...in various charts like line, pie and column charts. What a message to show? In what place?
I would put the message in the location that the user would expect to see the chart or if there is a standard error message area already in place in your application (e.g. the Firefox application has a standard error bar) then I'd use that. As far as what to say, be sure to tell the user how to get what they want (i.e. how to fix the problem) or if the data is not available and they should return later tell them to do so, and tell them why so they don't just think it's a bug.
Some examples of messages you might use:
You must select a numeric value to use as a measurement and one field to categorize the numeric measurement.
There is no data available for the time period you have chosen. Please choose a different time period.
If you don't have enough data to render the chart, then tell the user directly rather than go through the processing. Mostly, what happens is that I would select a bunch of parameters for which I need charts for, then after submitting the form and processing the whole page, the page returns an error saying there is not enough data.
Rather than this, let the user select parameters and upon form submission, check if the chart is 'renderable'. If it is, then show a loader and load the chart in a visually separate area. If you cannot, show the error message near the field selection.
If possible, give some indication. Like,
Data not available for the last 24 hours
There should be 3-6 words long error heading which in itself should be enough for the reader to understand what has gone wrong. BUT, this few words long heading might not convey different solutions which user would be equally want to know during early usage. That means error message may look somewhat like
Insufficient data to make a chart
Please select 2 or more cells with numeric value to make a pie chart.
Next time the user makes the same error, he would only want to look at the heading and understand what has gone wrong.