A r/.lintr => r/.lintr +7 -0
@@ 0,0 1,7 @@
+linters: linters_with_defaults(
+ line_length_linter = line_length_linter(80),
+ object_name_linter = NULL,
+ object_length_linter = object_length_linter(40),
+ object_usage_linter = NULL,
+ cyclocomp_linter = cyclocomp_linter(26)
+ )
A r/DESCRIPTION => r/DESCRIPTION +12 -0
@@ 0,0 1,12 @@
+Package: blspR
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R:
+ person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),
+ comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
+ license
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
A r/NAMESPACE => r/NAMESPACE +8 -0
@@ 0,0 1,8 @@
+# Generated by roxygen2: do not edit by hand
+
+# Load dynamic libraries (shared object files)
+useDynLib(blspR, .registration = TRUE, .fixes = "C_")
+
+
+# Export functions defined in R code
+export("blsp_test")
A r/R/blsp_r.R => r/R/blsp_r.R +4 -0
@@ 0,0 1,4 @@
+blsp_test <- function(a, b, c) {
+ result <- .Call(C_generate_data, a, b, c)#, PACKAGE = "blspR")
+ return(result)
+}
A r/cleanup => r/cleanup +5 -0
@@ 0,0 1,5 @@
+#!/bin/sh
+
+rm -f config.*
+rm -f src/Makevars
+rm -rf autom4te.cache
A r/configure => r/configure +2935 -0
@@ 0,0 1,2935 @@
+#! /bin/sh
+# Guess values for system-dependent variables and create Makefiles.
+# Generated by GNU Autoconf 2.71 for blspR 0.0.1.
+#
+#
+# Copyright (C) 1992-1996, 1998-2017, 2020-2021 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
+as_nop=:
+if test ${ZSH_VERSION+y} && (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 $as_nop
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+
+# Reset variables that may have inherited troublesome values from
+# the environment.
+
+# IFS needs to be set, to space, tab, and newline, in precisely that order.
+# (If _AS_PATH_WALK were called with IFS unset, it would have the
+# side effect of setting IFS to empty, thus disabling word splitting.)
+# Quoting is to prevent editors from complaining about space-tab.
+as_nl='
+'
+export as_nl
+IFS=" "" $as_nl"
+
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# Ensure predictable behavior from utilities with locale-dependent output.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# We cannot yet rely on "unset" to work, but we need these variables
+# to be unset--not just set to an empty or harmless value--now, to
+# avoid bugs in old shells (e.g. pre-3.0 UWIN ksh). This construct
+# also avoids known problems related to "unset" and subshell syntax
+# in other old shells (e.g. bash 2.01 and pdksh 5.2.14).
+for as_var in BASH_ENV ENV MAIL MAILPATH CDPATH
+do eval test \${$as_var+y} \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+
+# Ensure that fds 0, 1, and 2 are open.
+if (exec 3>&0) 2>/dev/null; then :; else exec 0</dev/null; fi
+if (exec 3>&1) 2>/dev/null; then :; else exec 1>/dev/null; fi
+if (exec 3>&2) ; then :; else exec 2>/dev/null; fi
+
+# The user is always right.
+if ${PATH_SEPARATOR+false} :; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# 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
+ case $as_dir in #(((
+ '') as_dir=./ ;;
+ */) ;;
+ *) as_dir=$as_dir/ ;;
+ esac
+ 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
+ printf "%s\n" "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+
+# Use a proper internal environment variable to ensure we don't fall
+ # into an infinite loop, continuously re-executing ourselves.
+ if test x"${_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'.
+printf "%s\n" "$0: could not re-execute with $CONFIG_SHELL" >&2
+exit 255
+ fi
+ # We don't want this to propagate to other subprocesses.
+ { _as_can_reexec=; unset _as_can_reexec;}
+if test "x$CONFIG_SHELL" = x; then
+ as_bourne_compatible="as_nop=:
+if test \${ZSH_VERSION+y} && (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 \$as_nop
+ 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 \$as_nop
+ exitcode=1; echo positional parameters were not saved.
+fi
+test x\$exitcode = x0 || exit 1
+blah=\$(echo \$(echo blah))
+test x\"\$blah\" = xblah || 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"
+ if (eval "$as_required") 2>/dev/null
+then :
+ as_have_required=yes
+else $as_nop
+ as_have_required=no
+fi
+ if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null
+then :
+
+else $as_nop
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+as_found=false
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ case $as_dir in #(((
+ '') as_dir=./ ;;
+ */) ;;
+ *) as_dir=$as_dir/ ;;
+ esac
+ 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 "$as_shell.exe"; } &&
+ as_run=a "$as_shell" -c "$as_bourne_compatible""$as_required" 2>/dev/null
+then :
+ CONFIG_SHELL=$as_shell as_have_required=yes
+ if as_run=a "$as_shell" -c "$as_bourne_compatible""$as_suggested" 2>/dev/null
+then :
+ break 2
+fi
+fi
+ done;;
+ esac
+ as_found=false
+done
+IFS=$as_save_IFS
+if $as_found
+then :
+
+else $as_nop
+ if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
+ as_run=a "$SHELL" -c "$as_bourne_compatible""$as_required" 2>/dev/null
+then :
+ CONFIG_SHELL=$SHELL as_have_required=yes
+fi
+fi
+
+
+ if test "x$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'.
+printf "%s\n" "$0: could not re-execute with $CONFIG_SHELL" >&2
+exit 255
+fi
+
+ if test x$as_have_required = xno
+then :
+ printf "%s\n" "$0: This script requires a shell more modern than all"
+ printf "%s\n" "$0: the shells that I found on your system."
+ if test ${ZSH_VERSION+y} ; then
+ printf "%s\n" "$0: In particular, zsh $ZSH_VERSION has bugs and should"
+ printf "%s\n" "$0: be upgraded to zsh 4.3.4 or later."
+ else
+ printf "%s\n" "$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_nop
+# ---------
+# Do nothing but, unlike ":", preserve the value of $?.
+as_fn_nop ()
+{
+ return $?
+}
+as_nop=as_fn_nop
+
+# as_fn_mkdir_p
+# -------------
+# Create "$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 $as_dir in #(
+ *\'*) as_qdir=`printf "%s\n" "$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 ||
+printf "%s\n" 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_nop
+ 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 $as_nop
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+# as_fn_nop
+# ---------
+# Do nothing but, unlike ":", preserve the value of $?.
+as_fn_nop ()
+{
+ return $?
+}
+as_nop=as_fn_nop
+
+# 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
+ printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ printf "%s\n" "$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 ||
+printf "%s\n" 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" ||
+ { printf "%s\n" "$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
+}
+
+
+# Determine whether it's possible to make 'echo' print without a newline.
+# These variables are no longer used directly by Autoconf, but are AC_SUBSTed
+# for compatibility with existing Makefiles.
+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
+
+# For backward compatibility with old third-party macros, we provide
+# the shell variables $as_echo and $as_echo_n. New code should use
+# AS_ECHO(["message"]) and AS_ECHO_N(["message"]), respectively.
+as_echo='printf %s\n'
+as_echo_n='printf %s'
+
+
+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='blspR'
+PACKAGE_TARNAME='blspr'
+PACKAGE_VERSION='0.0.1'
+PACKAGE_STRING='blspR 0.0.1'
+PACKAGE_BUGREPORT=''
+PACKAGE_URL=''
+
+ac_subst_vars='LTLIBOBJS
+LIBOBJS
+GSL_LIBS
+GSL_CFLAGS
+GSL_CONFIG
+target_alias
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+build_alias
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+ECHO_T
+ECHO_N
+ECHO_C
+DEFS
+mandir
+localedir
+libdir
+psdir
+pdfdir
+dvidir
+htmldir
+infodir
+docdir
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+runstatedir
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+sysconfdir
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+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
+'
+ ac_precious_vars='build_alias
+host_alias
+target_alias'
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+
+# Initialize some variables set by options.
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+ac_init_version=false
+ac_unrecognized_opts=
+ac_unrecognized_sep=
+# The variables have the same names as the options, with
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+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'
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+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.
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+ ac_prev=
+ continue
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+
+ case $ac_option in
+ *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+ *=) ac_optarg= ;;
+ *) ac_optarg=yes ;;
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+ case $ac_dashdash$ac_option in
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+ ac_dashdash=yes ;;
+
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+ 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 \
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+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
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+ cache_file=$ac_optarg ;;
+
+ --config-cache | -C)
+ cache_file=config.cache ;;
+
+ -datadir | --datadir | --datadi | --datad)
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+ datadir=$ac_optarg ;;
+
+ -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \
+ | --dataroo | --dataro | --datar)
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+ datarootdir=$ac_optarg ;;
+
+ -disable-* | --disable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
+ # Reject names that are not valid shell variable names.
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+ as_fn_error $? "invalid feature name: \`$ac_useropt'"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=no ;;
+
+ -docdir | --docdir | --docdi | --doc | --do)
+ ac_prev=docdir ;;
+ -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*)
+ docdir=$ac_optarg ;;
+
+ -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv)
+ ac_prev=dvidir ;;
+ -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*)
+ dvidir=$ac_optarg ;;
+
+ -enable-* | --enable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
+ # 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=$ac_useropt
+ ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=\$ac_optarg ;;
+
+ -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
+ | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
+ | --exec | --exe | --ex)
+ ac_prev=exec_prefix ;;
+ -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \
+ | --exec-pref=* | --exec-pre=* | --exec-pr=* | --exec-p=* | --exec-=* \
+ | --exec=* | --exe=* | --ex=*)
+ exec_prefix=$ac_optarg ;;
+
+ -gas | --gas | --ga | --g)
+ # Obsolete; use --with-gas.
