Commits

Chris Park  committed c9dd362

Added new tool MIed, similar to MIer however calculates MI between two dataset only using the union of the two gene sets. In contrast, MIer uses the sum of all genes among all datasets given to calculate MI. MIed allows MI to be constant even after adding new dataset into the integration.

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-# Copyright 1996, 1997, 1998, 1999, 2000, 2001, 2002
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+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
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-# Do all the work for Automake.                            -*- Autoconf -*-
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+AC_REQUIRE([AM_SET_LEADING_DOT])dnl
+_AM_IF_OPTION([tar-ustar], [_AM_PROG_TAR([ustar])],
+              [_AM_IF_OPTION([tar-pax], [_AM_PROG_TAR([pax])],
+	      		     [_AM_PROG_TAR([v7])])])
 _AM_IF_OPTION([no-dependencies],,
-[AC_PROVIDE_IFELSE([AC_PROG_][CC],
+[AC_PROVIDE_IFELSE([AC_PROG_CC],
                   [_AM_DEPENDENCIES(CC)],
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-                          defn([AC_PROG_][CC])[_AM_DEPENDENCIES(CC)])])dnl
-AC_PROVIDE_IFELSE([AC_PROG_][CXX],
+                  [define([AC_PROG_CC],
+                          defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl
+AC_PROVIDE_IFELSE([AC_PROG_CXX],
                   [_AM_DEPENDENCIES(CXX)],
-                  [define([AC_PROG_][CXX],
-                          defn([AC_PROG_][CXX])[_AM_DEPENDENCIES(CXX)])])dnl
+                  [define([AC_PROG_CXX],
+                          defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl
 ])
 ])
 
-# Copyright 2002  Free Software Foundation, Inc.
 
-# 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 2, or (at your option)
-# any later version.
+# When config.status generates a header, we must update the stamp-h file.
+# This file resides in the same directory as the config header
+# that is generated.  The stamp files are numbered to have different names.
 
-# 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.
+# Autoconf calls _AC_AM_CONFIG_HEADER_HOOK (when defined) in the
+# loop where config.status creates the headers, so we can generate
+# our stamp files there.
+AC_DEFUN([_AC_AM_CONFIG_HEADER_HOOK],
+[# Compute $1's index in $config_headers.
+_am_stamp_count=1
+for _am_header in $config_headers :; do
+  case $_am_header in
+    $1 | $1:* )
+      break ;;
+    * )
+      _am_stamp_count=`expr $_am_stamp_count + 1` ;;
+  esac
+done
+echo "timestamp for $1" >`AS_DIRNAME([$1])`/stamp-h[]$_am_stamp_count])
 
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+# Copyright (C) 2001, 2003, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
 
-# AM_AUTOMAKE_VERSION(VERSION)
-# ----------------------------
-# Automake X.Y traces this macro to ensure aclocal.m4 has been
-# generated from the m4 files accompanying Automake X.Y.
-AC_DEFUN([AM_AUTOMAKE_VERSION],[am__api_version="1.6"])
+# AM_PROG_INSTALL_SH
+# ------------------
+# Define $install_sh.
+AC_DEFUN([AM_PROG_INSTALL_SH],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+install_sh=${install_sh-"$am_aux_dir/install-sh"}
+AC_SUBST(install_sh)])
 
-# AM_SET_CURRENT_AUTOMAKE_VERSION
-# -------------------------------
-# Call AM_AUTOMAKE_VERSION so it can be traced.
-# This function is AC_REQUIREd by AC_INIT_AUTOMAKE.
-AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-	 [AM_AUTOMAKE_VERSION([1.6.3])])
-
-# Helper functions for option handling.                    -*- Autoconf -*-
-
-# Copyright 2001, 2002  Free Software Foundation, Inc.
-
-# 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 2, 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, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
+# Copyright (C) 2003, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
 
