Unable to do bundle install with bundler 2.6.1 for ruby 3.2 #8342

Bennet-Sunder · 2024-12-19T10:40:34Z

Bennet-Sunder
Dec 19, 2024

For my rails app when I do bundle install after upgrading my ruby version to 3.2.2 from 2.7.8 and also upgrading the bundler from 1.17.3 to 2.2.34 it fails with the below message

--- ERROR REPORT TEMPLATE -------------------------------------------------------

Errno::EPERM: Operation not permitted - /Applications/Cortex XDR.app/Contents/Library
  <internal:dir>:220:in `glob'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/rubygems_ext.rb:222:in `glob_files_in_dir'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/source/path.rb:176:in `load_spec_files'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/source/git.rb:211:in `load_spec_files'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/source/path.rb:107:in `local_specs'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/source/git.rb:178:in `specs'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/source.rb:59:in `spec_names'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/source_map.rb:20:in `block in all_requirements'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/source_map.rb:19:in `map'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/source_map.rb:19:in `all_requirements'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/definition.rb:779:in `source_requirements'
  /Users/bsunder/project_name/.bundle/plugin/gems/bootboot-0.2.2/lib/bootboot/bundler_patch.rb:35:in `source_requirements'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/definition.rb:264:in `resolve'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/definition.rb:175:in `resolve_remotely!'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/installer.rb:283:in `resolve_if_needed'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/installer.rb:82:in `block in run'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/process_lock.rb:12:in `block in lock'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/process_lock.rb:9:in `open'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/process_lock.rb:9:in `lock'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/installer.rb:71:in `run'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/installer.rb:23:in `install'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/cli/install.rb:60:in `run'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/cli.rb:253:in `block in install'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/settings.rb:131:in `temporary'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/cli.rb:252:in `install'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/vendor/thor/lib/thor/command.rb:27:in `run'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/vendor/thor/lib/thor/invocation.rb:127:in `invoke_command'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/vendor/thor/lib/thor.rb:392:in `dispatch'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/cli.rb:31:in `dispatch'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/vendor/thor/lib/thor/base.rb:485:in `start'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/cli.rb:25:in `start'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/exe/bundle:49:in `block in <top (required)>'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/lib/bundler/friendly_errors.rb:103:in `with_friendly_errors'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/gems/bundler-2.2.34/exe/bundle:37:in `<top (required)>'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/bin/bundle:25:in `load'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/bin/bundle:25:in `<main>'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/bin/ruby_executable_hooks:22:in `eval'
  /Users/bsunder/.rvm/gems/ruby-3.2.2@project_name/bin/ruby_executable_hooks:22:in `<main>'

Environment

Bundler       2.2.34
  Platforms   ruby, x86_64-darwin-23
Ruby          3.2.2p53 (2023-03-30 revision e51014f9c05aa65cbf203442d37fef7c12390015) [x86_64-darwin23]
  Full Path   /Users/bsunder/.rvm/rubies/ruby-3.2.2/bin/ruby
  Config Dir  /Users/bsunder/.rvm/rubies/ruby-3.2.2/etc
RubyGems      3.6.1
  Gem Home    /Users/bsunder/.gem/ruby/3.2.0
  Gem Path    /Users/bsunder/.gem/ruby/3.2.0
  User Home   /Users/bsunder
  User Path   /Users/bsunder/.gem/ruby/3.2.0
  Bin Dir     /Users/bsunder/.gem/ruby/3.2.0/bin
OpenSSL       
  Compiled    OpenSSL 1.1.1w  11 Sep 2023
  Loaded      OpenSSL 1.1.1w  11 Sep 2023
  Cert File   /usr/local/etc/openssl@1.1/cert.pem
  Cert Dir    /usr/local/etc/openssl@1.1/certs
Tools         
  Git         2.39.3 (Apple Git-146)
  RVM         1.29.12 (latest)
  rbenv       rbenv 1.3.0
  chruby      not installed