+ with_gas=yes ;;
+
+ -help | --help | --hel | --he | -h)
+ ac_init_help=long ;;
+ -help=r* | --help=r* | --hel=r* | --he=r* | -hr*)
+ ac_init_help=recursive ;;
+ -help=s* | --help=s* | --hel=s* | --he=s* | -hs*)
+ ac_init_help=short ;;
+
+ -host | --host | --hos | --ho)
+ ac_prev=host_alias ;;
+ -host=* | --host=* | --hos=* | --ho=*)
+ host_alias=$ac_optarg ;;
+
+ -htmldir | --htmldir | --htmldi | --htmld | --html | --htm | --ht)
+ ac_prev=htmldir ;;
+ -htmldir=* | --htmldir=* | --htmldi=* | --htmld=* | --html=* | --htm=* \
+ | --ht=*)
+ htmldir=$ac_optarg ;;
+
+ -includedir | --includedir | --includedi | --included | --include \
+ | --includ | --inclu | --incl | --inc)
+ ac_prev=includedir ;;
+ -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \
+ | --includ=* | --inclu=* | --incl=* | --inc=*)
+ includedir=$ac_optarg ;;
+
+ -infodir | --infodir | --infodi | --infod | --info | --inf)
+ ac_prev=infodir ;;
+ -infodir=* | --infodir=* | --infodi=* | --infod=* | --info=* | --inf=*)
+ infodir=$ac_optarg ;;
+
+ -libdir | --libdir | --libdi | --libd)
+ ac_prev=libdir ;;
+ -libdir=* | --libdir=* | --libdi=* | --libd=*)
+ libdir=$ac_optarg ;;
+
+ -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \
+ | --libexe | --libex | --libe)
+ ac_prev=libexecdir ;;
+ -libexecdir=* | --libexecdir=* | --libexecdi=* | --libexecd=* | --libexec=* \
+ | --libexe=* | --libex=* | --libe=*)
+ libexecdir=$ac_optarg ;;
+
+ -localedir | --localedir | --localedi | --localed | --locale)
+ ac_prev=localedir ;;
+ -localedir=* | --localedir=* | --localedi=* | --localed=* | --locale=*)
+ localedir=$ac_optarg ;;
+
+ -localstatedir | --localstatedir | --localstatedi | --localstated \
+ | --localstate | --localstat | --localsta | --localst | --locals)
+ ac_prev=localstatedir ;;
+ -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \
+ | --localstate=* | --localstat=* | --localsta=* | --localst=* | --locals=*)
+ localstatedir=$ac_optarg ;;
+
+ -mandir | --mandir | --mandi | --mand | --man | --ma | --m)
+ ac_prev=mandir ;;
+ -mandir=* | --mandir=* | --mandi=* | --mand=* | --man=* | --ma=* | --m=*)
+ mandir=$ac_optarg ;;
+
+ -nfp | --nfp | --nf)
+ # Obsolete; use --without-fp.
+ with_fp=no ;;
+
+ -no-create | --no-create | --no-creat | --no-crea | --no-cre \
+ | --no-cr | --no-c | -n)
+ no_create=yes ;;
+
+ -no-recursion | --no-recursion | --no-recursio | --no-recursi \
+ | --no-recurs | --no-recur | --no-recu | --no-rec | --no-re | --no-r)
+ no_recursion=yes ;;
+
+ -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \
+ | --oldinclude | --oldinclud | --oldinclu | --oldincl | --oldinc \
+ | --oldin | --oldi | --old | --ol | --o)
+ ac_prev=oldincludedir ;;
+ -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \
+ | --oldinclude=* | --oldinclud=* | --oldinclu=* | --oldincl=* | --oldinc=* \
+ | --oldin=* | --oldi=* | --old=* | --ol=* | --o=*)
+ oldincludedir=$ac_optarg ;;
+
+ -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
+ ac_prev=prefix ;;
+ -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
+ prefix=$ac_optarg ;;
+
+ -program-prefix | --program-prefix | --program-prefi | --program-pref \
+ | --program-pre | --program-pr | --program-p)
+ ac_prev=program_prefix ;;
+ -program-prefix=* | --program-prefix=* | --program-prefi=* \
+ | --program-pref=* | --program-pre=* | --program-pr=* | --program-p=*)
+ program_prefix=$ac_optarg ;;
+
+ -program-suffix | --program-suffix | --program-suffi | --program-suff \
+ | --program-suf | --program-su | --program-s)
+ ac_prev=program_suffix ;;
+ -program-suffix=* | --program-suffix=* | --program-suffi=* \
+ | --program-suff=* | --program-suf=* | --program-su=* | --program-s=*)
+ program_suffix=$ac_optarg ;;
+
+ -program-transform-name | --program-transform-name \
+ | --program-transform-nam | --program-transform-na \
+ | --program-transform-n | --program-transform- \
+ | --program-transform | --program-transfor \
+ | --program-transfo | --program-transf \
+ | --program-trans | --program-tran \
+ | --progr-tra | --program-tr | --program-t)
+ ac_prev=program_transform_name ;;
+ -program-transform-name=* | --program-transform-name=* \
+ | --program-transform-nam=* | --program-transform-na=* \
+ | --program-transform-n=* | --program-transform-=* \
+ | --program-transform=* | --program-transfor=* \
+ | --program-transfo=* | --program-transf=* \
+ | --program-trans=* | --program-tran=* \
+ | --progr-tra=* | --program-tr=* | --program-t=*)
+ program_transform_name=$ac_optarg ;;
+
+ -pdfdir | --pdfdir | --pdfdi | --pdfd | --pdf | --pd)
+ ac_prev=pdfdir ;;
+ -pdfdir=* | --pdfdir=* | --pdfdi=* | --pdfd=* | --pdf=* | --pd=*)
+ pdfdir=$ac_optarg ;;
+
+ -psdir | --psdir | --psdi | --psd | --ps)
+ ac_prev=psdir ;;
+ -psdir=* | --psdir=* | --psdi=* | --psd=* | --ps=*)
+ psdir=$ac_optarg ;;
+
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ silent=yes ;;
+
+ -runstatedir | --runstatedir | --runstatedi | --runstated \
+ | --runstate | --runstat | --runsta | --runst | --runs \
+ | --run | --ru | --r)
+ ac_prev=runstatedir ;;
+ -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
+ | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \
+ | --run=* | --ru=* | --r=*)
+ runstatedir=$ac_optarg ;;
+
+ -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
+ ac_prev=sbindir ;;
+ -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
+ | --sbi=* | --sb=*)
+ sbindir=$ac_optarg ;;
+
+ -sharedstatedir | --sharedstatedir | --sharedstatedi \
+ | --sharedstated | --sharedstate | --sharedstat | --sharedsta \
+ | --sharedst | --shareds | --shared | --share | --shar \
+ | --sha | --sh)
+ ac_prev=sharedstatedir ;;
+ -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \
+ | --sharedstated=* | --sharedstate=* | --sharedstat=* | --sharedsta=* \
+ | --sharedst=* | --shareds=* | --shared=* | --share=* | --shar=* \
+ | --sha=* | --sh=*)
+ sharedstatedir=$ac_optarg ;;
+
+ -site | --site | --sit)
+ ac_prev=site ;;
+ -site=* | --site=* | --sit=*)
+ site=$ac_optarg ;;
+
+ -srcdir | --srcdir | --srcdi | --srcd | --src | --sr)
+ ac_prev=srcdir ;;
+ -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*)
+ srcdir=$ac_optarg ;;
+
+ -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \
+ | --syscon | --sysco | --sysc | --sys | --sy)
+ ac_prev=sysconfdir ;;
+ -sysconfdir=* | --sysconfdir=* | --sysconfdi=* | --sysconfd=* | --sysconf=* \
+ | --syscon=* | --sysco=* | --sysc=* | --sys=* | --sy=*)
+ sysconfdir=$ac_optarg ;;
+
+ -target | --target | --targe | --targ | --tar | --ta | --t)
+ ac_prev=target_alias ;;
+ -target=* | --target=* | --targe=* | --targ=* | --tar=* | --ta=* | --t=*)
+ target_alias=$ac_optarg ;;
+
+ -v | -verbose | --verbose | --verbos | --verbo | --verb)
+ verbose=yes ;;
+
+ -version | --version | --versio | --versi | --vers | -V)
+ ac_init_version=: ;;
+
+ -with-* | --with-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid package name: \`$ac_useropt'"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
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+"with_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--with-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval with_$ac_useropt=\$ac_optarg ;;
+
+ -without-* | --without-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid package name: \`$ac_useropt'"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"with_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--without-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval with_$ac_useropt=no ;;
+
+ --x)
+ # Obsolete; use --with-x.
+ with_x=yes ;;
+
+ -x-includes | --x-includes | --x-include | --x-includ | --x-inclu \
+ | --x-incl | --x-inc | --x-in | --x-i)
+ ac_prev=x_includes ;;
+ -x-includes=* | --x-includes=* | --x-include=* | --x-includ=* | --x-inclu=* \
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+ x_includes=$ac_optarg ;;
+
+ -x-libraries | --x-libraries | --x-librarie | --x-librari \
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+ ac_prev=x_libraries ;;
+ -x-libraries=* | --x-libraries=* | --x-librarie=* | --x-librari=* \
+ | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
+ x_libraries=$ac_optarg ;;
+
+ -*) as_fn_error $? "unrecognized option: \`$ac_option'
+Try \`$0 --help' for more information"
+ ;;
+
+ *=*)
+ ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
+ # Reject names that are not valid shell variable names.
+ case $ac_envvar in #(
+ '' | [0-9]* | *[!_$as_cr_alnum]* )
+ as_fn_error $? "invalid variable name: \`$ac_envvar'" ;;
+ esac
+ eval $ac_envvar=\$ac_optarg
+ export $ac_envvar ;;
+
+ *)
+ # FIXME: should be removed in autoconf 3.0.
+ printf "%s\n" "$as_me: WARNING: you should use --build, --host, --target" >&2
+ expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null &&
+ printf "%s\n" "$as_me: WARNING: invalid host type: $ac_option" >&2
+ : "${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}"
+ ;;
+
+ esac
+done
+
+if test -n "$ac_prev"; then
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+ as_fn_error $? "missing argument to $ac_option"
+fi
+
+if test -n "$ac_unrecognized_opts"; then
+ case $enable_option_checking in
+ no) ;;
+ fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;;
+ *) printf "%s\n" "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;;
+ esac
+fi
+
+# Check all directory arguments for consistency.
+for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \
+ datadir sysconfdir sharedstatedir localstatedir includedir \
+ oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
+ libdir localedir mandir runstatedir
+do
+ eval ac_val=\$$ac_var
+ # Remove trailing slashes.
+ case $ac_val in
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+ ac_val=`expr "X$ac_val" : 'X\(.*[^/]\)' \| "X$ac_val" : 'X\(.*\)'`
+ eval $ac_var=\$ac_val;;
+ esac
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+ case $ac_val in
+ [\\/$]* | ?:[\\/]* ) continue;;
+ NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
+ esac
+ as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val"
+done
+
+# There might be people who depend on the old broken behavior: `$host'
+# used to hold the argument of --host etc.
+# FIXME: To remove some day.
+build=$build_alias
+host=$host_alias
+target=$target_alias
+
+# FIXME: To remove some day.
+if test "x$host_alias" != x; then
+ if test "x$build_alias" = x; then
+ cross_compiling=maybe
+ elif test "x$build_alias" != "x$host_alias"; then
+ cross_compiling=yes
+ fi
+fi
+
+ac_tool_prefix=
+test -n "$host_alias" && ac_tool_prefix=$host_alias-
+
+test "$silent" = yes && exec 6>/dev/null
+
+
+ac_pwd=`pwd` && test -n "$ac_pwd" &&
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+test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
+ as_fn_error $? "pwd does not report name of working directory"
+
+
+# Find the source files, if location was not specified.
