@@ -32,4 +32,5 @@

 ^src/cpp_tests/testGibbsSampler.o

 ^src/cpp_tests/testMatrix.o

 ^src/cpp_tests/testProposalQueue.o

-^src/cpp_tests/testRandom.o

\ No newline at end of file

+^src/cpp_tests/testRandom.o

+^src/cpp_tests/testSerialization.o

\ No newline at end of file

deleted file mode 100644

@@ -1,26 +0,0 @@

-# options file for running astyle to "beautify" c++ code

-# run using `astyle --options=.astylerc src/*.{cc,cpp,h}`

-

-# use 4 spaces instead of tabs

-indent=spaces=4

-convert-tabs

-

-# remove spaces in and around parenthesis except in front of headers

-# Example: foo ( bar, baz ); -> foo(bar, baz);

-unpad-paren

-

-# insert a space after if, while, for, etc (exception to previous rule)

-pad-header

-

-# pointer and reference operators to name

-align-pointer=name

-

-# ALWAYS use brackets, even if the conditional is one line

-# if not and you add more code later you can have problems...

-add-brackets

-

-# use linux line-endings

-lineend=linux

-

-# restrict lines to 80 characters

-max-code-length=120

deleted file mode 100644

@@ -1,13 +0,0 @@

-linters: with_defaults(

-    camel_case_linter = NULL, # 1066

-    assignment_linter = NULL, # 239

-    infix_spaces_linter = NULL, # 150

-    open_curly_linter = NULL, # 113

-    line_length_linter = NULL, # 111

-    spaces_left_parentheses_linter = NULL, # 53

-    single_quotes_linter = NULL, # 33

-    commented_code_linter = NULL, # 6

-    commas_linter = NULL,

-    NULL

-  )

-exclusions: list("R/RcppExports.R")

@@ -42,7 +42,7 @@

 #' data(SimpSim)

 #' result <- CoGAPS(SimpSim.D, SimpSim.S, nFactor=3, nOutputs=250)

 #' @export

-CoGAPS <- function(D, S, nFactor=7, nEquil=1000, nSample=1000, nOutputs=1000,

+CoGAPS <- function(D, S, nFactor=7, nEquil=250, nSample=250, nOutputs=1000,

 nSnapshots=0, alphaA=0.01, alphaP=0.01, maxGibbmassA=100, maxGibbmassP=100,

 seed=-1, messages=TRUE, singleCellRNASeq=FALSE, whichMatrixFixed='N',

 fixedPatterns=matrix(0), checkpointInterval=0, 

@@ -114,6 +114,7 @@ checkpointFile="gaps_checkpoint.out", nCores=1, ...)

 }

 #' Restart CoGAPS from Checkpoint File

+#' @export

 #'

 #' @details loads the state of a previous CoGAPS run from a file and

 #'  continues the run from that point

@@ -122,6 +123,9 @@ checkpointFile="gaps_checkpoint.out", nCores=1, ...)

 #' @param path path to checkpoint file

 #' @param checkpointFile name for future checkpooints made

 #' @return list with A and P matrix estimates

+#' @examples

+#' data(SimpSim)

+#' result <- CoGAPS(SimpSim.D, SimpSim.S, nFactor=3, nOutputs=250)

 CoGapsFromCheckpoint <- function(D, S, path, checkpointFile=NA)

 {

     if (is.na(checkpointFile))

@@ -103,4 +103,4 @@ NULL

 #' @docType data

 #' @name tf2ugFC

 #' @usage tf2ugFC

-NULL

\ No newline at end of file

+NULL

@@ -46,4 +46,4 @@ plotGAPS <- function(A, P, outputPDF="")

     {

         dev.off()

     }

-}

\ No newline at end of file

+}

new file mode 100644

@@ -0,0 +1,5644 @@

+#! /bin/sh

+# Guess values for system-dependent variables and create Makefiles.

+# Generated by GNU Autoconf 2.69 for CoGAPS 3.1.2.

+#

+#

+# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.

+#

+#

+# This configure script is free software; the Free Software Foundation

+# gives unlimited permission to copy, distribute and modify it.

+## -------------------- ##

+## M4sh Initialization. ##

+## -------------------- ##

+

+# Be more Bourne compatible

+DUALCASE=1; export DUALCASE # for MKS sh

+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :

+  emulate sh

+  NULLCMD=:

+  # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which

+  # is contrary to our usage.  Disable this feature.