Bundler Build Metadata

Built At          2023-02-06
Git SHA           78d3be232c
Released Version  true

Bundler settings

bootboot_env_prefix
  Set for your local app (/Users/bsunder/project_name/.bundle/config): "FS"
build.iconv
  Set for the current user (/Users/bsunder/.bundle/config): "--with-cppflags=-Wno-compound-token-split-by-macro -Wno-error=incompatible-function-pointer-types"
build.mysql2
  Set for the current user (/Users/bsunder/.bundle/config): "--with-cppflags=-Wno-compound-token-split-by-macro -Wno-error=incompatible-function-pointer-types"
build.pg
  Set for the current user (/Users/bsunder/.bundle/config): "--with-cppflags=-Wno-compound-token-split-by-macro -Wno-error=incompatible-function-pointer-types"
build.rbtrace
  Set for the current user (/Users/bsunder/.bundle/config): "--with-cppflags=-Wno-compound-token-split-by-macro -Wno-error=incompatible-function-pointer-types"
build.rugged
  Set for the current user (/Users/bsunder/.bundle/config): "--with-cppflags=-Wno-compound-token-split-by-macro -Wno-error=incompatible-function-pointer-types"
disable_shared_gems
  Set for your local app (/Users/bsunder/project_name/.bundle/config): true
gems.contribsys.com
  Set for the current user (/Users/bsunder/.bundle/config): "048e7e73:[REDACTED]"
path
  Set for your local app (/Users/bsunder/project_name/.bundle/config): "/Users/bsunder/.gem"
set
  Set for the current user (/Users/bsunder/.bundle/config): "--global default_bundler_version 2.5.18"

The issue seems to be only with respect to bundler 2.x versions, when I use the existing bundler 1.17.3 and ruby 3.1.0 I'm able to get this to works

I get a similar error when using the latest bundler 2.6.1 as well.

There was an error creating /Users/bsunder/.gem/ruby/3.2.0/bundler.lock.
The underlying system error is Errno::EPERM: Operation not permitted - /Applications/Cortex XDR.app/Contents/Library

deivid-rodriguez · 2024-12-19T11:48:39Z

deivid-rodriguez
Dec 19, 2024

Could you post the full error when using Bundler 2.6.1?

0 replies

Bennet-Sunder · 2024-12-19T16:57:02Z

Bennet-Sunder
Dec 19, 2024
Author

This is the error I get when I do

$ FS_NEXT=true bundle _2.6.1_ install --verbose
Bundler::GenericSystemCallError: There was an error creating `/Users/bsunder/.gem/ruby/3.3.0/bundler.lock`.
The underlying system error is Errno::EPERM: Operation not permitted - /Applications/Cortex XDR.app/Contents/Library
/Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/shared_helpers.rb:121:in `rescue in filesystem_access'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/shared_helpers.rb:104:in `filesystem_access'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/process_lock.rb:12:in `lock'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/installer.rb:71:in `run'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/installer.rb:23:in `install'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/cli/install.rb:72:in `run'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/cli.rb:247:in `block in install'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/settings.rb:159:in `temporary'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/cli.rb:246:in `install'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/vendor/thor/lib/thor/command.rb:28:in `run'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/vendor/thor/lib/thor/invocation.rb:127:in `invoke_command'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/vendor/thor/lib/thor.rb:538:in `dispatch'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/cli.rb:35:in `dispatch'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/vendor/thor/lib/thor/base.rb:584:in `start'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/cli.rb:29:in `start'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/exe/bundle:28:in `block in <top (required)>'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/lib/bundler/friendly_errors.rb:117:in `with_friendly_errors'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/gems/bundler-2.6.1/exe/bundle:20:in `<top (required)>'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/bin/bundle:25:in `load'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/bin/bundle:25:in `<main>'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/bin/ruby_executable_hooks:22:in `eval'
  /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/bin/ruby_executable_hooks:22:in `<main>'