+if test -z "$srcdir"; then
+ ac_srcdir_defaulted=yes
+ # Try the directory containing this script, then the parent directory.
+ ac_confdir=`$as_dirname -- "$as_myself" ||
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+ q
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+ /^X\(\/\/\)[^/].*/{
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+ /^X\(\/\/\)$/{
+ s//\1/
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+ /^X\(\/\).*/{
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+ s/.*/./; q'`
+ srcdir=$ac_confdir
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+fi
+if test ! -r "$srcdir/$ac_unique_file"; then
+ test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
+ as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir"
+fi
+ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
+ac_abs_confdir=`(
+ cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg"
+ pwd)`
+# When building in place, set srcdir=.
+if test "$ac_abs_confdir" = "$ac_pwd"; then
+ srcdir=.
+fi
+# Remove unnecessary trailing slashes from srcdir.
+# Double slashes in file names in object file debugging info
+# mess up M-x gdb in Emacs.
+case $srcdir in
+*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;;
+esac
+for ac_var in $ac_precious_vars; do
+ eval ac_env_${ac_var}_set=\${${ac_var}+set}
+ eval ac_env_${ac_var}_value=\$${ac_var}
+ eval ac_cv_env_${ac_var}_set=\${${ac_var}+set}
+ eval ac_cv_env_${ac_var}_value=\$${ac_var}
+done
+
+#
+# Report the --help message.
+#
+if test "$ac_init_help" = "long"; then
+ # Omit some internal or obsolete options to make the list less imposing.
+ # This message is too long to be a string in the A/UX 3.1 sh.
+ cat <<_ACEOF
+\`configure' configures blspR 0.0.1 to adapt to many kinds of systems.
+
+Usage: $0 [OPTION]... [VAR=VALUE]...
+
+To assign environment variables (e.g., CC, CFLAGS...), specify them as
+VAR=VALUE. See below for descriptions of some of the useful variables.
+
+Defaults for the options are specified in brackets.
+
+Configuration:
+ -h, --help display this help and exit
+ --help=short display options specific to this package
+ --help=recursive display the short help of all the included packages
+ -V, --version display version information and exit
+ -q, --quiet, --silent do not print \`checking ...' messages
+ --cache-file=FILE cache test results in FILE [disabled]
+ -C, --config-cache alias for \`--cache-file=config.cache'
+ -n, --no-create do not create output files
+ --srcdir=DIR find the sources in DIR [configure dir or \`..']
+
+Installation directories:
+ --prefix=PREFIX install architecture-independent files in PREFIX
+ [$ac_default_prefix]
+ --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX
+ [PREFIX]
+
+By default, \`make install' will install all the files in
+\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify
+an installation prefix other than \`$ac_default_prefix' using \`--prefix',
+for instance \`--prefix=\$HOME'.
+
+For better control, use the options below.
+
+Fine tuning of the installation directories:
+ --bindir=DIR user executables [EPREFIX/bin]
+ --sbindir=DIR system admin executables [EPREFIX/sbin]
+ --libexecdir=DIR program executables [EPREFIX/libexec]
+ --sysconfdir=DIR read-only single-machine data [PREFIX/etc]
+ --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
+ --localstatedir=DIR modifiable single-machine data [PREFIX/var]
+ --runstatedir=DIR modifiable per-process data [LOCALSTATEDIR/run]
+ --libdir=DIR object code libraries [EPREFIX/lib]
+ --includedir=DIR C header files [PREFIX/include]
+ --oldincludedir=DIR C header files for non-gcc [/usr/include]
+ --datarootdir=DIR read-only arch.-independent data root [PREFIX/share]
+ --datadir=DIR read-only architecture-independent data [DATAROOTDIR]
+ --infodir=DIR info documentation [DATAROOTDIR/info]
+ --localedir=DIR locale-dependent data [DATAROOTDIR/locale]
+ --mandir=DIR man documentation [DATAROOTDIR/man]
+ --docdir=DIR documentation root [DATAROOTDIR/doc/blspr]
+ --htmldir=DIR html documentation [DOCDIR]
+ --dvidir=DIR dvi documentation [DOCDIR]
+ --pdfdir=DIR pdf documentation [DOCDIR]
+ --psdir=DIR ps documentation [DOCDIR]
+_ACEOF
+
+ cat <<\_ACEOF
+_ACEOF
+fi
+
+if test -n "$ac_init_help"; then
+ case $ac_init_help in
+ short | recursive ) echo "Configuration of blspR 0.0.1:";;
+ esac
+ cat <<\_ACEOF
+
+Report bugs to the package provider.
+_ACEOF
+ac_status=$?
+fi
+
+if test "$ac_init_help" = "recursive"; then
+ # If there are subdirs, report their specific --help.
+ for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
+ test -d "$ac_dir" ||
+ { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } ||
+ continue
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`printf "%s\n" "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`printf "%s\n" "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+ cd "$ac_dir" || { ac_status=$?; continue; }
+ # Check for configure.gnu first; this name is used for a wrapper for
+ # Metaconfig's "Configure" on case-insensitive file systems.
+ if test -f "$ac_srcdir/configure.gnu"; then
+ echo &&
+ $SHELL "$ac_srcdir/configure.gnu" --help=recursive
+ elif test -f "$ac_srcdir/configure"; then
+ echo &&
+ $SHELL "$ac_srcdir/configure" --help=recursive
+ else
+ printf "%s\n" "$as_me: WARNING: no configuration information is in $ac_dir" >&2
+ fi || ac_status=$?
+ cd "$ac_pwd" || { ac_status=$?; break; }
+ done
+fi
+
+test -n "$ac_init_help" && exit $ac_status
+if $ac_init_version; then
+ cat <<\_ACEOF
+blspR configure 0.0.1
+generated by GNU Autoconf 2.71
+
+Copyright (C) 2021 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
+_ACEOF
+ exit
+fi
+
+## ------------------------ ##
+## Autoconf initialization. ##
+## ------------------------ ##
+ac_configure_args_raw=
+for ac_arg
+do
+ case $ac_arg in
+ *\'*)
+ ac_arg=`printf "%s\n" "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ as_fn_append ac_configure_args_raw " '$ac_arg'"
+done
+
+case $ac_configure_args_raw in
+ *$as_nl*)
+ ac_safe_unquote= ;;
+ *)
+ ac_unsafe_z='|&;<>()$`\\"*?[ '' ' # This string ends in space, tab.
+ ac_unsafe_a="$ac_unsafe_z#~"
+ ac_safe_unquote="s/ '\\([^$ac_unsafe_a][^$ac_unsafe_z]*\\)'/ \\1/g"
+ ac_configure_args_raw=` printf "%s\n" "$ac_configure_args_raw" | sed "$ac_safe_unquote"`;;
+esac
+
+cat >config.log <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by blspR $as_me 0.0.1, which was
+generated by GNU Autoconf 2.71. Invocation command line was
+
+ $ $0$ac_configure_args_raw
+
+_ACEOF
+exec 5>>config.log
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown`
+
+/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
+/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown`
+/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
+/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
+
+_ASUNAME
+
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ case $as_dir in #(((
+ '') as_dir=./ ;;
+ */) ;;
+ *) as_dir=$as_dir/ ;;
+ esac
+ printf "%s\n" "PATH: $as_dir"
+ done
+IFS=$as_save_IFS
+
+} >&5
+
+cat >&5 <<_ACEOF
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+_ACEOF
+
+
+# Keep a trace of the command line.
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Strip out --silent because we don't want to record it for future runs.
+# Also quote any args containing shell meta-characters.
+# Make two passes to allow for proper duplicate-argument suppression.
+ac_configure_args=
+ac_configure_args0=
+ac_configure_args1=
+ac_must_keep_next=false
+for ac_pass in 1 2
+do
+ for ac_arg
+ do
+ case $ac_arg in
+ -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ continue ;;
+ *\'*)
+ ac_arg=`printf "%s\n" "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ case $ac_pass in
+ 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
+ 2)
+ as_fn_append ac_configure_args1 " '$ac_arg'"
+ if test $ac_must_keep_next = true; then
+ ac_must_keep_next=false # Got value, back to normal.
+ else
+ case $ac_arg in
+ *=* | --config-cache | -C | -disable-* | --disable-* \
+ | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
+ | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
+ | -with-* | --with-* | -without-* | --without-* | --x)
+ case "$ac_configure_args0 " in
+ "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
+ esac
+ ;;
+ -* ) ac_must_keep_next=true ;;
+ esac
+ fi
+ as_fn_append ac_configure_args " '$ac_arg'"
+ ;;
+ esac
+ done
+done
+{ ac_configure_args0=; unset ac_configure_args0;}
+{ ac_configure_args1=; unset ac_configure_args1;}
+
+# When interrupted or exit'd, cleanup temporary files, and complete
+# config.log. We remove comments because anyway the quotes in there
+# would cause problems or look ugly.
+# WARNING: Use '\'' to represent an apostrophe within the trap.
+# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
+trap 'exit_status=$?
+ # Sanitize IFS.
+ IFS=" "" $as_nl"
+ # Save into config.log some information that might help in debugging.
+ {
+ echo
+
+ printf "%s\n" "## ---------------- ##
+## Cache variables. ##
+## ---------------- ##"
+ echo
+ # The following way of writing the cache mishandles newlines in values,
+(
+ for ac_var in `(set) 2>&1 | sed -n '\''s/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'\''`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+printf "%s\n" "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+ (set) 2>&1 |
+ case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ sed -n \
+ "s/'\''/'\''\\\\'\'''\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\''\\2'\''/p"
+ ;; #(
+ *)
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+)
+ echo
+
+ printf "%s\n" "## ----------------- ##
+## Output variables. ##
+## ----------------- ##"
+ echo
+ for ac_var in $ac_subst_vars
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`printf "%s\n" "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ printf "%s\n" "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+
+ if test -n "$ac_subst_files"; then
+ printf "%s\n" "## ------------------- ##
+## File substitutions. ##
+## ------------------- ##"
+ echo
+ for ac_var in $ac_subst_files
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`printf "%s\n" "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ printf "%s\n" "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+ fi
+
+ if test -s confdefs.h; then
+ printf "%s\n" "## ----------- ##
+## confdefs.h. ##
+## ----------- ##"
+ echo
+ cat confdefs.h
+ echo
+ fi
+ test "$ac_signal" != 0 &&
+ printf "%s\n" "$as_me: caught signal $ac_signal"
+ printf "%s\n" "$as_me: exit $exit_status"
+ } >&5
+ rm -f core *.core core.conftest.* &&
+ rm -f -r conftest* confdefs* conf$$* $ac_clean_files &&
+ exit $exit_status
+' 0
+for ac_signal in 1 2 13 15; do
+ trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
+done
+ac_signal=0
+
+# confdefs.h avoids OS command line length limits that DEFS can exceed.
