler-1.3.0.gemspec
Bundle complete! 1 Gemfile dependency, 3 gems now installed.
Bundled gems are installed into `./bundle`

$ bundle list
Could not find rake-compiler-1.3.0 in locally installed gems
Install missing gems with `bundle install`.

[Edouard-chin]

It's probably related to the bundler change where passing flags to bundle no longer persist it in the config (previously passing --standalone would persist the BUNDLE_PATH: bundle in your config).

I feel like we should make an exception to this flag and continue setting the BUNDLE_PATH 🤔 .
Edit: Actually, maybe not, I'm not sure.

[junaruga]

Thanks for your response. Could you rename this thread's title to a better name, once you find the root cause of this issue?

[JonRowe]

This also seem to affects binstubs, if you run:

bundle install --standalone

Then this will fail:

bundle binstubs --all --standalone
# or bundle binstubs some_gem --standalone