+  alias -g '${1+"$@"}'='"$@"'

+  setopt NO_GLOB_SUBST

+else

+  case `(set -o) 2>/dev/null` in #(

+  *posix*) :

+    set -o posix ;; #(

+  *) :

+     ;;

+esac

+fi

+

+

+as_nl='

+'

+export as_nl

+# Printing a long string crashes Solaris 7 /usr/bin/printf.

+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'

+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo

+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo

+# Prefer a ksh shell builtin over an external printf program on Solaris,

+# but without wasting forks for bash or zsh.

+if test -z "$BASH_VERSION$ZSH_VERSION" \

+    && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then

+  as_echo='print -r --'

+  as_echo_n='print -rn --'

+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then

+  as_echo='printf %s\n'

+  as_echo_n='printf %s'

+else

+  if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then

+    as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'

+    as_echo_n='/usr/ucb/echo -n'

+  else

+    as_echo_body='eval expr "X$1" : "X\\(.*\\)"'

+    as_echo_n_body='eval

+      arg=$1;

+      case $arg in #(

+      *"$as_nl"*)

+	expr "X$arg" : "X\\(.*\\)$as_nl";

+	arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;

+      esac;

+      expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"

+    '

+    export as_echo_n_body

+    as_echo_n='sh -c $as_echo_n_body as_echo'

+  fi

+  export as_echo_body

+  as_echo='sh -c $as_echo_body as_echo'

+fi

+

+# The user is always right.

+if test "${PATH_SEPARATOR+set}" != set; then

+  PATH_SEPARATOR=:

+  (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {

+    (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||

+      PATH_SEPARATOR=';'

+  }

+fi

+

+

+# IFS

+# We need space, tab and new line, in precisely that order.  Quoting is

+# there to prevent editors from complaining about space-tab.

+# (If _AS_PATH_WALK were called with IFS unset, it would disable word

+# splitting by setting IFS to empty value.)

+IFS=" ""	$as_nl"

+

+# Find who we are.  Look in the path if we contain no directory separator.

+as_myself=

+case $0 in #((

+  *[\\/]* ) as_myself=$0 ;;

+  *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR

+for as_dir in $PATH

+do

+  IFS=$as_save_IFS

+  test -z "$as_dir" && as_dir=.

+    test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break

+  done

+IFS=$as_save_IFS

+

+     ;;

+esac

+# We did not find ourselves, most probably we were run as `sh COMMAND'

+# in which case we are not to be found in the path.

+if test "x$as_myself" = x; then

+  as_myself=$0

+fi

+if test ! -f "$as_myself"; then

+  $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2

+  exit 1

+fi

+

+# Unset variables that we do not need and which cause bugs (e.g. in

+# pre-3.0 UWIN ksh).  But do not cause bugs in bash 2.01; the "|| exit 1"

+# suppresses any "Segmentation fault" message there.  '((' could

+# trigger a bug in pdksh 5.2.14.

+for as_var in BASH_ENV ENV MAIL MAILPATH

+do eval test x\${$as_var+set} = xset \

+  && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :

+done

+PS1='$ '

+PS2='> '

+PS4='+ '

+

+# NLS nuisances.

+LC_ALL=C

+export LC_ALL

+LANGUAGE=C

+export LANGUAGE

+

+# CDPATH.

+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH

+

+# Use a proper internal environment variable to ensure we don't fall

+  # into an infinite loop, continuously re-executing ourselves.

+  if test x"${_as_can_reexec}" != xno && test "x$CONFIG_SHELL" != x; then

+    _as_can_reexec=no; export _as_can_reexec;

+    # We cannot yet assume a decent shell, so we have to provide a

+# neutralization value for shells without unset; and this also

+# works around shells that cannot unset nonexistent variables.

+# Preserve -v and -x to the replacement shell.

+BASH_ENV=/dev/null

+ENV=/dev/null

+(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV

+case $- in # ((((

+  *v*x* | *x*v* ) as_opts=-vx ;;

+  *v* ) as_opts=-v ;;

+  *x* ) as_opts=-x ;;

+  * ) as_opts= ;;

+esac

+exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}

+# Admittedly, this is quite paranoid, since all the known shells bail

+# out after a failed `exec'.

+$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2

+as_fn_exit 255

+  fi

+  # We don't want this to propagate to other subprocesses.