 # serial 2
 
+# Check whether the underlying file-system supports filenames
+# with a leading dot.  For instance MS-DOS doesn't.
+AC_DEFUN([AM_SET_LEADING_DOT],
+[rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+  am__leading_dot=.
+else
+  am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+AC_SUBST([am__leading_dot])])
+
+# Check to see how 'make' treats includes.	            -*- Autoconf -*-
+
+# Copyright (C) 2001, 2002, 2003, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 3
+
+# AM_MAKE_INCLUDE()
+# -----------------
+# Check to see how make treats includes.
+AC_DEFUN([AM_MAKE_INCLUDE],
+[am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+	@echo done
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+AC_MSG_CHECKING([for style of include used by $am_make])
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# We grep out `Entering directory' and `Leaving directory'
+# messages which can occur if `w' ends up in MAKEFLAGS.
+# In particular we don't look at `^make:' because GNU make might
+# be invoked under some other name (usually "gmake"), in which
+# case it prints its new name instead of `make'.
+if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then
+   am__include=include
+   am__quote=
+   _am_result=GNU
+fi
+# Now try BSD make style include.
+if test "$am__include" = "#"; then
+   echo '.include "confinc"' > confmf
+   if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then
+      am__include=.include
+      am__quote="\""
+      _am_result=BSD
+   fi
+fi
+AC_SUBST([am__include])
+AC_SUBST([am__quote])
+AC_MSG_RESULT([$_am_result])
+rm -f confinc confmf
+])
+
+# Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
+
+# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2005
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 4
+
+# AM_MISSING_PROG(NAME, PROGRAM)
+# ------------------------------
+AC_DEFUN([AM_MISSING_PROG],
+[AC_REQUIRE([AM_MISSING_HAS_RUN])
+$1=${$1-"${am_missing_run}$2"}
+AC_SUBST($1)])
+
+
+# AM_MISSING_HAS_RUN
+# ------------------
+# Define MISSING if not defined so far and test if it supports --run.
+# If it does, set am_missing_run to use it, otherwise, to nothing.
+AC_DEFUN([AM_MISSING_HAS_RUN],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing"
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+  am_missing_run="$MISSING --run "
+else
+  am_missing_run=
+  AC_MSG_WARN([`missing' script is too old or missing])
+fi
+])
+
+# Copyright (C) 2003, 2004, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_MKDIR_P
+# ---------------
+# Check whether `mkdir -p' is supported, fallback to mkinstalldirs otherwise.
+#
+# Automake 1.8 used `mkdir -m 0755 -p --' to ensure that directories
+# created by `make install' are always world readable, even if the
+# installer happens to have an overly restrictive umask (e.g. 077).
+# This was a mistake.  There are at least two reasons why we must not
+# use `-m 0755':
+#   - it causes special bits like SGID to be ignored,
+#   - it may be too restrictive (some setups expect 775 directories).
+#
+# Do not use -m 0755 and let people choose whatever they expect by
+# setting umask.
+#
+# We cannot accept any implementation of `mkdir' that recognizes `-p'.
+# Some implementations (such as Solaris 8's) are not thread-safe: if a
+# parallel make tries to run `mkdir -p a/b' and `mkdir -p a/c'
+# concurrently, both version can detect that a/ is missing, but only
+# one can create it and the other will error out.  Consequently we
+# restrict ourselves to GNU make (using the --version option ensures
+# this.)
+AC_DEFUN([AM_PROG_MKDIR_P],
+[if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then
+  # We used to keeping the `.' as first argument, in order to
+  # allow $(mkdir_p) to be used without argument.  As in
+  #   $(mkdir_p) $(somedir)
+  # where $(somedir) is conditionally defined.  However this is wrong
+  # for two reasons:
+  #  1. if the package is installed by a user who cannot write `.'
+  #     make install will fail,
+  #  2. the above comment should most certainly read
+  #     $(mkdir_p) $(DESTDIR)$(somedir)
+  #     so it does not work when $(somedir) is undefined and
+  #     $(DESTDIR) is not.
+  #  To support the latter case, we have to write
+  #     test -z "$(somedir)" || $(mkdir_p) $(DESTDIR)$(somedir),
+  #  so the `.' trick is pointless.
+  mkdir_p='mkdir -p --'
+else
+  # On NextStep and OpenStep, the `mkdir' command does not
+  # recognize any option.  It will interpret all options as
+  # directories to create, and then abort because `.' already
+  # exists.
+  for d in ./-p ./--version;
+  do
+    test -d $d && rmdir $d
+  done
+  # $(mkinstalldirs) is defined by Automake if mkinstalldirs exists.
+  if test -f "$ac_aux_dir/mkinstalldirs"; then
+    mkdir_p='$(mkinstalldirs)'
+  else
+    mkdir_p='$(install_sh) -d'
+  fi
+fi
+AC_SUBST([mkdir_p])])
+
+# Helper functions for option handling.                     -*- Autoconf -*-
+
+# Copyright (C) 2001, 2002, 2003, 2005  Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 3
+
 # _AM_MANGLE_OPTION(NAME)
 # -----------------------
 AC_DEFUN([_AM_MANGLE_OPTION],
 AC_DEFUN([_AM_IF_OPTION],
 [m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
 