+rm -f -r conftest* confdefs.h
+
+printf "%s\n" "/* confdefs.h */" > confdefs.h
+
+# Predefined preprocessor variables.
+
+printf "%s\n" "#define PACKAGE_NAME \"$PACKAGE_NAME\"" >>confdefs.h
+
+printf "%s\n" "#define PACKAGE_TARNAME \"$PACKAGE_TARNAME\"" >>confdefs.h
+
+printf "%s\n" "#define PACKAGE_VERSION \"$PACKAGE_VERSION\"" >>confdefs.h
+
+printf "%s\n" "#define PACKAGE_STRING \"$PACKAGE_STRING\"" >>confdefs.h
+
+printf "%s\n" "#define PACKAGE_BUGREPORT \"$PACKAGE_BUGREPORT\"" >>confdefs.h
+
+printf "%s\n" "#define PACKAGE_URL \"$PACKAGE_URL\"" >>confdefs.h
+
+
+# Let the site file select an alternate cache file if it wants to.
+# Prefer an explicitly selected file to automatically selected ones.
+if test -n "$CONFIG_SITE"; then
+ ac_site_files="$CONFIG_SITE"
+elif test "x$prefix" != xNONE; then
+ ac_site_files="$prefix/share/config.site $prefix/etc/config.site"
+else
+ ac_site_files="$ac_default_prefix/share/config.site $ac_default_prefix/etc/config.site"
+fi
+
+for ac_site_file in $ac_site_files
+do
+ case $ac_site_file in #(
+ */*) :
+ ;; #(
+ *) :
+ ac_site_file=./$ac_site_file ;;
+esac
+ if test -f "$ac_site_file" && test -r "$ac_site_file"; then
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
+printf "%s\n" "$as_me: loading site script $ac_site_file" >&6;}
+ sed 's/^/| /' "$ac_site_file" >&5
+ . "$ac_site_file" \
+ || { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+printf "%s\n" "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "failed to load site script $ac_site_file
+See \`config.log' for more details" "$LINENO" 5; }
+ fi
+done
+
+if test -r "$cache_file"; then
+ # Some versions of bash will fail to source /dev/null (special files
+ # actually), so we avoid doing that. DJGPP emulates it as a regular file.
+ if test /dev/null != "$cache_file" && test -f "$cache_file"; then
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
+printf "%s\n" "$as_me: loading cache $cache_file" >&6;}
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) . "$cache_file";;
+ *) . "./$cache_file";;
+ esac
+ fi
+else
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
+printf "%s\n" "$as_me: creating cache $cache_file" >&6;}
+ >$cache_file
+fi
+
+# Check that the precious variables saved in the cache have kept the same
+# value.
+ac_cache_corrupted=false
+for ac_var in $ac_precious_vars; do
+ eval ac_old_set=\$ac_cv_env_${ac_var}_set
+ eval ac_new_set=\$ac_env_${ac_var}_set
+ eval ac_old_val=\$ac_cv_env_${ac_var}_value
+ eval ac_new_val=\$ac_env_${ac_var}_value
+ case $ac_old_set,$ac_new_set in
+ set,)
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+printf "%s\n" "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,set)
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5
+printf "%s\n" "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,);;
+ *)
+ if test "x$ac_old_val" != "x$ac_new_val"; then
+ # differences in whitespace do not lead to failure.
+ ac_old_val_w=`echo x $ac_old_val`
+ ac_new_val_w=`echo x $ac_new_val`
+ if test "$ac_old_val_w" != "$ac_new_val_w"; then
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
+printf "%s\n" "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
+ ac_cache_corrupted=:
+ else
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
+printf "%s\n" "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
+ eval $ac_var=\$ac_old_val
+ fi
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
+printf "%s\n" "$as_me: former value: \`$ac_old_val'" >&2;}
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5
+printf "%s\n" "$as_me: current value: \`$ac_new_val'" >&2;}
+ fi;;
+ esac
+ # Pass precious variables to config.status.
+ if test "$ac_new_set" = set; then
+ case $ac_new_val in
+ *\'*) ac_arg=$ac_var=`printf "%s\n" "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+ *) ac_arg=$ac_var=$ac_new_val ;;
+ esac
+ case " $ac_configure_args " in
+ *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
+ *) as_fn_append ac_configure_args " '$ac_arg'" ;;
+ esac
+ fi
+done
+if $ac_cache_corrupted; then
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+printf "%s\n" "$as_me: error: in \`$ac_pwd':" >&2;}
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
+printf "%s\n" "$as_me: error: changes in the environment can compromise the build" >&2;}
+ as_fn_error $? "run \`${MAKE-make} distclean' and/or \`rm $cache_file'
+ and start over" "$LINENO" 5
+fi
+## -------------------- ##
+## Main body of script. ##
+## -------------------- ##
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+## Use gsl-config to find arguments for compiler and linker flags
+##
+## Check for non-standard programs: gsl-config(1)
+# Extract the first word of "gsl-config", so it can be a program name with args.
+set dummy gsl-config; ac_word=$2
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+printf %s "checking for $ac_word... " >&6; }
+if test ${ac_cv_path_GSL_CONFIG+y}
+then :
+ printf %s "(cached) " >&6
+else $as_nop
+ case $GSL_CONFIG in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_GSL_CONFIG="$GSL_CONFIG" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ case $as_dir in #(((
+ '') as_dir=./ ;;
+ */) ;;
+ *) as_dir=$as_dir/ ;;
+ esac
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then
+ ac_cv_path_GSL_CONFIG="$as_dir$ac_word$ac_exec_ext"
+ printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+fi
+GSL_CONFIG=$ac_cv_path_GSL_CONFIG
+if test -n "$GSL_CONFIG"; then
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $GSL_CONFIG" >&5
+printf "%s\n" "$GSL_CONFIG" >&6; }
+else
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5
+printf "%s\n" "no" >&6; }
+fi
+
+
+## If gsl-config was found, let's use it
+if test "${GSL_CONFIG}" != ""; then
+ # Use gsl-config for header and linker arguments
+ GSL_CFLAGS=`${GSL_CONFIG} --cflags`
+ GSL_LIBS=`${GSL_CONFIG} --libs`
+else
+ as_fn_error $? "gsl-config not found, is GSL installed?" "$LINENO" 5
+fi
+
+# Now substitute these variables in src/Makevars.in to create src/Makevars
+
+
+
+ac_config_files="$ac_config_files src/Makevars"
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems. If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, we kill variables containing newlines.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(
+ for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
+printf "%s\n" "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) { eval $ac_var=; unset $ac_var;} ;;
+ esac ;;
+ esac
+ done
+
+ (set) 2>&1 |
+ case $as_nl`(ac_space=' '; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ # `set' does not quote correctly, so add quotes: double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \.
+ sed -n \
+ "s/'/'\\\\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
+ ;; #(
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+) |
+ sed '
+ /^ac_cv_env_/b end
+ t clear
+ :clear
+ s/^\([^=]*\)=\(.*[{}].*\)$/test ${\1+y} || &/
+ t end
+ s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+ :end' >>confcache
+if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
+ if test -w "$cache_file"; then
+ if test "x$cache_file" != "x/dev/null"; then
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
+printf "%s\n" "$as_me: updating cache $cache_file" >&6;}
+ if test ! -f "$cache_file" || test -h "$cache_file"; then
+ cat confcache >"$cache_file"
+ else
+ case $cache_file in #(
+ */* | ?:*)
+ mv -f confcache "$cache_file"$$ &&
+ mv -f "$cache_file"$$ "$cache_file" ;; #(
+ *)
+ mv -f confcache "$cache_file" ;;
+ esac
+ fi
+ fi
+ else
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
+printf "%s\n" "$as_me: not updating unwritable cache $cache_file" >&6;}
+ fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+# Transform confdefs.h into DEFS.
+# Protect against shell expansion while executing Makefile rules.
+# Protect against Makefile macro expansion.
+#
+# If the first sed substitution is executed (which looks for macros that
+# take arguments), then branch to the quote section. Otherwise,
+# look for a macro that doesn't take arguments.
+ac_script='
+:mline
+/\\$/{
+ N
+ s,\\\n,,
+ b mline
+}
+t clear
+:clear
+s/^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\)/-D\1=\2/g
+t quote
+s/^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)/-D\1=\2/g
+t quote
+b any
+:quote
+s/[ `~#$^&*(){}\\|;'\''"<>?]/\\&/g
+s/\[/\\&/g
+s/\]/\\&/g
+s/\$/$$/g
+H
+:any
+${
+ g
+ s/^\n//
+ s/\n/ /g
+ p
+}
+'
+DEFS=`sed -n "$ac_script" confdefs.h`
+
+
+ac_libobjs=
+ac_ltlibobjs=
+U=
+for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
+ # 1. Remove the extension, and $U if already installed.
+ ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
+ ac_i=`printf "%s\n" "$ac_i" | sed "$ac_script"`
+ # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
+ # will be set to the directory where LIBOBJS objects are built.
+ as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
+done
+LIBOBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+
+: "${CONFIG_STATUS=./config.status}"
+ac_write_fail=0
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
+printf "%s\n" "$as_me: creating $CONFIG_STATUS" >&6;}
+as_write_fail=0
+cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+
+SHELL=\${CONFIG_SHELL-$SHELL}
+export SHELL
+_ASEOF
+cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+as_nop=:
+if test ${ZSH_VERSION+y} && (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 $as_nop
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
+fi
+
+
+
+# Reset variables that may have inherited troublesome values from
+# the environment.
+
+# IFS needs to be set, to space, tab, and newline, in precisely that order.
+# (If _AS_PATH_WALK were called with IFS unset, it would have the
+# side effect of setting IFS to empty, thus disabling word splitting.)
+# Quoting is to prevent editors from complaining about space-tab.
+as_nl='
+'
+export as_nl
+IFS=" "" $as_nl"
+
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# Ensure predictable behavior from utilities with locale-dependent output.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# We cannot yet rely on "unset" to work, but we need these variables
+# to be unset--not just set to an empty or harmless value--now, to
+# avoid bugs in old shells (e.g. pre-3.0 UWIN ksh). This construct
+# also avoids known problems related to "unset" and subshell syntax
+# in other old shells (e.g. bash 2.01 and pdksh 5.2.14).
+for as_var in BASH_ENV ENV MAIL MAILPATH CDPATH
+do eval test \${$as_var+y} \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
+done
+
+# Ensure that fds 0, 1, and 2 are open.