+          { _as_can_reexec=; unset _as_can_reexec;}

+if test "x$CONFIG_SHELL" = x; then

+  as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :

+  emulate sh

+  NULLCMD=:

+  # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which

+  # is contrary to our usage.  Disable this feature.

+  alias -g '\${1+\"\$@\"}'='\"\$@\"'

+  setopt NO_GLOB_SUBST

+else

+  case \`(set -o) 2>/dev/null\` in #(

+  *posix*) :

+    set -o posix ;; #(

+  *) :

+     ;;

+esac

+fi

+"

+  as_required="as_fn_return () { (exit \$1); }

+as_fn_success () { as_fn_return 0; }

+as_fn_failure () { as_fn_return 1; }

+as_fn_ret_success () { return 0; }

+as_fn_ret_failure () { return 1; }

+

+exitcode=0

+as_fn_success || { exitcode=1; echo as_fn_success failed.; }

+as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }

+as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }

+as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }

+if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :

+

+else

+  exitcode=1; echo positional parameters were not saved.

+fi

+test x\$exitcode = x0 || exit 1

+test -x / || exit 1"

+  as_suggested="  as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO

+  as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO

+  eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&

+  test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1

+test \$(( 1 + 1 )) = 2 || exit 1"

+  if (eval "$as_required") 2>/dev/null; then :

+  as_have_required=yes

+else

+  as_have_required=no

+fi

+  if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :

+

+else

+  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR

+as_found=false

+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH

+do

+  IFS=$as_save_IFS

+  test -z "$as_dir" && as_dir=.

+  as_found=:

+  case $as_dir in #(

+	 /*)

+	   for as_base in sh bash ksh sh5; do

+	     # Try only shells that exist, to save several forks.

+	     as_shell=$as_dir/$as_base

+	     if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&

+		    { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :

+  CONFIG_SHELL=$as_shell as_have_required=yes

+		   if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :

+  break 2

+fi

+fi

+	   done;;

+       esac

+  as_found=false

+done

+$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&

+	      { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :

+  CONFIG_SHELL=$SHELL as_have_required=yes

+fi; }

+IFS=$as_save_IFS

+

+

+      if test "x$CONFIG_SHELL" != x; then :

+  export CONFIG_SHELL

+             # We cannot yet assume a decent shell, so we have to provide a

+# neutralization value for shells without unset; and this also

+# works around shells that cannot unset nonexistent variables.

+# Preserve -v and -x to the replacement shell.

+BASH_ENV=/dev/null

+ENV=/dev/null

+(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV

+case $- in # ((((

+  *v*x* | *x*v* ) as_opts=-vx ;;

+  *v* ) as_opts=-v ;;

+  *x* ) as_opts=-x ;;

+  * ) as_opts= ;;

+esac

+exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}

+# Admittedly, this is quite paranoid, since all the known shells bail

+# out after a failed `exec'.

+$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2

+exit 255

+fi

+

+    if test x$as_have_required = xno; then :

+  $as_echo "$0: This script requires a shell more modern than all"

+  $as_echo "$0: the shells that I found on your system."

+  if test x${ZSH_VERSION+set} = xset ; then

+    $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"

+    $as_echo "$0: be upgraded to zsh 4.3.4 or later."

+  else

+    $as_echo "$0: Please tell bug-autoconf@gnu.org about your system,

+$0: including any error possibly output before this

+$0: message. Then install a modern shell, or manually run

+$0: the script under such a shell if you do have one."

+  fi

+  exit 1

+fi

+fi

+fi

+SHELL=${CONFIG_SHELL-/bin/sh}

+export SHELL

+# Unset more variables known to interfere with behavior of common tools.

+CLICOLOR_FORCE= GREP_OPTIONS=

+unset CLICOLOR_FORCE GREP_OPTIONS

+

+## --------------------- ##

+## M4sh Shell Functions. ##

+## --------------------- ##

+# as_fn_unset VAR

+# ---------------

+# Portably unset VAR.

+as_fn_unset ()

+{

+  { eval $1=; unset $1;}

+}

+as_unset=as_fn_unset

+

+# as_fn_set_status STATUS

+# -----------------------

+# Set $? to STATUS, without forking.

+as_fn_set_status ()

+{

+  return $1

+} # as_fn_set_status

+

+# as_fn_exit STATUS

+# -----------------

+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.

+as_fn_exit ()

+{

+  set +e

+  as_fn_set_status $1

+  exit $1

+} # as_fn_exit

+

+# as_fn_mkdir_p

+# -------------

+# Create "$as_dir" as a directory, including parents if necessary.