+# Check to make sure that the build environment is sane.    -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005
+# Free Software Foundation, Inc.
 #
-# Check to make sure that the build environment is sane.
-#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
 
-# Copyright 1996, 1997, 2000, 2001 Free Software Foundation, Inc.
-
-# 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 2, 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, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
-
-# serial 3
+# serial 4
 
 # AM_SANITY_CHECK
 # ---------------
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-#  -*- Autoconf -*-
-
-
-# Copyright 1997, 1999, 2000, 2001 Free Software Foundation, Inc.
-
-# 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 2, 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, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
-
-# serial 3
-
-# AM_MISSING_PROG(NAME, PROGRAM)
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-AC_DEFUN([AM_MISSING_PROG],
-[AC_REQUIRE([AM_MISSING_HAS_RUN])
-$1=${$1-"${am_missing_run}$2"}
-AC_SUBST($1)])
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-# AM_MISSING_HAS_RUN
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-# If it does, set am_missing_run to use it, otherwise, to nothing.
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-# Use eval to expand $SHELL
-if eval "$MISSING --run true"; then
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-  am_missing_run=
-  AC_MSG_WARN([`missing' script is too old or missing])
-fi
-])
-
-# AM_AUX_DIR_EXPAND
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-# Copyright 2001 Free Software Foundation, Inc.
-
-# This program is free software; you can redistribute it and/or modify
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-# 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, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
-
-# For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets
-# $ac_aux_dir to `$srcdir/foo'.  In other projects, it is set to
-# `$srcdir', `$srcdir/..', or `$srcdir/../..'.
+# Copyright (C) 2001, 2003, 2005  Free Software Foundation, Inc.
 #
-# Of course, Automake must honor this variable whenever it calls a
-# tool from the auxiliary directory.  The problem is that $srcdir (and
-# therefore $ac_aux_dir as well) can be either absolute or relative,
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-# it makes $ac_aux_dir quite unusable in subdirectories: in the top
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-AC_PREREQ([2.50])
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-AC_DEFUN([AM_AUX_DIR_EXPAND], [
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-
-# AM_PROG_INSTALL_SH
-# ------------------
-# Define $install_sh.
-
-# Copyright 2001 Free Software Foundation, Inc.
-
-# This program is free software; you can redistribute it and/or modify
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-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
-
-AC_DEFUN([AM_PROG_INSTALL_SH],
-[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-install_sh=${install_sh-"$am_aux_dir/install-sh"}
-AC_SUBST(install_sh)])
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
 
 # AM_PROG_INSTALL_STRIP
-
-# Copyright 2001 Free Software Foundation, Inc.
-
-# 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 2, 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, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
-
+# ---------------------
 # One issue with vendor `install' (even GNU) is that you can't
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 AC_SUBST([INSTALL_STRIP_PROGRAM])])
 
