FULL PRODUCT VERSION :
java version "1.7.0_85"
Java(TM) SE Runtime Environment (build 1.7.0_85-b15)


ADDITIONAL OS VERSION INFORMATION :
Linux 2.6.39-400.211.1.el6uek.x86_64 #1 SMP Fri Nov 15 
13:39:16 PST 2013 x86_64 x86_64 x86_64 GNU/Linux


A DESCRIPTION OF THE PROBLEM :
Java 8 seems to have it fixed.

The problem occurs in Java 7



STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
                         Java 8 produces

OK I found           F()  with the argument 'one'
OK I found   as.factor()  with the argument 'two'
OK I found      factor()  with the argument 'three'
OK I found           F()  with the argument 'four'

                         Java 7 produces
OK I found           F()  with the argument 'one'
OK I found   as.factor()  with the argument 'two'
OK I found      factor()  with the argument 'three'



import java.util.regex.Matcher;
import java.util.regex.Pattern;

import static java.lang.System.out;

/**
 * @author Dmitry Golovashkin. Created on 10/28/16.
 */
public class Main {

  private static void asFactor(final String formula) {
    final String functionName = "\\b((as\\.)?factor|F)\\b"; // factor(ID), as.factor(ID), or F(ID).
    final String space = "\\s*";
    final String leftParenthesis = "\\(";
    final String id = "([^)]*)"; // May include leading/trailing space.
    final String rightParenthesis = "\\)";
    final String asFactorRegex = functionName + space + leftParenthesis + id + rightParenthesis;

    final Pattern asFactorPattern = Pattern.compile(asFactorRegex);
    final Matcher matcher = asFactorPattern.matcher(formula);
    final StringBuffer sb = new StringBuffer();

    while (matcher.find()) {
      final String factorName = matcher.group(3).trim();
      out.printf("OK I found  %10s()  with the argument \'%s\'%n", matcher.group(1), matcher.group(3));
    }
  }

  public static void main(String[] args) {
    final String formula = "y ~ F(one) + as.factor(two) + factor(three) + F(four)";
    out.println("input formula " + formula);
    out.println();

    asFactor(formula);
  }
}


EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
I was expecting to see

                         Java 8 produces (correct)

OK I found           F()  with the argument 'one'
OK I found   as.factor()  with the argument 'two'
OK I found      factor()  with the argument 'three'
OK I found           F()  with the argument 'four'


However Java 7 matches just three.

ACTUAL -
                         Java 7 produces
OK I found           F()  with the argument 'one'
OK I found   as.factor()  with the argument 'two'
OK I found      factor()  with the argument 'three'

and this is incorrect.
Java 8 produces the correct result.

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import static java.lang.System.out;

/**
 * @author Dmitry Golovashkin. Created on 10/28/16.
 *        dmitry.golovashkin@oracle.com
 */
public class Main {

  private static void asFactor(final String formula) {
    final String functionName = "\\b((as\\.)?factor|F)\\b"; // factor(ID), as.factor(ID), or F(ID).
    final String space = "\\s*";
    final String leftParenthesis = "\\(";
    final String id = "([^)]*)"; // May include leading/trailing space.
    final String rightParenthesis = "\\)";
    final String asFactorRegex = functionName + space + leftParenthesis + id + rightParenthesis;

    final Pattern asFactorPattern = Pattern.compile(asFactorRegex);
    final Matcher matcher = asFactorPattern.matcher(formula);
    final StringBuffer sb = new StringBuffer();

    while (matcher.find()) {
      final String factorName = matcher.group(3).trim();
      out.printf("OK I found  %10s()  with the argument \'%s\'%n", matcher.group(1), matcher.group(3));
    }
  }

  public static void main(String[] args) {
    final String formula = "y ~ F(one) + as.factor(two) + factor(three) + F(four)";
    out.println("input formula " + formula);
    out.println();

    asFactor(formula);
  }
}

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