+as_fn_mkdir_p ()

+{

+

+  case $as_dir in #(

+  -*) as_dir=./$as_dir;;

+  esac

+  test -d "$as_dir" || eval $as_mkdir_p || {

+    as_dirs=

+    while :; do

+      case $as_dir in #(

+      *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(

+      *) as_qdir=$as_dir;;

+      esac

+      as_dirs="'$as_qdir' $as_dirs"

+      as_dir=`$as_dirname -- "$as_dir" ||

+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \

+	 X"$as_dir" : 'X\(//\)[^/]' \| \

+	 X"$as_dir" : 'X\(//\)$' \| \

+	 X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||

+$as_echo X"$as_dir" |

+    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{

+	    s//\1/

+	    q

+	  }

+	  /^X\(\/\/\)[^/].*/{

+	    s//\1/

+	    q

+	  }

+	  /^X\(\/\/\)$/{

+	    s//\1/

+	    q

+	  }

+	  /^X\(\/\).*/{

+	    s//\1/

+	    q

+	  }

+	  s/.*/./; q'`

+      test -d "$as_dir" && break

+    done

+    test -z "$as_dirs" || eval "mkdir $as_dirs"

+  } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"

+

+

+} # as_fn_mkdir_p

+

+# as_fn_executable_p FILE

+# -----------------------

+# Test if FILE is an executable regular file.

+as_fn_executable_p ()

+{

+  test -f "$1" && test -x "$1"

+} # as_fn_executable_p

+# as_fn_append VAR VALUE

+# ----------------------

+# Append the text in VALUE to the end of the definition contained in VAR. Take

+# advantage of any shell optimizations that allow amortized linear growth over

+# repeated appends, instead of the typical quadratic growth present in naive

+# implementations.

+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :

+  eval 'as_fn_append ()

+  {

+    eval $1+=\$2

+  }'

+else

+  as_fn_append ()

+  {

+    eval $1=\$$1\$2

+  }

+fi # as_fn_append

+

+# as_fn_arith ARG...

+# ------------------

+# Perform arithmetic evaluation on the ARGs, and store the result in the

+# global $as_val. Take advantage of shells that can avoid forks. The arguments

+# must be portable across $(()) and expr.

+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :

+  eval 'as_fn_arith ()

+  {

+    as_val=$(( $* ))

+  }'

+else

+  as_fn_arith ()

+  {

+    as_val=`expr "$@" || test $? -eq 1`

+  }

+fi # as_fn_arith

+

+

+# as_fn_error STATUS ERROR [LINENO LOG_FD]

+# ----------------------------------------

+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are

+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the

+# script with STATUS, using 1 if that was 0.

+as_fn_error ()

+{

+  as_status=$1; test $as_status -eq 0 && as_status=1

+  if test "$4"; then

+    as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack

+    $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4

+  fi

+  $as_echo "$as_me: error: $2" >&2

+  as_fn_exit $as_status

+} # as_fn_error

+

+if expr a : '\(a\)' >/dev/null 2>&1 &&

+   test "X`expr 00001 : '.*\(...\)'`" = X001; then

+  as_expr=expr

+else

+  as_expr=false

+fi

+

+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then

+  as_basename=basename

+else

+  as_basename=false

+fi

+

+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then

+  as_dirname=dirname

+else

+  as_dirname=false

+fi

+

+as_me=`$as_basename -- "$0" ||

+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \

+	 X"$0" : 'X\(//\)$' \| \

+	 X"$0" : 'X\(/\)' \| . 2>/dev/null ||

+$as_echo X/"$0" |

+    sed '/^.*\/\([^/][^/]*\)\/*$/{

+	    s//\1/

+	    q

+	  }

+	  /^X\/\(\/\/\)$/{

+	    s//\1/

+	    q

+	  }

+	  /^X\/\(\/\).*/{

+	    s//\1/

+	    q

+	  }

+	  s/.*/./; q'`

+

+# Avoid depending upon Character Ranges.