-# serial 4						-*- Autoconf -*-
+# Check how to create a tarball.                            -*- Autoconf -*-
 
-# Copyright 1999, 2000, 2001 Free Software Foundation, Inc.
-
-# 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 2, 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, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
-
-
-# There are a few dirty hacks below to avoid letting `AC_PROG_CC' be
-# written in clear, in which case automake, when reading aclocal.m4,
-# will think it sees a *use*, and therefore will trigger all it's
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-
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-# ----------------------
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+# Copyright (C) 2004, 2005  Free Software Foundation, Inc.
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-# We don't AC_REQUIRE the corresponding AC_PROG_CC since the latter was
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-# This macro is AC_REQUIREd in _AM_DEPENDENCIES
-AC_DEFUN([AM_SET_DEPDIR],
-[rm -f .deps 2>/dev/null
-mkdir .deps 2>/dev/null
-if test -d .deps; then
-  DEPDIR=.deps
-else
-  # MS-DOS does not allow filenames that begin with a dot.
-  DEPDIR=_deps
-fi
-rmdir .deps 2>/dev/null
-AC_SUBST([DEPDIR])
-])
-
-
-# AM_DEP_TRACK
-# ------------
-AC_DEFUN([AM_DEP_TRACK],
-[AC_ARG_ENABLE(dependency-tracking,
-[  --disable-dependency-tracking Speeds up one-time builds
-  --enable-dependency-tracking  Do not reject slow dependency extractors])
-if test "x$enable_dependency_tracking" != xno; then
-  am_depcomp="$ac_aux_dir/depcomp"
-  AMDEPBACKSLASH='\'
-fi
-AM_CONDITIONAL([AMDEP], [test "x$enable_dependency_tracking" != xno])
-AC_SUBST([AMDEPBACKSLASH])
-])
-
-# Generate code to set up dependency tracking.   -*- Autoconf -*-
-
-# Copyright 1999, 2000, 2001, 2002 Free Software Foundation, Inc.
-
-# 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 2, 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, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
-
-#serial 2
-
-# _AM_OUTPUT_DEPENDENCY_COMMANDS
-# ------------------------------
-AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
-[for mf in $CONFIG_FILES; do
-  # Strip MF so we end up with the name of the file.
-  mf=`echo "$mf" | sed -e 's/:.*$//'`
-  # Check whether this is an Automake generated Makefile or not.
-  # We used to match only the files named `Makefile.in', but
-  # some people rename them; so instead we look at the file content.
-  # Grep'ing the first line is not enough: some people post-process
-  # each Makefile.in and add a new line on top of each file to say so.
-  # So let's grep whole file.
-  if grep '^#.*generated by automake' $mf > /dev/null 2>&1; then
-    dirpart=`AS_DIRNAME("$mf")`
-  else
-    continue
-  fi
-  grep '^DEP_FILES *= *[[^ @%:@]]' < "$mf" > /dev/null || continue
-  # Extract the definition of DEP_FILES from the Makefile without
-  # running `make'.
-  DEPDIR=`sed -n -e '/^DEPDIR = / s///p' < "$mf"`
-  test -z "$DEPDIR" && continue
-  # When using ansi2knr, U may be empty or an underscore; expand it
-  U=`sed -n -e '/^U = / s///p' < "$mf"`
-  test -d "$dirpart/$DEPDIR" || mkdir "$dirpart/$DEPDIR"
-  # We invoke sed twice because it is the simplest approach to
-  # changing $(DEPDIR) to its actual value in the expansion.
-  for file in `sed -n -e '
-    /^DEP_FILES = .*\\\\$/ {
-      s/^DEP_FILES = //
-      :loop
-	s/\\\\$//
-	p
-	n
-	/\\\\$/ b loop
-      p
-    }
-    /^DEP_FILES = / s/^DEP_FILES = //p' < "$mf" | \
-       sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
-    # Make sure the directory exists.
-    test -f "$dirpart/$file" && continue
-    fdir=`AS_DIRNAME(["$file"])`
-    AS_MKDIR_P([$dirpart/$fdir])
-    # echo "creating $dirpart/$file"
-    echo '# dummy' > "$dirpart/$file"
-  done
-done
-])# _AM_OUTPUT_DEPENDENCY_COMMANDS
-
-
-# AM_OUTPUT_DEPENDENCY_COMMANDS
-# -----------------------------
-# This macro should only be invoked once -- use via AC_REQUIRE.
-#
-# This code is only required when automatic dependency tracking
-# is enabled.  FIXME.  This creates each `.P' file that we will
-# need in order to bootstrap the dependency handling code.
-AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
-[AC_CONFIG_COMMANDS([depfiles],
-     [test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS],
-     [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
-])
-
-# Copyright 2001 Free Software Foundation, Inc.             -*- Autoconf -*-
-
-# 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 2, 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, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
 