And also below code returns

FS_NEXT=true bundle _2.6.1_ env

Bundler             2.6.1
  Platforms         ruby, x86_64-darwin-23
Ruby                3.3.5p100 (2024-09-03 revision ef084cc8f4958c1b6e4ead99136631bef6d8ddba) [x86_64-darwin-23]
  Full Path         /Users/bsunder/.rvm/rubies/ruby-3.3.5/bin/ruby
  Config Dir        /Users/bsunder/.rvm/rubies/ruby-3.3.5/etc
RubyGems            3.5.16
  Gem Home          /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name
  Gem Path          /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name:/Users/bsunder/.rvm/rubies/ruby-3.3.5/lib/ruby/gems/3.3.0
  User Home         /Users/bsunder
  User Path         /Users/bsunder/.gem/ruby/3.3.0
  Bin Dir           /Users/bsunder/.rvm/gems/ruby-3.3.5@project_name/bin
Tools               
  Git               2.39.3 (Apple Git-146)
  RVM               1.29.12 (latest)
  rbenv             rbenv 1.3.0
  chruby            not installed
  rubygems-bundler  (1.4.5)

Bundler Build Metadata

Built At          2024-12-17
Git SHA           00a344e02c8
Released Version  true

Bundler settings

bootboot_env_prefix
  Set for your local app (/Users/bsunder/project_name/.bundle/config): "FS"
build.iconv
  Set for the current user (/Users/bsunder/.bundle/config): "--with-cppflags=-Wno-compound-token-split-by-macro -Wno-error=incompatible-function-pointer-types"
build.mysql2
  Set for the current user (/Users/bsunder/.bundle/config): "--with-cppflags=-Wno-compound-token-split-by-macro -Wno-error=incompatible-function-pointer-types"
build.pg
  Set for the current user (/Users/bsunder/.bundle/config): "--with-cppflags=-Wno-compound-token-split-by-macro -Wno-error=incompatible-function-pointer-types"
build.rbtrace
  Set for the current user (/Users/bsunder/.bundle/config): "--with-cppflags=-Wno-compound-token-split-by-macro -Wno-error=incompatible-function-pointer-types"
build.rugged
  Set for the current user (/Users/bsunder/.bundle/config): "--with-cppflags=-Wno-compound-token-split-by-macro -Wno-error=incompatible-function-pointer-types"
clean
  Set for your local app (/Users/bsunder/project_name/.bundle/config): true
disable_shared_gems
  Set for your local app (/Users/bsunder/project_name/.bundle/config): true
path
  Set for your local app (/Users/bsunder/project_name/.bundle/config): "/Users/bsunder/.gem"
set
  Set for the current user (/Users/bsunder/.bundle/config): "--global default_bundler_version 2.5.18"

RUBY VERSION
ruby 2.6.9p207

BUNDLED WITH
1.17.3

0 replies

deivid-rodriguez · 2024-12-19T17:02:14Z

deivid-rodriguez
Dec 19, 2024

What are the permissions of /Users/bsunder/.gem/ruby/3.3.0/? Does touch /Users/bsunder/.gem/ruby/3.3.0/bundler.lock succeed?

0 replies

Bennet-Sunder · 2024-12-19T17:11:21Z

Bennet-Sunder
Dec 19, 2024
Author

ls -ld /Users/bsunder/.gem/ruby/3.3.0

returns

drwxr-xr-x@ 12 bsunder  staff  384 Dec 19 22:39 /Users/bsunder/.gem/ruby/3.3.0

And

touch /Users/bsunder/.gem/ruby/3.3.0/bundler.lock

does succeed.

0 replies

deivid-rodriguez · 2024-12-19T17:19:58Z

deivid-rodriguez
Dec 19, 2024

Can you also upgrade RubyGems with gem update --system and try again?

0 replies

Bennet-Sunder · 2024-12-19T19:20:10Z

Bennet-Sunder
Dec 19, 2024
Author

It didn't work even with the latest rubygems i.e 3.6.1.
However I seem to have narrowed down the issue, it looks like load_spec_files from Bundler::Source calls

Gem::Util.glob_files_in_dir('/**/*.gemspec', 'gem_directory')

which for some reason seems to set off the palo alto network traps.

Errno::EPERM (Operation not permitted - /Library/Application Support/PaloAltoNetworks/Traps/edr)

I'll have this checked internally and get back incase bundle still can't install after fixing this as well.

Thanks

0 replies

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Unable to do bundle install with bundler 2.6.1 for ruby 3.2 #8342

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Environment

Bundler Build Metadata

Bundler settings

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