Fixed bug in mem allocation and cleaned up config files

configure.ac

@@ -107,16 +107,6 @@ AS_IF([test "x$enable_win" = "xyes"],[CC="i686-w64-mingw32-gcc"])
 AS_IF([test "x$enable_win" = "xyes"],AC_DEFINE([WIN32],[1],[WIN32 tag on]))
 AM_CONDITIONAL([WANT_WIN], [test "$enable_win" = yes])
 
-
-dnl AC_ARG_ENABLE([beagle], [AS_HELP_STRING([--enable-beagle], [Compute likelihoods using BEAGLE library.])], [beagle=yes],[beagle=no])
-dnl AS_IF([test "x$enable_beagle" = "xyes"],[PKG_CHECK_MODULES([BEAGLE],[hmsbeagle-1])])
-dnl AS_IF([test "x$enable_beagle" = "xyes"],
-dnl       [CFLAGS="${CFLAGS} ${BEAGLE_CFLAGS} ${BEAGLE_LIBS} -lstdc++"],
-dnl       [CFLAGS=${CFLAGS}])
-AS_IF([test "x$enable_beagle" = "xyes"], AC_DEFINE([BEAGLE],[1],[BEAGLE tag on]))
-AM_CONDITIONAL([WANT_BEAGLE], [test "$enable_beagle" = yes])
-
-
 AC_ARG_ENABLE([phytime],[AS_HELP_STRING([--enable-phytime],[Compile PhyTime])],[phytime=yes],[phytime=no])
 AM_CONDITIONAL([WANT_PHYTIME], [test "$phytime" = yes])
 if test "$phytime" = yes; then
@@ -130,30 +120,12 @@ if test "$phyml" = yes; then
 fi
 
 
-AC_ARG_ENABLE([tiporder],[AS_HELP_STRING([--enable-tiporder],[Compile tiporder])],[tiporder=yes],[tiporder=no])
-AM_CONDITIONAL([WANT_TIPORDER], [test "$tiporder" = yes])
-if test "$tiporder" = yes; then
-   AC_DEFINE([TIPORDER],[1],[TIPORDER tag on])
-fi
-
-AC_ARG_ENABLE([part],[AS_HELP_STRING([--enable-part],[Compile Part])],[part=yes],[part=no])
-AM_CONDITIONAL([WANT_PART], [test "$part" = yes])
-if test "$part" = yes; then
-   AC_DEFINE([PART],[1],[PART tag on])
-fi
-
 AC_ARG_ENABLE([rwrap],[AS_HELP_STRING([--enable-rwrap],[Compile Rwrap])],[rwrap=yes],[rwrap=no])
 AM_CONDITIONAL([WANT_RWRAP], [test "$rwrap" = yes])
 if test "$rwrap" = yes; then
    AC_DEFINE([RWRAP],[1],[RWRAP tag on])
 fi
 
-AC_ARG_ENABLE([phycont],[AS_HELP_STRING([--enable-phycont],[Compile PhyCont])],[phycont=yes],[phycont=no])
-AM_CONDITIONAL([WANT_PHYCONT], [test "$phycont" = yes])
-if test "$phycont" = yes; then
-   AC_DEFINE([PHYCONT],[1],[PHYCONT tag on])
-fi
-
 AC_ARG_ENABLE([rf],[AS_HELP_STRING([--enable-rf],[Compile RF])],[rf=yes],[rf=no])
 AM_CONDITIONAL([WANT_RF], [test "$rf" = yes])
 if test "$rf" = yes; then
@@ -172,25 +144,6 @@ if test "$evolve" = yes; then
    AC_DEFINE([EVOLVE],[1],[EVOLVE tag on])
 fi
 
-AC_ARG_ENABLE([invitee],[AS_HELP_STRING([--enable-invitee],[Compile invitee])],[invitee=yes],[invitee=no])
-AM_CONDITIONAL([WANT_INVITEE], [test "$invitee" = yes])
-if test "$invitee" = yes; then
-   AC_DEFINE([INVITEE],[1],[INVITEE tag on])
-fi
-
-AC_ARG_ENABLE([geo],[AS_HELP_STRING([--enable-geo],[Compile geo])],[geo=yes],[geo=no])
-AM_CONDITIONAL([WANT_GEO], [test "$geo" = yes])
-if test "$geo" = yes; then
-   AC_DEFINE([GEO],[1],[GEO tag on])
-fi
-
-AC_ARG_ENABLE([checkpoint],[AS_HELP_STRING([--enable-checkpoint],[Compile checkpoint])],[checkpoint=yes],[checkpoint=no])
-AM_CONDITIONAL([WANT_CHECKPOINT], [test "$checkpoint" = yes])
-if test "$checkpoint" = yes; then
-   AC_DEFINE([CHECKPOINT],[1],[CHECKPOINT tag on])
-fi
-
-
 AC_ARG_ENABLE([phyrex],[AS_HELP_STRING([--enable-phyrex],[Compile phyrex])],[phyrex=yes],[phyrex=no])
 AM_CONDITIONAL([WANT_PHYREX], [test "$phyrex" = yes])
 if test "$phyrex" = yes; then
@@ -217,16 +170,10 @@ if test "$date" = yes; then
 fi
 
 if test "$phytime" = no; then
-if test "$tiporder" = no; then
-if test "$part" = no; then
 if test "$rwrap" = no; then
-if test "$phycont" = no; then
 if test "$test" = no; then
 if test "$rf" = no; then
-if test "$invitee" = no; then
-if test "$geo" = no; then
 if test "$evolve" = no; then
-if test "$checkpoint" = no; then
 if test "$phyrex" = no; then
 if test "$phyrexsim" = no; then
 if test "$date" = no; then
@@ -239,12 +186,6 @@ fi
 fi
 fi
 fi
-fi
-fi
-fi
-fi
-fi
-fi
 
 AC_CONFIG_FILES([Makefile src/Makefile doc/Makefile])
 AC_OUTPUT