 # serial 2
 
-# AM_MAKE_INCLUDE()
-# -----------------
-# Check to see how make treats includes.
-AC_DEFUN([AM_MAKE_INCLUDE],
-[am_make=${MAKE-make}
-cat > confinc << 'END'
-doit:
-	@echo done
-END
-# If we don't find an include directive, just comment out the code.
-AC_MSG_CHECKING([for style of include used by $am_make])
-am__include="#"
-am__quote=
-_am_result=none
-# First try GNU make style include.
-echo "include confinc" > confmf
-# We grep out `Entering directory' and `Leaving directory'
-# messages which can occur if `w' ends up in MAKEFLAGS.
-# In particular we don't look at `^make:' because GNU make might
-# be invoked under some other name (usually "gmake"), in which
-# case it prints its new name instead of `make'.
-if test "`$am_make -s -f confmf 2> /dev/null | fgrep -v 'ing directory'`" = "done"; then
-   am__include=include
-   am__quote=
-   _am_result=GNU
-fi
-# Now try BSD make style include.
-if test "$am__include" = "#"; then
-   echo '.include "confinc"' > confmf
-   if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then
-      am__include=.include
-      am__quote="\""
-      _am_result=BSD
-   fi
-fi
-AC_SUBST(am__include)
-AC_SUBST(am__quote)
-AC_MSG_RESULT($_am_result)
-rm -f confinc confmf
-])
+# _AM_PROG_TAR(FORMAT)
+# --------------------
+# Check how to create a tarball in format FORMAT.
+# FORMAT should be one of `v7', `ustar', or `pax'.
+#
+# Substitute a variable $(am__tar) that is a command
+# writing to stdout a FORMAT-tarball containing the directory
+# $tardir.
+#     tardir=directory && $(am__tar) > result.tar
+#
+# Substitute a variable $(am__untar) that extract such
+# a tarball read from stdin.
+#     $(am__untar) < result.tar
+AC_DEFUN([_AM_PROG_TAR],
+[# Always define AMTAR for backward compatibility.
+AM_MISSING_PROG([AMTAR], [tar])
+m4_if([$1], [v7],
+     [am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'],
+     [m4_case([$1], [ustar],, [pax],,
+              [m4_fatal([Unknown tar format])])
+AC_MSG_CHECKING([how to create a $1 tar archive])
+# Loop over all known methods to create a tar archive until one works.
+_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
+_am_tools=${am_cv_prog_tar_$1-$_am_tools}
+# Do not fold the above two line into one, because Tru64 sh and
+# Solaris sh will not grok spaces in the rhs of `-'.
+for _am_tool in $_am_tools
+do
+  case $_am_tool in
+  gnutar)
+    for _am_tar in tar gnutar gtar;
+    do
+      AM_RUN_LOG([$_am_tar --version]) && break
+    done
+    am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+    am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+    am__untar="$_am_tar -xf -"
+    ;;
+  plaintar)
+    # Must skip GNU tar: if it does not support --format= it doesn't create
+    # ustar tarball either.
+    (tar --version) >/dev/null 2>&1 && continue
+    am__tar='tar chf - "$$tardir"'
+    am__tar_='tar chf - "$tardir"'
+    am__untar='tar xf -'
+    ;;
+  pax)
+    am__tar='pax -L -x $1 -w "$$tardir"'
+    am__tar_='pax -L -x $1 -w "$tardir"'
+    am__untar='pax -r'
+    ;;
+  cpio)
+    am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+    am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+    am__untar='cpio -i -H $1 -d'
+    ;;
+  none)
+    am__tar=false
+    am__tar_=false
+    am__untar=false
+    ;;
+  esac
 
