While deploying an Ruby update to an old application these days, we encountered the following misleading error:

*** [err :: some-host.makandra.de] You are trying to install in deployment mode after changing
*** [err :: some-host.makandra.de] your Gemfile. Run `bundle install` elsewhere and add the
*** [err :: some-host.makandra.de] updated Gemfile.lock to version control.
*** [err :: some-host.makandra.de] 
*** [err :: some-host.makandra.de] You have deleted from the Gemfile:
*** [err :: some-host.makandra.de] *

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We found out a newer version of bundler runs on the machines to be deployed to (see bundle -v, it was 2.0.1 in our case) while in the Gemfile.lock an old version of bundler is mentioned in the BUNDLED_WITH block:

BUNDLED WITH
   1.17.1

This broke during deployment while Capistrano tries to run bundle --deployment --quiet --without development test. On our development machines bundle install run successfully.

Fix this by making sure both sides use the same major versions of bundler (preferably 2.x).