+if (exec 3>&0) 2>/dev/null; then :; else exec 0</dev/null; fi
+if (exec 3>&1) 2>/dev/null; then :; else exec 1>/dev/null; fi
+if (exec 3>&2) ; then :; else exec 2>/dev/null; fi
+
+# The user is always right.
+if ${PATH_SEPARATOR+false} :; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+
+# 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
+ case $as_dir in #(((
+ '') as_dir=./ ;;
+ */) ;;
+ *) as_dir=$as_dir/ ;;
+ esac
+ 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
+ printf "%s\n" "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
+fi
+
+
+
+# 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
+ printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ printf "%s\n" "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+
+
+# 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_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+
+# 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_nop
+ 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 $as_nop
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
+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 ||
+printf "%s\n" 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
+
+
+# Determine whether it's possible to make 'echo' print without a newline.
+# These variables are no longer used directly by Autoconf, but are AC_SUBSTed
+# for compatibility with existing Makefiles.
+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
+
+# For backward compatibility with old third-party macros, we provide
+# the shell variables $as_echo and $as_echo_n. New code should use
+# AS_ECHO(["message"]) and AS_ECHO_N(["message"]), respectively.
+as_echo='printf %s\n'
+as_echo_n='printf %s'
+
+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
+
+
+# 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 $as_dir in #(
+ *\'*) as_qdir=`printf "%s\n" "$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 ||
+printf "%s\n" 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 $as_dir"
+
+
+} # as_fn_mkdir_p
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p='mkdir -p "$as_dir"'
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+
+# as_fn_executable_p FILE
+# -----------------------
+# Test if FILE is an executable regular file.
+as_fn_executable_p ()
+{
+ test -f "$1" && test -x "$1"
+} # as_fn_executable_p
+as_test_x='test -x'
+as_executable_p=as_fn_executable_p
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$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'"
+
+
+exec 6>&1
+## ----------------------------------- ##
+## Main body of $CONFIG_STATUS script. ##
+## ----------------------------------- ##
+_ASEOF
+test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# Save the log message, to keep $0 and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling.
+ac_log="
+This file was extended by blspR $as_me 0.0.1, which was
+generated by GNU Autoconf 2.71. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+_ACEOF
+
+case $ac_config_files in *"
+"*) set x $ac_config_files; shift; ac_config_files=$*;;
+esac
+
+
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+# Files that config.status was made for.
+config_files="$ac_config_files"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ac_cs_usage="\
+\`$as_me' instantiates files and other configuration actions
+from templates according to the current configuration. Unless the files
+and actions are specified as TAGs, all are instantiated by default.
+
+Usage: $0 [OPTION]... [TAG]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number and configuration settings, then exit
+ --config print configuration, then exit
+ -q, --quiet, --silent
+ do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+
+Configuration files:
+$config_files
+
+Report bugs to the package provider."
+
+_ACEOF
+ac_cs_config=`printf "%s\n" "$ac_configure_args" | sed "$ac_safe_unquote"`
+ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\''/g"`
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_config='$ac_cs_config_escaped'
+ac_cs_version="\\
+blspR config.status 0.0.1
+configured by $0, generated by GNU Autoconf 2.71,
+ with options \\"\$ac_cs_config\\"
+
+Copyright (C) 2021 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+
+ac_pwd='$ac_pwd'
+srcdir='$srcdir'
+test -n "\$AWK" || AWK=awk
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# The default lists apply if the user does not specify any file.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=?*)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ --*=)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=
+ ac_shift=:
+ ;;
+ *)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
+ printf "%s\n" "$ac_cs_version"; exit ;;
+ --config | --confi | --conf | --con | --co | --c )
+ printf "%s\n" "$ac_cs_config"; exit ;;
+ --debug | --debu | --deb | --de | --d | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`printf "%s\n" "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ '') as_fn_error $? "missing file argument" ;;
+ esac
+ as_fn_append CONFIG_FILES " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --he | --h | --help | --hel | -h )
+ printf "%s\n" "$ac_cs_usage"; exit ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) as_fn_error $? "unrecognized option: \`$1'
+Try \`$0 --help' for more information." ;;
+
+ *) as_fn_append ac_config_targets " $1"
+ ac_need_defaults=false ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+if \$ac_cs_recheck; then
+ set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ shift
+ \printf "%s\n" "running CONFIG_SHELL=$SHELL \$*" >&6
+ CONFIG_SHELL='$SHELL'
+ export CONFIG_SHELL
+ exec "\$@"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
+## Running $as_me. ##
+_ASBOX
+ printf "%s\n" "$ac_log"
+} >&5
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+
+# Handling of arguments.
+for ac_config_target in $ac_config_targets
+do
+ case $ac_config_target in
+ "src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;;
+
+ *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
+ esac
+done
+
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test ${CONFIG_FILES+y} || CONFIG_FILES=$config_files
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason against having it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Hook for its removal unless debugging.
+# Note that there is a small window in which the directory will not be cleaned:
+# after its creation but before its name has been assigned to `$tmp'.
+$debug ||
+{
+ tmp= ac_tmp=
+ trap 'exit_status=$?
+ : "${ac_tmp:=$tmp}"
+ { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
+' 0
+ trap 'as_fn_exit 1' 1 2 13 15
+}
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
+ test -d "$tmp"
+} ||
+{
+ tmp=./conf$$-$RANDOM
+ (umask 077 && mkdir "$tmp")
+} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
+ac_tmp=$tmp
+
+# Set up the scripts for CONFIG_FILES section.
+# No need to generate them if there are no CONFIG_FILES.
+# This happens for instance with `./config.status config.h'.
+if test -n "$CONFIG_FILES"; then
+
+
+ac_cr=`echo X | tr X '\015'`
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
+# But we know of no other shell where ac_cr would be empty at this
+# point, so we can use a bashism as a fallback.
+if test "x$ac_cr" = x; then
+ eval ac_cr=\$\'\\r\'
+fi
+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
+ ac_cs_awk_cr='\\r'
+else
+ ac_cs_awk_cr=$ac_cr
+fi
+
+echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
+_ACEOF
+
+
+{
+ echo "cat >conf$$subs.awk <<_ACEOF" &&
+ echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
+ echo "_ACEOF"
+} >conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+ . ./conf$$subs.sh ||
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+
+ ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
+ if test $ac_delim_n = $ac_delim_num; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+rm -f conf$$subs.sh
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK &&
+_ACEOF
+sed -n '
+h
+s/^/S["/; s/!.*/"]=/
+p
+g
+s/^[^!]*!//
+:repl
+t repl
+s/'"$ac_delim"'$//
+t delim
+:nl
+h
+s/\(.\{148\}\)..*/\1/
+t more1
+s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
+p
+n
+b repl
+:more1
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t nl
+:delim
+h
+s/\(.\{148\}\)..*/\1/
+t more2
+s/["\\]/\\&/g; s/^/"/; s/$/"/
+p
+b
+:more2
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t delim
+' <conf$$subs.awk | sed '
+/^[^""]/{
+ N
+ s/\n//
+}
+' >>$CONFIG_STATUS || ac_write_fail=1
+rm -f conf$$subs.awk
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+_ACAWK
+cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
+ for (key in S) S_is_set[key] = 1
+ FS = ""
+
+}
+{
+ line = $ 0
+ nfields = split(line, field, "@")
+ substed = 0
+ len = length(field[1])
+ for (i = 2; i < nfields; i++) {
+ key = field[i]
+ keylen = length(key)
+ if (S_is_set[key]) {
+ value = S[key]
+ line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
+ len += length(value) + length(field[++i])
+ substed = 1
+ } else
+ len += 1 + keylen
+ }
+
+ print line
+}
+
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
+ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
+else
+ cat
+fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
+ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5
+_ACEOF
+
+# VPATH may cause trouble with some makes, so we remove sole $(srcdir),
+# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{
+h
+s///
+s/^/:/
+s/[ ]*$/:/
+s/:\$(srcdir):/:/g
+s/:\${srcdir}:/:/g
+s/:@srcdir@:/:/g
+s/^:*//
+s/:*$//
+x
+s/\(=[ ]*\).*/\1/
+G
+s/\n//
+s/^[^=]*=[ ]*$//
+}'
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+fi # test -n "$CONFIG_FILES"
+
+
+eval set X " :F $CONFIG_FILES "
+shift
+for ac_tag
+do
+ case $ac_tag in
+ :[FHLC]) ac_mode=$ac_tag; continue;;
+ esac
+ case $ac_mode$ac_tag in
+ :[FHL]*:*);;
+ :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;;
+ :[FH]-) ac_tag=-:-;;
+ :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
+ esac
+ ac_save_IFS=$IFS
+ IFS=:
+ set x $ac_tag
+ IFS=$ac_save_IFS
+ shift
+ ac_file=$1
+ shift
+
+ case $ac_mode in
+ :L) ac_source=$1;;
+ :[FH])
+ ac_file_inputs=
+ for ac_f
+ do
+ case $ac_f in
+ -) ac_f="$ac_tmp/stdin";;
+ *) # Look for the file first in the build tree, then in the source tree
+ # (if the path is not absolute). The absolute path cannot be DOS-style,
+ # because $ac_f cannot contain `:'.
+ test -f "$ac_f" ||
+ case $ac_f in
+ [\\/$]*) false;;
+ *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
+ esac ||
+ as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;;
+ esac
+ case $ac_f in *\'*) ac_f=`printf "%s\n" "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
+ as_fn_append ac_file_inputs " '$ac_f'"
+ done
+
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ configure_input='Generated from '`
+ printf "%s\n" "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
+ `' by configure.'
+ if test x"$ac_file" != x-; then
+ configure_input="$ac_file. $configure_input"
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
+printf "%s\n" "$as_me: creating $ac_file" >&6;}
+ fi
+ # Neutralize special characters interpreted by sed in replacement strings.
+ case $configure_input in #(
+ *\&* | *\|* | *\\* )
+ ac_sed_conf_input=`printf "%s\n" "$configure_input" |
+ sed 's/[\\\\&|]/\\\\&/g'`;; #(
+ *) ac_sed_conf_input=$configure_input;;
+ esac
+
+ case $ac_tag in
+ *:-:* | *:-) cat >"$ac_tmp/stdin" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;;
+ esac
+ ;;
+ esac
+
+ ac_dir=`$as_dirname -- "$ac_file" ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
+printf "%s\n" X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ as_dir="$ac_dir"; as_fn_mkdir_p
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`printf "%s\n" "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
+ ac_top_builddir_sub=`printf "%s\n" "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+
+ case $ac_mode in
+ :F)
+ #
+ # CONFIG_FILE
+ #
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# If the template does not know about datarootdir, expand it.
+# FIXME: This hack should be removed a few years after 2.60.