-# AM_CONDITIONAL                                              -*- Autoconf -*-
+  # If the value was cached, stop now.  We just wanted to have am__tar
+  # and am__untar set.
+  test -n "${am_cv_prog_tar_$1}" && break
 
-# Copyright 1997, 2000, 2001 Free Software Foundation, Inc.
+  # tar/untar a dummy directory, and stop if the command works
+  rm -rf conftest.dir
+  mkdir conftest.dir
+  echo GrepMe > conftest.dir/file
+  AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+  rm -rf conftest.dir
+  if test -s conftest.tar; then
+    AM_RUN_LOG([$am__untar <conftest.tar])
+    grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+  fi
+done
+rm -rf conftest.dir
 
-# 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 2, or (at your option)
-# any later version.
+AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+AC_SUBST([am__tar])
+AC_SUBST([am__untar])
+]) # _AM_PROG_TAR
 
-# 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, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
-
-# serial 5
-
-AC_PREREQ(2.52)
-
-# AM_CONDITIONAL(NAME, SHELL-CONDITION)
-# -------------------------------------
-# Define a conditional.
-AC_DEFUN([AM_CONDITIONAL],
-[ifelse([$1], [TRUE],  [AC_FATAL([$0: invalid condition: $1])],
-        [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
-AC_SUBST([$1_TRUE])
-AC_SUBST([$1_FALSE])
-if $2; then
-  $1_TRUE=
-  $1_FALSE='#'
-else
-  $1_TRUE='#'
-  $1_FALSE=
-fi
-AC_CONFIG_COMMANDS_PRE(
-[if test -z "${$1_TRUE}" && test -z "${$1_FALSE}"; then
-  AC_MSG_ERROR([conditional \"$1\" was never defined.
-Usually this means the macro was only invoked conditionally.])
-fi])])
-
 # include <unistd.h>
 #endif"
 
-ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO AMTAR install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM AWK SET_MAKE CXX CXXFLAGS LDFLAGS CPPFLAGS ac_ct_CXX EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CXXDEPMODE CC CFLAGS ac_ct_CC CCDEPMODE RANLIB ac_ct_RANLIB CXXCPP EGREP LIBOBJS POW_LIB prog_gengetopt prog_gengetopt_dir GENGETOPT_PREFIX GENGETOPT_CFLAGS GENGETOPT_LIBS LOG4CPP_PREFIX LOG4CPP_CFLAGS LOG4CPP_LIBS SMILE_PREFIX SMILE_CFLAGS SMILE_LIBS SVM_PERF_PREFIX SVM_PERF_CFLAGS SVM_PERF_LIBS VOWPAL_WABBIT_PREFIX VOWPAL_WABBIT_CFLAGS VOWPAL_WABBIT_LIBS BOOST_CFLAGS BOOST_LIBS READLINE_PREFIX READLINE_CFLAGS READLINE_LIBS PTHREAD_PREFIX PTHREAD_CFLAGS PTHREAD_LIBS sleipnirdocdir SLEIPNIR_PREFIX SLEIPNIR_CFLAGS SLEIPNIR_LIBS WITH_TOOLS_TRUE WITH_TOOLS_FALSE WITH_SMILE_TOOLS_TRUE WITH_SMILE_TOOLS_FALSE WITH_SVM_TOOLS_TRUE WITH_SVM_TOOLS_FALSE WITH_VW_TOOLS_TRUE WITH_VW_TOOLS_FALSE WITH_READLINE_TOOLS_TRUE WITH_READLINE_TOOLS_FALSE WITH_BOOST_TOOLS_TRUE WITH_BOOST_TOOLS_FALSE WITH_GENGETOPT_TRUE WITH_GENGETOPT_FALSE LTLIBOBJS'
+ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM mkdir_p AWK SET_MAKE am__leading_dot AMTAR am__tar am__untar CXX CXXFLAGS LDFLAGS CPPFLAGS ac_ct_CXX EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE CC CFLAGS ac_ct_CC CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE RANLIB ac_ct_RANLIB CXXCPP EGREP LIBOBJS POW_LIB prog_gengetopt prog_gengetopt_dir GENGETOPT_PREFIX GENGETOPT_CFLAGS GENGETOPT_LIBS LOG4CPP_PREFIX LOG4CPP_CFLAGS LOG4CPP_LIBS SMILE_PREFIX SMILE_CFLAGS SMILE_LIBS SVM_PERF_PREFIX SVM_PERF_CFLAGS SVM_PERF_LIBS VOWPAL_WABBIT_PREFIX VOWPAL_WABBIT_CFLAGS VOWPAL_WABBIT_LIBS BOOST_CFLAGS BOOST_LIBS READLINE_PREFIX READLINE_CFLAGS READLINE_LIBS PTHREAD_PREFIX PTHREAD_CFLAGS PTHREAD_LIBS sleipnirdocdir SLEIPNIR_PREFIX SLEIPNIR_CFLAGS SLEIPNIR_LIBS WITH_TOOLS_TRUE WITH_TOOLS_FALSE WITH_SMILE_TOOLS_TRUE WITH_SMILE_TOOLS_FALSE WITH_SVM_TOOLS_TRUE WITH_SVM_TOOLS_FALSE WITH_VW_TOOLS_TRUE WITH_VW_TOOLS_FALSE WITH_READLINE_TOOLS_TRUE WITH_READLINE_TOOLS_FALSE WITH_BOOST_TOOLS_TRUE WITH_BOOST_TOOLS_FALSE WITH_GENGETOPT_TRUE WITH_GENGETOPT_FALSE LTLIBOBJS'
 ac_subst_files=''
 
 # Initialize some variables set by options.
 Optional Features:
   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
-  --disable-dependency-tracking Speeds up one-time builds
-  --enable-dependency-tracking  Do not reject slow dependency extractors
+  --disable-dependency-tracking  speeds up one-time build
+  --enable-dependency-tracking   do not reject slow dependency extractors
 
 Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
 #AC_CONFIG_HEADER([config.h])
 #AM_CONFIG_HEADER([config.h])
 
-am__api_version="1.6"
+am__api_version="1.9"
 ac_aux_dir=
 for ac_dir in $srcdir $srcdir/.. $srcdir/../..; do
   if test -f $ac_dir/install-sh; then
 program_transform_name=`echo $program_transform_name | sed -f conftest.sed`
 rm conftest.sed
 
