ALl code in R is licensed under GPL-2
Java package xcms.jar is licensed under GPL-2 as stated in the source code
/**************************************************************************
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
***************************************************************************/


JARP library is licensed under LGPL as stated in the source code
http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/jrap/stax/software/
/****************************************************************************
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
  *   it under the terms of the GNU Lesser General Public License as        *
  *   published by the Free Software Foundation; either version 2 of the    *
  *   License, or (at your option) any later version.                       *
  *                                                                         *
  ***************************************************************************/