+ac_datarootdir_hack=; ac_datarootdir_seen=
+ac_sed_dataroot='
+/datarootdir/ {
+ p
+ q
+}
+/@datadir@/p
+/@docdir@/p
+/@infodir@/p
+/@localedir@/p
+/@mandir@/p'
+case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
+*datarootdir*) ac_datarootdir_seen=yes;;
+*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+printf "%s\n" "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ ac_datarootdir_hack='
+ s&@datadir@&$datadir&g
+ s&@docdir@&$docdir&g
+ s&@infodir@&$infodir&g
+ s&@localedir@&$localedir&g
+ s&@mandir@&$mandir&g
+ s&\\\${datarootdir}&$datarootdir&g' ;;
+esac
+_ACEOF
+
+# Neutralize VPATH when `$srcdir' = `.'.
+# Shell code in configure.ac might set extrasub.
+# FIXME: do we really want to maintain this feature?
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_sed_extra="$ac_vpsub
+$extrasub
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s|@configure_input@|$ac_sed_conf_input|;t t
+s&@top_builddir@&$ac_top_builddir_sub&;t t
+s&@top_build_prefix@&$ac_top_build_prefix&;t t
+s&@srcdir@&$ac_srcdir&;t t
+s&@abs_srcdir@&$ac_abs_srcdir&;t t
+s&@top_srcdir@&$ac_top_srcdir&;t t
+s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
+s&@builddir@&$ac_builddir&;t t
+s&@abs_builddir@&$ac_abs_builddir&;t t
+s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
+$ac_datarootdir_hack
+"
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \
+ >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+
+test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
+ { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } &&
+ { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \
+ "$ac_tmp/out"`; test -z "$ac_out"; } &&
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&5
+printf "%s\n" "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+which seems to be undefined. Please make sure it is defined" >&2;}
+
+ rm -f "$ac_tmp/stdin"
+ case $ac_file in
+ -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";;
+ *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";;
+ esac \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ ;;
+
+
+
+ esac
+
+done # for ac_tag
+
+
+as_fn_exit 0
+_ACEOF
+ac_clean_files=$ac_clean_files_save
+
+test $ac_write_fail = 0 ||
+ as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded. So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status. When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+ ac_cs_success=:
+ ac_config_status_args=
+ test "$silent" = yes &&
+ ac_config_status_args="$ac_config_status_args --quiet"
+ exec 5>/dev/null
+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+ exec 5>>config.log
+ # Use ||, not &&, to avoid exiting from the if with $? = 1, which
+ # would make configure fail if this is the last instruction.
+ $ac_cs_success || as_fn_exit 1
+fi
+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+printf "%s\n" "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
+fi
+
+
A r/configure.ac => r/configure.ac +21 -0
@@ 0,0 1,21 @@
+AC_INIT([blspR], [0.0.1])
+
+## Use gsl-config to find arguments for compiler and linker flags
+##
+## Check for non-standard programs: gsl-config(1)
+AC_PATH_PROG([GSL_CONFIG], [gsl-config])
+## If gsl-config was found, let's use it
+if test "${GSL_CONFIG}" != ""; then
+ # Use gsl-config for header and linker arguments
+ GSL_CFLAGS=`${GSL_CONFIG} --cflags`
+ GSL_LIBS=`${GSL_CONFIG} --libs`
+else
+ AC_MSG_ERROR([gsl-config not found, is GSL installed?])
+fi
+
+# Now substitute these variables in src/Makevars.in to create src/Makevars
+AC_SUBST(GSL_CFLAGS)
+AC_SUBST(GSL_LIBS)
+
+AC_CONFIG_FILES([src/Makevars])
+AC_OUTPUT
A r/src/.gitignore => r/src/.gitignore +3 -0
@@ 0,0 1,3 @@
+*.o
+*.so
+*.dll
A r/src/Makevars.in => r/src/Makevars.in +14 -0
@@ 0,0 1,14 @@
+# set by configure
+GSL_CFLAGS = @GSL_CFLAGS@
+GSL_LIBS = @GSL_LIBS@
+
+# combine with standard arguments for R
+PKG_CPPFLAGS = $(GSL_CFLAGS) #-I../inst/c
+PKG_LIBS = $(GSL_LIBS)
+
+#OBJECTS =$(SOURCES_CPP:.cpp=.o) $(SOURCES_C:.c=.o)
+SOURCES=$(wildcard ../../src/**/*.c ../../src/*.c ./*.c)
+OBJECTS=$(patsubst %.c, %.o, $(SOURCES)) # list *.c -> *.o
+
+
+#all : $(SHLIB)
A r/src/blsp_r.c => r/src/blsp_r.c +57 -0
@@ 0,0 1,57 @@
+#include <R.h>
+#include <Rdefines.h>
+#include <Rinternals.h>
+
+
+#include "../../src/blsp.h"
+#include "../../src/blsp_data.h"
+#include "../../src/sampler.h"
+
+SEXP generate_data(SEXP data_vector, SEXP doy_vector, SEXP year_idx_vector) {
+
+
+ int n_obs = length(data_vector);
+ int n_years = length(year_idx_vector);
+
+
+ double *data_vec = REAL(data_vector);
+ double *doy_vec = REAL(doy_vector);
+ int *year_idx_vec = INTEGER(year_idx_vector);
+
+ SEXP theta_matrix;
+ PROTECT(theta_matrix = Rf_allocMatrix(REALSXP, n_years, 7));
+
+ BLSP_Data_t *BLSP_Data = BLSP_Data_alloc(n_years, n_obs);
+
+ gsl_vector_view pp = gsl_vector_view_array(data_vec, n_obs);
+ BLSP_Data->obs = &pp.vector;
+
+ gsl_vector_view pv = gsl_vector_view_array(doy_vec, n_obs);
+ BLSP_Data->doy = &pv.vector;
+
+ for (size_t i = 1; i < n_years + 1; ++i) {
+ gsl_vector_set(BLSP_Data->year_idx, i,
+ gsl_vector_get(BLSP_Data->year_idx, i - 1) +
+ year_idx_vec[i - 1]);
+ }
+
+
+ double theta_mean[7] = {-2.030660, 0.9576184, 119.2568116,
+ 8.7140161, 291.0681806, 9.9803594,
+ -6.6876395};
+
+ double theta_sd[7] = {0.03324139, 0.02499047, 0.46365685,
+ 0.35526145, 0.75144906, 0.55121990,
+ 0.09682220};
+
+ gsl_matrix* theta = blsp_sampler(BLSP_Data, theta_mean, theta_sd, 0.8, 7000, 2000);
+
+ for (int i = 0; i < n_years; i++) {
+ for (int p = 0; p < 7; p++) {
+ REAL(theta_matrix)[i + n_years*p] = gsl_matrix_get(theta, i, p);
+ }
+ }
+
+ UNPROTECT(1);
+ return theta_matrix;
+}
A r/src/blsp_r.h => r/src/blsp_r.h +5 -0
@@ 0,0 1,5 @@
+#include <R.h>
+#include <Rinternals.h>
+#include <R_ext/Rdynload.h>
+
+SEXP generate_data(SEXP data_vector, SEXP doy_vector, SEXP year_idx_vector);
A r/src/init.c => r/src/init.c +18 -0
@@ 0,0 1,18 @@
+#define R_NO_REMAP
+#include <R.h>
+#include <Rinternals.h>
+#include <R_ext/Rdynload.h>
+#include "blsp_r.h"
+
+
+
+static const R_CallMethodDef CallEntries[] = {
+ {"generate_data", (DL_FUNC) &generate_data, 3},
+ {NULL, NULL, 0}
+};
+
+void R_init_blspR(DllInfo *dll) {
+ R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+ R_useDynamicSymbols(dll, TRUE);
+ R_forceSymbols(dll, TRUE);
+}
A r/testing.R => r/testing.R +8 -0
@@ 0,0 1,8 @@
+data_path <- file.path("../test_data.Rdata")
+
+load(data_path)
+ls()
+
+devtools::load_all()
+
+blspR::blsp_test(unlist(y), unlist(t), yr_idx)
A src/blsp.c => src/blsp.c +35 -0
@@ 0,0 1,35 @@
+#include "blsp.h"
+
+BLSP_Model_t *BLSP_Model_alloc(size_t year_cnt, size_t obs_cnt,
+ size_t parameter_cnt) {
+
+ BLSP_Model_t *BLSP_Model = malloc(sizeof(BLSP_Model));
+
+ if (BLSP_Model == NULL) {
+ printf("Couldn't allocate memory for BLSP_Model\n");
+ exit(EXIT_FAILURE);
+ }
+
+ BLSP_Model->theta_mean_vector = gsl_vector_calloc(parameter_cnt);
+ BLSP_Model->theta_stddev_vector = gsl_vector_calloc(parameter_cnt);
+ BLSP_Model->global_log_likelihood_vector = gsl_vector_calloc(parameter_cnt);
+
+ BLSP_Model->theta_hat_matrix = gsl_matrix_calloc(year_cnt, parameter_cnt);
+ BLSP_Model->attempts_matrix = gsl_matrix_calloc(year_cnt, parameter_cnt);
+ BLSP_Model->acceptence_matrix = gsl_matrix_calloc(year_cnt, parameter_cnt);
+ BLSP_Model->metropolis_hastings_matrix =
+ gsl_matrix_calloc(year_cnt, parameter_cnt);
+
+ // NOTE: Surely there is a way to allocate all the needed memory in a single
+ // gsl_block for the vectors and matricies at once?
