На этот вопрос уже есть ответ здесь :
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package ninja is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
deepak@ubuntu:~$ sudo apt-get install cscope
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package cscope is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
Это должно зафиксировать его:
sudo apt-get clean
sudo mv /var/lib/apt/lists /tmp
sudo apt-get clean
sudo apt-get update
Затем попробовали еще раз.