Bundler "Your Gemfile.lock is corrupt" in CI

Bundler validates the structure of Gemfile.lock before installing. When a gem appears in one section but not the matching one - usually after a bad merge or a hand-edit - Bundler calls the lockfile corrupt and refuses to install from it.

What this error means

bundle install fails with "Your Gemfile.lock is corrupt. The following gem is missing from the DEPENDENCIES section: '<gem>'." Often the lockfile contains leftover merge-conflict markers.

bundler

Your Gemfile.lock is corrupt. The following gem is missing from the
DEPENDENCIES section: 'nokogiri'

Common causes

A merge conflict was resolved incorrectly

Two branches changed Gemfile.lock and the resolution left the GEM, DEPENDENCIES, and BUNDLED WITH sections out of sync.

The lockfile was hand-edited

A manual edit removed or duplicated a gem entry, breaking the invariant Bundler expects between sections.

How to fix it

Regenerate the lockfile cleanly

Let Bundler rewrite a consistent lockfile from the Gemfile rather than patching it by hand.

Terminal

# discard the broken lock and re-resolve
rm Gemfile.lock
bundle install
git add Gemfile.lock

Check for leftover conflict markers

Open Gemfile.lock and search for <<<<<<<, =======, >>>>>>>.
Resolve the conflict in the Gemfile, then regenerate the lock with bundle install.
Commit the regenerated lockfile, not a hand-merged one.

How to prevent it

Resolve Gemfile.lock conflicts by re-running bundle install, never by hand-merging sections.
Avoid editing Gemfile.lock manually; change the Gemfile and let Bundler regenerate.
Add a CI check that bundle install --frozen produces no diff.