+ /* size_t memory_block_size = */
+ /* ((year_cnt * parameter_cnt) * 4) + (parameter_cnt * 3); */
+
+ /* gsl_block *memory_block = gsl_block_calloc(memory_block_size); */
+
+ /* size_t stride = sizeof(double); */
+
+ /* gsl_vector_alloc_from_block(memory_block, 0, parameter_cnt, stride); */
+
+ return BLSP_Model;
+}
A src/blsp.h => src/blsp.h +23 -0
@@ 0,0 1,23 @@
+#ifndef BLSP_H_
+#define BLSP_H_
+#include "common.h"
+
+typedef struct BLSP_Model {
+ gsl_vector *theta_mean_vector;
+ gsl_vector *theta_stddev_vector;
+
+ gsl_matrix *theta_hat_matrix;
+
+ gsl_vector *global_log_likelihood_vector;
+ gsl_matrix *attempts_matrix;
+ gsl_matrix *acceptence_matrix;
+
+ gsl_matrix *metropolis_hastings_matrix;
+
+} BLSP_Model_t;
+
+BLSP_Model_t *BLSP_Model_alloc(size_t year_cnt, size_t obs_cnt,
+ size_t parameter_cnt);
+
+
+#endif
A src/blsp_data.c => src/blsp_data.c +64 -0
@@ 0,0 1,64 @@
+#include "blsp_data.h"
+
+BLSP_Data_t *BLSP_Data_alloc(size_t n_years, size_t n_obs) {
+ BLSP_Data_t *BLSP_Data = malloc(sizeof(BLSP_Data_t));
+ if (BLSP_Data == NULL) {
+ printf("Couldn't allocate memory for BLSP_Data\n");
+ exit(EXIT_FAILURE);
+ }
+
+ BLSP_Data->n_years = n_years;
+ BLSP_Data->n_obs = n_obs;
+
+ // right now we are overidding these externally so we just wont allocate them
+ // BLSP_Data->obs = gsl_vector_calloc(n_obs);
+ // BLSP_Data->doy = gsl_vector_calloc(n_obs);
+ BLSP_Data->year_idx = gsl_vector_calloc(n_years + 1);
+
+ return BLSP_Data;
+}
+
+
+void BLSP_Data_free(BLSP_Data_t* BLSP_Data) {
+ free(BLSP_Data->obs);
+ free(BLSP_Data->doy);
+ free(BLSP_Data->year_idx);
+ free(BLSP_Data);
+}
+
+unsigned int BLSP_Data_get_year(BLSP_Data_t *BLSP_Data, size_t i) {
+ return gsl_vector_get(BLSP_Data->year_idx, i);
+}
+
+
+double BLSP_Data_get_doy(BLSP_Data_t *BLSP_Data, size_t i) {
+ return gsl_vector_get(BLSP_Data->doy, i);
+}
+
+gsl_vector_view BLSP_Data_get_year_doy(BLSP_Data_t *BLSP_Data, size_t year_idx) {
+ size_t idx_s, idx_e;
+
+ if (year_idx > (BLSP_Data->n_years) - 1)
+ exit(EXIT_FAILURE); // TODO: Add message
+
+ idx_s = BLSP_Data_get_year(BLSP_Data, year_idx);
+ idx_e = BLSP_Data_get_year(BLSP_Data, year_idx + 1);
+
+ return gsl_vector_subvector(BLSP_Data->doy, idx_s, idx_e - idx_s);
+}
+
+double BLSP_Data_get_obs(BLSP_Data_t *BLSP_Data, size_t i) {
+ return gsl_vector_get(BLSP_Data->obs, i);
+}
+
+gsl_vector_view BLSP_Data_get_year_obs(BLSP_Data_t *BLSP_Data, size_t year_idx) {
+ size_t idx_s, idx_e;
+
+ if (year_idx > (BLSP_Data->n_years) - 1)
+ exit(EXIT_FAILURE); // TODO: Add message
+
+ idx_s = BLSP_Data_get_year(BLSP_Data, year_idx);
+ idx_e = BLSP_Data_get_year(BLSP_Data, year_idx + 1);
+
+ return gsl_vector_subvector(BLSP_Data->obs, idx_s, idx_e - idx_s);
+}
R src/ts_data.h => src/blsp_data.h +13 -11
@@ 1,5 1,5 @@
-#ifndef TS_DATA_H_
-#define TS_DATA_H_
+#ifndef BLSP_DATA_H_
+#define BLSP_DATA_H_
#include "common.h"
@@ 30,25 30,27 @@
*
*/
-typedef struct TS_Data {
+
+// Observation
+typedef struct BLSP_Data {
unsigned int n_years; // Total number of years
unsigned int n_obs; // total number of observations
gsl_vector *obs; // GSL vector holding signal data
gsl_vector *doy; // GLS vector holding DOY for each observation
gsl_vector *year_idx; // GSL vector holding idx for each year
-} TS_Data_t;
+} BLSP_Data_t;
-TS_Data_t *TS_Data_alloc(size_t n_years, size_t n_obs);
-void TS_Data_free(TS_Data_t* TS_Data);
+BLSP_Data_t *BLSP_Data_alloc(size_t n_years, size_t n_obs);
+void BLSP_Data_free(BLSP_Data_t* BLSP_Data);
-unsigned int TS_Data_get_year(TS_Data_t *TS_Data, size_t i);
+unsigned int BLSP_Data_get_year(BLSP_Data_t *BLSP_Data, size_t i);
-double TS_Data_get_doy(TS_Data_t *TS_Data, size_t i);
-gsl_vector_view TS_Data_get_year_doy(TS_Data_t *TS_Data, size_t year_idx);
+double BLSP_Data_get_doy(BLSP_Data_t *BLSP_Data, size_t i);
+gsl_vector_view BLSP_Data_get_year_doy(BLSP_Data_t *BLSP_Data, size_t year_idx);
-double TS_Data_get_obs(TS_Data_t *TS_Data, size_t i);
-gsl_vector_view TS_Data_get_year_obs(TS_Data_t *TS_Data, size_t year_idx);
+double BLSP_Data_get_obs(BLSP_Data_t *BLSP_Data, size_t i);
+gsl_vector_view BLSP_Data_get_year_obs(BLSP_Data_t *BLSP_Data, size_t year_idx);
#endif // !TS_DATA_H_
A src/blsp_math.c => src/blsp_math.c +74 -0
@@ 0,0 1,74 @@
+#include "blsp_math.h"
+
+/*
+ * Double logistic function with greendown parameter (Elmore et al., 2012)
+ */
+double vi_double_logistic(double doy, gsl_vector *parameter_vector) {
+
+ double m1_l = gsl_cdf_logistic_P(gsl_vector_get(parameter_vector, 0), 1);
+ double m7_l = gsl_cdf_logistic_P(gsl_vector_get(parameter_vector, 6), 1);
+
+ double term1, // (m2 - m7 * t)
+ term2, // 1 / (1 + e^((m3 - t) / m4))
+ term3; // 1 / (1 + e^((m5 - t) / m6))
+ int status = 0;
+
+ gsl_sf_result_e10 term2_exp;
+ gsl_sf_result_e10 term3_exp;
+ term1 = gsl_vector_get(parameter_vector, 1) - m7_l * doy;
+
+ gsl_sf_exp_e10_e((gsl_vector_get(parameter_vector, 2) - doy) /
+ gsl_vector_get(parameter_vector, 3),
+ &term2_exp);
+ term2 = (1 / (1 + term2_exp.val));
+
+ gsl_sf_exp_e10_e((gsl_vector_get(parameter_vector, 4) - doy) /
+ gsl_vector_get(parameter_vector, 5),
+ &term3_exp);
+
+ term3 = (1 / (1 + term3_exp.val));
+
+ return m1_l + term1 * (term2 - term3);
+}
+
+/*
+ * Safely compute /log/ probabilty from normal distribution.
+ * Adapated from dnorm.c & dnorm4() from R Core.
+ */
+double log_norm(double x, double mu, double sigma) {
+ double xx;
+ xx = (x - mu) / sigma;
+ xx = fabs(xx);
+ return -(M_LN_SQRT_2PI + 0.5 * xx * xx + gsl_sf_log(sigma));
+}
+
+
+double log_likelihood_ratio(double candidate_value,
+ double candidate_log_likelihood, double mean_local,
+ double current_log_likelihood, double mean_global,
+ double stddev_global) {
+
+ // Compute values to compute accetence ratio
+ double log_1 = log_norm(candidate_value, mean_global, stddev_global);
+ double log_2 = log_norm(mean_local, mean_global, stddev_global);
+
+ return (candidate_log_likelihood - current_log_likelihood) + log_1 - log_2;
+}
+
+double draw_ran_gaussian(gsl_rng *RNG_ptr, double mean, double sttdev) {
+ // Draw a candidate for parameter
+ return gsl_ran_gaussian(RNG_ptr, sttdev) + mean;
+}
+
+double vi_log_likelihood(gsl_vector *vi_vector, gsl_vector *doy_vector,
+ gsl_vector *param_vector, size_t size, double sigma) {
+ double final_likelihood = 0, A_i, B_i;
+ for (size_t i = 0; i < size; ++i) {
+ A_i = gsl_vector_get(vi_vector, i);
+ B_i = gsl_vector_get(doy_vector, i);
+ final_likelihood += log_norm(
+ gsl_vector_get(vi_vector, i),
+ vi_double_logistic(gsl_vector_get(doy_vector, i), param_vector), sigma);
+ }
+ return final_likelihood;
+}
A src/blsp_math.h => src/blsp_math.h +24 -0
@@ 0,0 1,24 @@
+#ifndef BLSP_MATH_H_
+#define BLSP_MATH_H_
+
+#include "common.h"
+
+#define M_LN_SQRT_2PI 0.918938533204672741780329736406
+
+double vi_double_logistic(double doy, gsl_vector *parameter_vector);
+
+double log_norm(double x, double mu, double sigma);
+
+double log_likelihood_ratio(double candidate_value,
+ double candidate_log_likelihood, double mean_local,
+ double current_log_likelihood, double mean_global,
+ double stddev_global);
+
+
+double draw_ran_gaussian(gsl_rng *RNG_ptr, double mean, double sttdev);
+
+
+double vi_log_likelihood(gsl_vector *vi_vector, gsl_vector *doy_vector,
+ gsl_vector *param_vector, size_t size, double sigma);
+
+#endif
A src/sampler.c => src/sampler.c +308 -0
@@ 0,0 1,308 @@
+#include "blsp.h"
+#include "blsp_data.h"
+#include "blsp_math.h"
+#include "common.h"
+#define PARAMETER_COUNT 7
+#define BURN_STEPS 50
+
+gsl_matrix *blsp_sampler(BLSP_Data_t *TS_Data, double *theta_mean, double *theta_sd,
+ double sigma, size_t iterations, size_t burn) {
+
+ size_t observation_count = TS_Data->n_obs;
+ size_t year_count = TS_Data->n_years;
+ double m = 0.1;
+ double w = year_count / (year_count + m);
+
+ gsl_vector *theta_mean_vector;
+ gsl_vector *theta_sd_vector;
+ gsl_vector *current_log_like;
+ gsl_vector *theta_hat_candidate_vector;
+
+ gsl_matrix *theta_hat;
+ gsl_matrix *attempts;
+ gsl_matrix *acceptences;
+ gsl_matrix *metropolis_hastings_matrix;
+
+
+ // Create random number generator
+ const gsl_rng_type *RNG_t;
+ gsl_rng *RNG_ptr;
+ gsl_rng_env_setup();
+ RNG_t = gsl_rng_taus;
+ RNG_ptr = gsl_rng_alloc(RNG_t);
+ gsl_rng_set(RNG_ptr, 1);
+
+ /* BLSP_Model_t *BLSP_Model = */
+ /* BLSP_Model_alloc(year_count, observation_count, PARAMETER_COUNT); */
+
+ gsl_vector_view initial_theta_hat =
+ gsl_vector_view_array(theta_mean, PARAMETER_COUNT);
+ gsl_vector_view initial_theta_sd =
+ gsl_vector_view_array(theta_sd, PARAMETER_COUNT);
+
+ theta_mean_vector = gsl_vector_alloc(PARAMETER_COUNT);
+ gsl_vector_memcpy(theta_mean_vector, &initial_theta_hat.vector);
+ theta_sd_vector = gsl_vector_alloc(PARAMETER_COUNT);
+ gsl_vector_memcpy(theta_sd_vector, &initial_theta_sd.vector);
+
+ // Initialize matrix of parameter means
+ // The state of each parameter for each year is stored
+ theta_hat = gsl_matrix_alloc(year_count, PARAMETER_COUNT);
+ for (size_t j = 0; j < year_count; ++j) {
+ gsl_matrix_set_row(theta_hat, j, &initial_theta_hat.vector);
+ }
+
+ // INITIAL LOG LIKELIHOOD
+ // Initialize empty (zeroed) vector to hold log likelihoods
+ current_log_like = gsl_vector_calloc(year_count);
+ for (size_t year = 0; year < TS_Data->n_years; ++year) {
+ // Variable to store summed log likelihood for each year
+ double year_i_log_likelihood = 0;
+ // Get value vectors for year i
+
+ gsl_vector_view year_i_obs = BLSP_Data_get_year_obs(TS_Data, year);
+ gsl_vector_view year_i_doy = BLSP_Data_get_year_doy(TS_Data, year);
+
+ // Get parameter vector for year i
+ gsl_vector_view curr_theta_hat = gsl_matrix_row(theta_hat, year);
+
+ double ll = vi_log_likelihood(&year_i_obs.vector, &year_i_doy.vector,
+ &curr_theta_hat.vector,
+ year_i_obs.vector.size, sigma);
+
+ // Set log likelihood
+ gsl_vector_set(current_log_like, year, year_i_log_likelihood);
+ }
+
+ // Set up matrix for attempts and for acceptences for metropolis hastings
+ attempts = gsl_matrix_alloc(year_count, PARAMETER_COUNT);
+ gsl_matrix_set_all(attempts, 0.1);
+
+ acceptences = gsl_matrix_alloc(year_count, PARAMETER_COUNT);
+ gsl_matrix_set_all(acceptences, 0.1);
+
+ // Set up metropolis hastings grid and initialize
+ // This stores the current standard deviation for sampling a specific
+ // parameter in a specific year.
