To fix it simply run the following commands

sudo update-alternatives --install /usr/bin/java java /usr/lib/jvm/jdk-11.0.1/bin/java 3
sudo update-alternatives --config java

The first correct the errors you made where you had /usr/lib/jvm it should have been /usr/bin/java. The second command gives you the opportunity to pick the default version you want.

It turns out the fix is to run the following commands:

sudo rm /usr/bin/jar
sudo rm /var/lib/alternatives/jar
sudo alternatives --install /usr/bin/jar jar /usr/java/latest/bin/jar 20000

you can confirm that the steps above worked with:

which jar

I'd say that those steps are pretty generic and could be used for other alternative applications too.

See http://johnglotzer.blogspot.com/2012/09/alternatives-install-gets-stuck-failed.html for more information.

To restore your /usr/bin/java link, you should run

sudo update-java-alternatives -a

If you were using Debian 9 (as mentioned initially), you shouldn’t have run into these issues, since OpenJDK 8 is the default there and OpenJDK 7 isn’t even available. To fix things so that you can run version 52 classes (i.e. Java 8 classes), install OpenJDK 8:

sudo apt install openjdk-8-jre

On Debian 8 you can install OpenJDK 8 from backports:

echo deb http://archive.debian.org/debian jessie-backports main | sudo tee /etc/apt/sources.list.d/jessie-backports.list
echo 'Acquire::Check-Valid-Until "false";' | sudo tee -a /etc/apt/apt.conf
sudo apt update
sudo apt -t jessie-backports install openjdk-8-jre

(See Failed to fetch jessie backports repository for details.)

You’ll then need to specifically choose OpenJDK 8 as the default:

sudo update-java-alternatives -s java-1.8.0-openjdk-amd64

(To see the possible values, run /usr/sbin/update-java-alternatives -l.)

The javac binary (and probably other java binaries) is/are not in your user's $PATH environment variable. There are several ways you can address this:

1. Add /usr/lib/jvm/java-6-open-jdk/bin to your user's $PATH environment variable. You can do this by adding a line similar to the following in your user's .bash_profile:

   export PATH=${PATH}:/usr/lib/jvm/java-6-open-jdk/bin

   You'll have to restart your terminal session for it to take effect.

2. Create symbolic links to the java binaries from some directory that's already part of your path (such as /usr/bin)

   sudo ln -s /usr/lib/jvm/java-6-open-jdk/bin/java /usr/bin/
sudo ln -s /usr/lib/jvm/java-6-open-jdk/bin/javac /usr/bin/

   BTW: There are several other java executables in /usr/lib/jvm/java-6-open-jdk/bin. I've shown the symlink commands for java and javac above. You should run similar command for any other executables you may want to use.

3. Use the fully qualified path directly on the command line:

   $ /usr/lib/jvm/java-6-open-jdk/bin/javac

Update:

Apparently, there is an elegant, but Ubuntu-specific solution to this problem. When on an Ubuntu system, use update-java-alternatives.

This is because there are some 32-bit libraries missing in your Ubuntu 64-bit. Run:

apt-get install libc6-i386

you can refer to this Stack Overflow post for more information

you have installed the wrong architecture of java (32bit on top of a 64bit system or viceversa)

This is a $PATH issue. $PATH is an environment variable that contains a list of directories to search when looking for an executable. You can see your current $PATH via echo $PATH.

javac: command not found indicates javac is not in any of the directories in your $PATH. You need to add the directory with javac in it into your $PATH, or add javac to one of the directories in your $PATH -- but the former is much preferable.

To temporarily add a directory for your current shell:

export PATH=/some/directory:$PATH

If you want to use that permanently, add the same line to ~/.bashrc. For example, I use JDK 8 on the pi that I have installed to /usr/local, so I have a line:

export PATH=/usr/local/jdk1.8.0/bin:$PATH

That directory contains java, javac, jar, etc.

You mentioned that java appears in be in your path since "java -version comes up with the java number and package so java is definitely installed" although you do not actually say what that number and package are. I suspect you have multiple versions installed, one of which is just a jre and thus does not include javac.