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the workspace directory is clean and does not contain any hidden files hence .catkin_tools is not present.

No, but:

Workspace:                   /home/usr/Desktop

it's likely there is a .catkin_tools directory in /home/usr/Desktop.

What is the output of ls -al $HOME/Desktop/.catkin_tools?

The rest of the warnings/errors you are getting follow from this. If $HOME/Desktop is the workspace according to catkin_tools, there is no src space (as that would be in $HOME/Desktop/workspace/src).

the workspace directory is clean and does not contain any hidden files hence .catkin_tools is not present.

No, but:

Workspace:                   /home/usr/Desktop

it's likely there is a .catkin_tools directory in /home/usr/Desktop.

What is the output of ls -al $HOME/Desktop/.catkin_tools?

The rest of the warnings/errors you are getting follow from this. If $HOME/Desktop is the workspace according to catkin_tools, there is no src space (as that would be in $HOME/Desktop/workspace/src).


Edit:

I didn't knew i had it on my desktop, but why should that matter? I can have multiple workspaces, what if desktop is a workspace, I cannot have any other workspace inside it?

Multiple workspaces is completely supported. But you just can't nest workspaces (ie: workspaces inside other workspaces).

If you want to have multiple workspaces, make them siblings or place them in entirely different directories.

the workspace directory is clean and does not contain any hidden files hence .catkin_tools is not present.

No, but:

Workspace:                   /home/usr/Desktop

it's likely there is a .catkin_tools directory in /home/usr/Desktop.

What is the output of ls -al $HOME/Desktop/.catkin_tools?

The rest of the warnings/errors you are getting follow from this. If $HOME/Desktop is the workspace according to catkin_tools, there is no src space (as that would be in $HOME/Desktop/workspace/src).


Edit:

I didn't knew i had it on my desktop, but why should that matter? I can have multiple workspaces, what if desktop is a workspace, I cannot have any other workspace inside it?

Multiple Having multiple workspaces is completely supported. But you just can't nest workspaces (ie: workspaces inside other workspaces).

If you want to have multiple workspaces, make them siblings or place them in entirely different directories.

the workspace directory is clean and does not contain any hidden files hence .catkin_tools is not present.

No, but:

Workspace:                   /home/usr/Desktop

it's likely there is a .catkin_tools directory in /home/usr/Desktop.

What is the output of ls -al $HOME/Desktop/.catkin_tools?

The rest of the warnings/errors you are getting follow from this. If $HOME/Desktop is the workspace according to catkin_tools, there is no src space (as that would be in $HOME/Desktop/workspace/src).


Edit:

I didn't knew i had it on my desktop, but why should that matter? I can have multiple workspaces, what if desktop is a workspace, I cannot have any other workspace inside it?

Having multiple workspaces is completely supported. But you just can't nest workspaces (ie: workspaces inside other workspaces).

If you want to have multiple workspaces, make them siblings or place them in entirely different directories.

It might also be informative to take a look at wiki/catkin/workspaces. Specifically: workspace overlaying.