Gitlab broke after system update

After we ran apt-get update && apt-get upgrade the other day, gitlab stopped working.

We cannot run backup or anything, and updates fail.

Trying to reinstall gems we get:

Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

/usr/local/bin/ruby extconf.rb

checking for gmake… no
checking for make… yes
checking for cmake… yes
checking for pkg-config… yes
-DCMAKE_BUILD_TYPE=RelWithDebInfo -G “Unix Makefiles”
– /usr/bin/make
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers. Check the mkmf.log file for more details. You may
need configuration options.

Provided configuration options:
–without-opt-include={opt-dir}/include --with-opt-lib --without-opt-lib={opt-dir}/lib
extconf.rb:13:in sys': ERROR: '/usr/bin/make' failed (RuntimeError) from extconf.rb:71:in block (2 levels) in ’
from extconf.rb:69:in chdir' from extconf.rb:69:in block in ’
from extconf.rb:66:in chdir' from extconf.rb:66:in

extconf failed, exit code 1

Gem files will remain installed in /home/git/gitlab/vendor/bundle/ruby/2.1.0/gems/rugged-0.24.0 for inspection.
Results logged to

An error occurred while installing rugged (0.24.0), and Bundler cannot continue.
Make sure that gem install rugged -v '0.24.0' succeeds before bundling.

In Gemfile:
gemnasium-gitlab-service was resolved to 0.2.6, which depends on

Trying to make a backup, we get:

Could not find activesupport- in any of the sources
Run bundle install to install missing gems.

We have not touched gitlab so are completely unsure what has happened, and the logs show us nothing.

Which version of GitLab were you running? Which OS and version are you using?

Gitlab version 8.13.5

Ubuntu 16.04.3 LTS.

The system had Ruby 2.1.8, it’s now on 2.3.1.

Not sure but did you try the steps in the following stackoverflow thread?