-
 # expand $ac_aux_dir to an absolute path
 am_aux_dir=`cd $ac_aux_dir && pwd`
 
 echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
 fi
 
+if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then
+  # We used to keeping the `.' as first argument, in order to
+  # allow $(mkdir_p) to be used without argument.  As in
+  #   $(mkdir_p) $(somedir)
+  # where $(somedir) is conditionally defined.  However this is wrong
+  # for two reasons:
+  #  1. if the package is installed by a user who cannot write `.'
+  #     make install will fail,
+  #  2. the above comment should most certainly read
+  #     $(mkdir_p) $(DESTDIR)$(somedir)
+  #     so it does not work when $(somedir) is undefined and
+  #     $(DESTDIR) is not.
+  #  To support the latter case, we have to write
+  #     test -z "$(somedir)" || $(mkdir_p) $(DESTDIR)$(somedir),
+  #  so the `.' trick is pointless.
+  mkdir_p='mkdir -p --'
+else
+  # On NextStep and OpenStep, the `mkdir' command does not
+  # recognize any option.  It will interpret all options as
+  # directories to create, and then abort because `.' already
+  # exists.
+  for d in ./-p ./--version;
+  do
+    test -d $d && rmdir $d
+  done
+  # $(mkinstalldirs) is defined by Automake if mkinstalldirs exists.
+  if test -f "$ac_aux_dir/mkinstalldirs"; then
+    mkdir_p='$(mkinstalldirs)'
+  else
+    mkdir_p='$(install_sh) -d'
+  fi
+fi
+
 for ac_prog in gawk mawk nawk awk
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
   SET_MAKE="MAKE=${MAKE-make}"
 fi
 
- # test to see if srcdir already configured
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+  am__leading_dot=.
+else
+  am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+# test to see if srcdir already configured
 if test "`cd $srcdir && pwd`" != "`pwd`" &&
    test -f $srcdir/config.status; then
   { { echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5
    { (exit 1); exit 1; }; }
 fi
 
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+  if (cygpath --version) >/dev/null 2>/dev/null; then
+    CYGPATH_W='cygpath -w'
+  else
+    CYGPATH_W=echo
+  fi
+fi
+
+
 # Define the identity of the package.
- PACKAGE=libsleipnir
- VERSION=1.0.0
+ PACKAGE='libsleipnir'
+ VERSION='1.0.0'
 
 
 cat >>confdefs.h <<_ACEOF
 
 MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
 
-
-AMTAR=${AMTAR-"${am_missing_run}tar"}
-
 install_sh=${install_sh-"$am_aux_dir/install-sh"}
 
 # Installed binaries are usually stripped using `strip' when the user
 
 # We need awk for the "check" target.  The system "awk" is bad on
 # some platforms.
+# Always define AMTAR for backward compatibility.
+
+AMTAR=${AMTAR-"${am_missing_run}tar"}
+
+am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
+
+
 
 
 
 ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
 ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
 ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-rm -f .deps 2>/dev/null
-mkdir .deps 2>/dev/null
-if test -d .deps; then
-  DEPDIR=.deps
-else
-  # MS-DOS does not allow filenames that begin with a dot.
-  DEPDIR=_deps
-fi
-rmdir .deps 2>/dev/null
-
+DEPDIR="${am__leading_dot}deps"
 
           ac_config_commands="$ac_config_commands depfiles"
 
 
 am_make=${MAKE-make}
 cat > confinc << 'END'
-doit:
+am__doit:
 	@echo done
+.PHONY: am__doit
 END
 # If we don't find an include directive, just comment out the code.
 echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5
 # In particular we don't look at `^make:' because GNU make might
 # be invoked under some other name (usually "gmake"), in which
 # case it prints its new name instead of `make'.
-if test "`$am_make -s -f confmf 2> /dev/null | fgrep -v 'ing directory'`" = "done"; then
+if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then
    am__include=include
    am__quote=
    _am_result=GNU
   # using a relative directory.
   cp "$am_depcomp" conftest.dir
   cd conftest.dir
+  # We will build objects and dependencies in a subdirectory because
+  # it helps to detect inapplicable dependency modes.  For instance
+  # both Tru64's cc and ICC support -MD to output dependencies as a
+  # side effect of compilation, but ICC will put the dependencies in
+  # the current directory while Tru64 will put them in the object
+  # directory.
+  mkdir sub
 
   am_cv_CXX_dependencies_compiler_type=none
   if test "$am_compiler_list" = ""; then
      am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
   fi
   for depmode in $am_compiler_list; do
+    # Setup a source with many dependencies, because some compilers
+    # like to wrap large dependency lists on column 80 (with \), and