+as_cr_letters='abcdefghijklmnopqrstuvwxyz'

+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'

+as_cr_Letters=$as_cr_letters$as_cr_LETTERS

+as_cr_digits='0123456789'

+as_cr_alnum=$as_cr_Letters$as_cr_digits

+

+

+  as_lineno_1=$LINENO as_lineno_1a=$LINENO

+  as_lineno_2=$LINENO as_lineno_2a=$LINENO

+  eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&

+  test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {

+  # Blame Lee E. McMahon (1931-1989) for sed's syntax.  :-)

+  sed -n '

+    p

+    /[$]LINENO/=

+  ' <$as_myself |

+    sed '

+      s/[$]LINENO.*/&-/

+      t lineno

+      b

+      :lineno

+      N

+      :loop

+      s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/

+      t loop

+      s/-\n.*//

+    ' >$as_me.lineno &&

+  chmod +x "$as_me.lineno" ||

+    { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }

+

+  # If we had to re-execute with $CONFIG_SHELL, we're ensured to have

+  # already done that, so ensure we don't try to do so again and fall

+  # in an infinite loop.  This has already happened in practice.

+  _as_can_reexec=no; export _as_can_reexec

+  # Don't try to exec as it changes $[0], causing all sort of problems

+  # (the dirname of $[0] is not the place where we might find the

+  # original and so on.  Autoconf is especially sensitive to this).

+  . "./$as_me.lineno"

+  # Exit status is that of the last command.

+  exit

+}

+

+ECHO_C= ECHO_N= ECHO_T=

+case `echo -n x` in #(((((

+-n*)

+  case `echo 'xy\c'` in

+  *c*) ECHO_T='	';;	# ECHO_T is single tab character.

+  xy)  ECHO_C='\c';;

+  *)   echo `echo ksh88 bug on AIX 6.1` > /dev/null

+       ECHO_T='	';;

+  esac;;

+*)

+  ECHO_N='-n';;

+esac

+

+rm -f conf$$ conf$$.exe conf$$.file

+if test -d conf$$.dir; then

+  rm -f conf$$.dir/conf$$.file

+else

+  rm -f conf$$.dir

+  mkdir conf$$.dir 2>/dev/null

+fi

+if (echo >conf$$.file) 2>/dev/null; then

+  if ln -s conf$$.file conf$$ 2>/dev/null; then

+    as_ln_s='ln -s'

+    # ... but there are two gotchas:

+    # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.

+    # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.

+    # In both cases, we have to default to `cp -pR'.

+    ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||

+      as_ln_s='cp -pR'

+  elif ln conf$$.file conf$$ 2>/dev/null; then

+    as_ln_s=ln

+  else

+    as_ln_s='cp -pR'

+  fi

+else

+  as_ln_s='cp -pR'

+fi

+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file

+rmdir conf$$.dir 2>/dev/null

+

+if mkdir -p . 2>/dev/null; then

+  as_mkdir_p='mkdir -p "$as_dir"'

+else

+  test -d ./-p && rmdir ./-p

+  as_mkdir_p=false

+fi

+

+as_test_x='test -x'

+as_executable_p=as_fn_executable_p

+

+# Sed expression to map a string onto a valid CPP name.

+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"

+

+# Sed expression to map a string onto a valid variable name.

+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"

+

+

+test -n "$DJDIR" || exec 7<&0 </dev/null

+exec 6>&1

+

+# Name of the host.

+# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,

+# so uname gets run too.

+ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`

+

+#

+# Initializations.

+#

+ac_default_prefix=/usr/local

+ac_clean_files=

+ac_config_libobj_dir=.

+LIBOBJS=

+cross_compiling=no

+subdirs=

+MFLAGS=

+MAKEFLAGS=

+

+# Identity of this package.

+PACKAGE_NAME='CoGAPS'

+PACKAGE_TARNAME='cogaps'

+PACKAGE_VERSION='3.1.2'

+PACKAGE_STRING='CoGAPS 3.1.2'

+PACKAGE_BUGREPORT=''

+PACKAGE_URL=''

+

+ac_subst_vars='LTLIBOBJS

+LIBOBJS

+GAPS_LIBS

+GAPS_CXX_FLAGS

+GAPS_CPP_FLAGS

+SED

+CXXCPP

+OBJEXT

+EXEEXT

+ac_ct_CXX

+CPPFLAGS

+LDFLAGS

+CXXFLAGS

+CXX

+target_alias

+host_alias

+build_alias

+LIBS

+ECHO_T

+ECHO_N

+ECHO_C

+DEFS

+mandir

+localedir

+libdir

+psdir

+pdfdir

+dvidir

+htmldir

+infodir

+docdir

+oldincludedir

+includedir

+runstatedir

+localstatedir

+sharedstatedir

+sysconfdir

+datadir

+datarootdir

+libexecdir

+sbindir

+bindir

+program_transform_name

+prefix

+exec_prefix

+PACKAGE_URL

+PACKAGE_BUGREPORT

+PACKAGE_STRING

+PACKAGE_VERSION

+PACKAGE_TARNAME

+PACKAGE_NAME

+PATH_SEPARATOR

+SHELL'

