ADDITIONAL SYSTEM INFORMATION :
Observable both with Java 8 and 11 EA:

$ java -version
java version "1.8.0_40"
Java(TM) SE Runtime Environment (build 1.8.0_40-b25)
Java HotSpot(TM) 64-Bit Server VM (build 25.40-b25, mixed mode)

$ java -version
java version "11-ea" 2018-09-25
Java(TM) SE Runtime Environment 18.9 (build 11-ea+15)
Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11-ea+15, mixed mode)

A DESCRIPTION OF THE PROBLEM :
java.util.Formatter (and hence String.format) accepts a 'width' field for the `%` modifier, together with an optional `-` flag for left alignment, but ignores both.

For example, the format `"~~%5%~~"` should render as `"~~ %~~"` but renders as just `"~~%~~"` without the spaces.

The Javadoc specifically requests the spaces at https://docs.oracle.com/javase/10/docs/api/java/util/Formatter.html#dper

Either the implementation or the Javadoc is erroneous. Arguably, a third reasonable specification *and* implementation would be to throw a `java.util.IllegalFormatWidthException` exception instead, as is the case for the `%5n` modifier.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Compile and run the `Test.java` file provided below.

$ javac Test.java
$ java Test


EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
~~ %~~
~~% ~~
~~ %~~
~~% ~~

(with the appropriate spaces)
ACTUAL -
~~%~~
~~%~~
~~%~~
~~%~~

(without the appropriate spaces)

---------- BEGIN SOURCE ----------
// Test.java
import java.util.Formatter;

public class Test {
    public static void main(String[] args) {
        // Expected: "~~ %~~", actual: "~~%~~"
        System.out.println(String.format("~~%5%~~", 5));

        // Expected: "~~% ~~", actual: "~~%~~"
        System.out.println(String.format("~~%-5%~~", 5));

        // Expected: "~~ %~~", actual: "~~%~~"
        System.out.println(new Formatter().format("~~%5%~~", 5).toString());

        // Expected: "~~% ~~", actual: "~~%~~"
        System.out.println(new Formatter().format("~~%-5%~~", 5).toString());
    }
}

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Write out the spaces in the format string instead:

String.format("~~ %%~~")
String.format("~~%% ~~")

FREQUENCY : always