Solve consistency between apt-get and dpkg tree

gistfile1.md

Cause

I face this problem because I accidentally try to install MongoDB 3.0.x (from http://repo.mongodb.org/apt/ubuntu) while actually a MongoDB 2.6.8 (provided by ubuntu) is already installed in the same computer. Therefore, both mongod and mongo commands are still point to the old version (which doesn't work actually). Since the official installation document said that "You cannot install this package concurrently with the mongodb, mongodb-server, or mongodb-clients packages provided by Ubuntu", this just cannot work.

A better way is to first completely uninstalled the older version before install the new one, but I already missed that time. So

sudo apt-get purge mongodb mongodb-clients mongodb-server mongodb-dev
sudo apt-get purge mongodb-10gen

cannot remove it completely (not sure whether that's the exact case), and \usr\bin\mongo and \usr\bin\mongod are still point to the old mongodb (which has already been removed). Therefore, I have to manually

sudo rm /usr/bin/mongo
sudo rm /usr/bin/mongod
sudo rm /var/lib/mongodb # for the old data?

After that, there's a dpkg deadlock which shows something goes wrong, and (not sure whether I am doing right) I also removed it.

To make /usr/bin/mongo etc point to the new mongodb, I sudo apt-get remove mongodb-org but it only remove ~40kb things. After I reinstall it, it doesn't overwrite /usr/bin/mongo etc. I am not sure whether that's because I used to do

beta@landlubber:~$ echo "mongodb-org hold" | sudo dpkg --set-selections
beta@landlubber:~$ echo "mongodb-org-server hold" | sudo dpkg --set-selections
beta@landlubber:~$ echo "mongodb-org-shell hold" | sudo dpkg --set-selections
beta@landlubber:~$ echo "mongodb-org-mongos hold" | sudo dpkg --set-selections
beta@landlubber:~$ echo "mongodb-org-tools hold" | sudo dpkg --set-selections 

in the installation process.

Found the problem

To call sudo dkpg --get-selections, there are lines

mongodb-org					hold
mongodb-org-mongos				hold
mongodb-org-server				hold
mongodb-org-shell				hold
mongodb-org-tools				hold

Their values can be changed by to install or deinstall by echo "mongodb-org-tools hold" | sudo dpkg --set-selections etc, but the lines are always in there. After apt-get remove, although apt-get said the package has been removed, dpkg -s mongodb-org can still give a bunch of information (which shows dpkg still treat the packages to be installed). Therefore, here's an inconsistency between apt-get and dpkg.

Solution

Manually and mandatory delete the dpkg setup using

sudo dpkg --purge mongodb-org
sudo dpkg --purge mongodb-org-mongos
sudo dpkg --purge mongodb-org-server
sudo dpkg --purge mongodb-org-shell
sudo dpkg --purge mongodb-org-tools

After that, dpkg -s mongodb-org shows that the package is not installed, and echo "mongodb-org-tools hold" | sudo dpkg --set-selections nolonger has anything about these items. And if we sudo apt-get install -y mongodb-org, some 50mb will be installed, and /usr/bin/mongo and /usr/bin/mongod will be back.

In this case, if running mongo, the system may complain something like

2015-04-23T14:54:45.367+0800 I STORAGE  In File::open(), ::open for '/home/beta/.mongorc.js' failed with errno:13 Permission denied
The ".mongorc.js" file located in your home folder could not be executed

that is because the .mongorc.js is still the one from the old mongodb. Just remove that file and run again.