+ac_subst_files=''

+ac_user_opts='

+enable_option_checking

+enable_debug

+enable_warnings

+enable_simd

+'

+      ac_precious_vars='build_alias

+host_alias

+target_alias

+CXX

+CXXFLAGS

+LDFLAGS

+LIBS

+CPPFLAGS

+CCC

+CXXCPP'

+

+

+# Initialize some variables set by options.

+ac_init_help=

+ac_init_version=false

+ac_unrecognized_opts=

+ac_unrecognized_sep=

+# The variables have the same names as the options, with

+# dashes changed to underlines.

+cache_file=/dev/null

+exec_prefix=NONE

+no_create=

+no_recursion=

+prefix=NONE

+program_prefix=NONE

+program_suffix=NONE

+program_transform_name=s,x,x,

+silent=

+site=

+srcdir=

+verbose=

+x_includes=NONE

+x_libraries=NONE

+

+# Installation directory options.

+# These are left unexpanded so users can "make install exec_prefix=/foo"

+# and all the variables that are supposed to be based on exec_prefix

+# by default will actually change.

+# Use braces instead of parens because sh, perl, etc. also accept them.

+# (The list follows the same order as the GNU Coding Standards.)

+bindir='${exec_prefix}/bin'

+sbindir='${exec_prefix}/sbin'

+libexecdir='${exec_prefix}/libexec'

+datarootdir='${prefix}/share'

+datadir='${datarootdir}'

+sysconfdir='${prefix}/etc'

+sharedstatedir='${prefix}/com'

+localstatedir='${prefix}/var'

+runstatedir='${localstatedir}/run'

+includedir='${prefix}/include'

+oldincludedir='/usr/include'

+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'

+infodir='${datarootdir}/info'

+htmldir='${docdir}'

+dvidir='${docdir}'

+pdfdir='${docdir}'

+psdir='${docdir}'

+libdir='${exec_prefix}/lib'

+localedir='${datarootdir}/locale'

+mandir='${datarootdir}/man'

+

+ac_prev=

+ac_dashdash=

+for ac_option

+do

+  # If the previous option needs an argument, assign it.

+  if test -n "$ac_prev"; then

+    eval $ac_prev=\$ac_option

+    ac_prev=

+    continue

+  fi

+

+  case $ac_option in

+  *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;

+  *=)   ac_optarg= ;;

+  *)    ac_optarg=yes ;;

+  esac

+

+  # Accept the important Cygnus configure options, so we can diagnose typos.

+

+  case $ac_dashdash$ac_option in

+  --)

+    ac_dashdash=yes ;;

+

+  -bindir | --bindir | --bindi | --bind | --bin | --bi)

+    ac_prev=bindir ;;

+  -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)

+    bindir=$ac_optarg ;;

+

+  -build | --build | --buil | --bui | --bu)

+    ac_prev=build_alias ;;

+  -build=* | --build=* | --buil=* | --bui=* | --bu=*)

+    build_alias=$ac_optarg ;;

+

+  -cache-file | --cache-file | --cache-fil | --cache-fi \

+  | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)

+    ac_prev=cache_file ;;

+  -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \

+  | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)

+    cache_file=$ac_optarg ;;

+

+  --config-cache | -C)

+    cache_file=config.cache ;;

+

+  -datadir | --datadir | --datadi | --datad)

+    ac_prev=datadir ;;

+  -datadir=* | --datadir=* | --datadi=* | --datad=*)

+    datadir=$ac_optarg ;;

+

+  -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \

+  | --dataroo | --dataro | --datar)

+    ac_prev=datarootdir ;;

+  -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \

+  | --dataroot=* | --dataroo=* | --dataro=* | --datar=*)

+    datarootdir=$ac_optarg ;;

+

+  -disable-* | --disable-*)

+    ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`

+    # Reject names that are not valid shell variable names.

+    expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&

+      as_fn_error $? "invalid feature name: $ac_useropt"

+    ac_useropt_orig=$ac_useropt

+    ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`

+    case $ac_user_opts in

+      *"

+"enable_$ac_useropt"