+ metropolis_hastings_matrix = gsl_matrix_alloc(year_count, PARAMETER_COUNT);
+ for (size_t j = 0; j < year_count; ++j) {
+ gsl_matrix_set_row(metropolis_hastings_matrix, j, theta_sd_vector);
+ }
+ gsl_matrix_scale(metropolis_hastings_matrix, 5.0);
+
+ // Initialize a vector to hold a /copy/ of the current year's vector so that
+ // we can update the years parameter vector with the current parameters draw
+ // without overwriting the value in the original theta_hat matrix until we
+ // decide to accept the candidate draw.
+ theta_hat_candidate_vector =
+ gsl_vector_calloc(PARAMETER_COUNT); // Candidate vector
+
+ // Declare vector views to be initalized with each year at each iteration
+ gsl_vector_view year_i_obs;
+ gsl_vector_view year_i_doy;
+ gsl_vector_view theta_hat_year;
+
+ for (size_t iter = 0; iter < iterations; ++iter) {
+ for (size_t year = 0; year < year_count; ++year) {
+
+ // Create vector views for the data in the current year
+ year_i_obs = BLSP_Data_get_year_obs(TS_Data, year);
+ year_i_doy = BLSP_Data_get_year_doy(TS_Data, year);
+ theta_hat_year = gsl_matrix_row(theta_hat, year);
+
+ for (size_t param = 0; param < PARAMETER_COUNT; ++param) {
+
+ // Increment attempt matrix
+ gsl_matrix_set(attempts, year, param,
+ gsl_matrix_get(attempts, year, param) + 1);
+
+ // memcopy so we can change the current parameter without setting it in
+ // the original
+ gsl_vector_memcpy(theta_hat_candidate_vector, &theta_hat_year.vector);
+
+ // Draw a candidate for parameter from gaussian distribution
+ double candidate_draw = draw_ran_gaussian(
+ RNG_ptr, gsl_matrix_get(theta_hat, year, param),
+ gsl_matrix_get(metropolis_hastings_matrix, year, param));
+
+ gsl_vector_set(theta_hat_candidate_vector, param, candidate_draw);
+
+ // Compute the candidate log likelihood for current year
+ double candidate_year_i_log_likelihood = vi_log_likelihood(
+ &year_i_obs.vector, &year_i_doy.vector, theta_hat_candidate_vector,
+ year_i_doy.vector.size, sigma);
+
+ /* for (size_t obs_i = 0; obs_i < year_i_obs.vector.size; ++obs_i) { */
+ /* // Compute simulated VI */
+ /* double doy_i = gsl_vector_get(&year_i_doy.vector, obs_i); */
+ /* vi_sim = vi_double_logistic(doy_i, theta_hat_candidate_vector); */
+
+ /* // Draw logp(x) */
+ /* ll_draw = log_norm(gsl_vector_get(&year_i_obs.vector, obs_i),
+ * vi_sim, */
+ /* sigma); */
+
+ /* // Sum up log likelihood */
+ /* candidate_year_i_log_likelihood += ll_draw; */
+ /* } */
+
+ // Compute acceptance ratio
+ double R = log_likelihood_ratio(
+ candidate_draw, candidate_year_i_log_likelihood,
+ gsl_matrix_get(theta_hat, year, param),
+ gsl_vector_get(current_log_like, year),
+ gsl_vector_get(theta_mean_vector, param),
+ gsl_vector_get(theta_sd_vector, param));
+
+ // Decide to accept or reject
+ double acceptence_prob = logl(gsl_ran_flat(RNG_ptr, 0, 1));
+
+ if (acceptence_prob < R) {
+ double current_acceptences = gsl_matrix_get(acceptences, year, param);
+
+ gsl_matrix_set(theta_hat, year, param, candidate_draw);
+ gsl_vector_set(current_log_like, year,
+ candidate_year_i_log_likelihood);
+ gsl_matrix_set(acceptences, year, param, current_acceptences + 1);
+ }
+
+ // Tune metropolis hastings samples
+ if (iter < burn) {
+ double attempt_cnt = gsl_matrix_get(attempts, year, param);
+ double acceptence_cnt = gsl_matrix_get(acceptences, year, param);
+
+ // Tune every 50 iterations
+ if (attempt_cnt > BURN_STEPS) {
+ double current_sample_stddev =
+ gsl_matrix_get(metropolis_hastings_matrix, year, param);
+
+ // If acceptence rate is low, tighten stddev
+ if (acceptence_cnt / attempt_cnt < 0.2) {
+ gsl_matrix_set(metropolis_hastings_matrix, year, param,
+ 0.8 * current_sample_stddev);
+ }
+
+ // If acceptence rate is high, expand sttdev
+ if (acceptence_cnt / attempt_cnt > 0.6) {
+ gsl_matrix_set(metropolis_hastings_matrix, year, param,
+ 1.2 * current_sample_stddev);
+ }
+
+ // Reset the attempt and acceptence value for current parameter
+ gsl_matrix_set(acceptences, year, param, 0);
+ gsl_matrix_set(attempts, year, param, 0);
+ }
+ }
+ } // End metropolis hastings for parameter vector
+
+ // TODO: Store parameters here
+ } // End year loop
+
+ // **** GIBBS *************************************************************
+ // Sample for global mean and stddev
+
+ // THETA MEAN *************************************************************
+ // Update the vector storing global mean for each parameter
+ //
+ // NOTE: When refactoring, see if it's faster to use BLAS to calculate
+ // column means instead of iterating fully over each column:
+ // gsl_blas_dgemv(CblasTrans, 1.0 / theta_hat->size1, theta_hat,
+ // scale_vector, 0.0, col_means);
+
+ for (size_t p = 0; p < PARAMETER_COUNT; ++p) {
+ double column_mean = 0, column_sum = 0;
+ double theta_mean_draw = 0;
+
+ // calculate column mean for parameter p
+ for (size_t year = 0; year < TS_Data->n_years; ++year) {
+ double th_p = gsl_matrix_get(theta_hat, year, p);
+ column_sum += th_p;
+ }
+ column_mean = column_sum / TS_Data->n_years;
+
+ theta_mean_draw = draw_ran_gaussian(
+ RNG_ptr, w * column_mean + (1 - w) * theta_mean[p],
+ gsl_vector_get(theta_sd_vector, p) / sqrtl((year_count + 0.1)));
+
+ gsl_vector_set(theta_mean_vector, p, theta_mean_draw);
+ } // END THETA MEAN UPDATE
+
+ // THETA STDDEV ***********************************************************
+ // Update the vector storing global stddev for each parameter
+ // 1. Calculate SSE
+ // 2. Draw new stddev from gamma dist
+
+ for (size_t p = 0; p < PARAMETER_COUNT; ++p) {
+ // 1. SSE for parameter p
+ double xi = 0, xj = 0, stddev_sse = 0;
+ double sse_i = 0;
+ double sse_2 = 0;
+ for (size_t year = 0; year < TS_Data->n_years; ++year) {
+ xi = gsl_matrix_get(theta_hat, year, p);
+ xj = gsl_vector_get(theta_mean_vector, p); // move this out (future)
+ sse_i = xi - xj;
+ sse_2 = gsl_pow_2(sse_i);
+
+ stddev_sse += sse_2;
+ }
+
+ // 2. Draw new stddev from gamma dist
+ double gamma_a = 0, gamma_b = 0, theta_stddev_p = 0;
+ // Compute parameters
+ gamma_a = year_count / 2.0 + 0.1;
+ gamma_b = stddev_sse / 2.0 + 0.1;
+
+ // Draw sample
+ theta_stddev_p = gsl_ran_gamma(RNG_ptr, gamma_a, 1.0 / gamma_b);
+
+ // intermediate variable for debugging
+ double theta_stddev_p_final = 1 / sqrtl(theta_stddev_p);
+
+ gsl_vector_set(theta_sd_vector, p, theta_stddev_p_final);
+ } // END THETA STDDEV UPDATE
+
+ // GLOBAL STDDEV **********************************************************
+ // update overall standard dev (noise)
+ double sse_sim = 0;
+ for (size_t year = 0; year < TS_Data->n_years; ++year) {
+ // 1. Calculate VI SSE for each year and add to SSE
+
+ // Get value vectors for year i
+ gsl_vector_view year_i_obs = BLSP_Data_get_year_obs(TS_Data, year);
+ gsl_vector_view year_i_doy = BLSP_Data_get_year_doy(TS_Data, year);
+
+ // We use the scale vector as a temporary place to memcpy our parameter
+ // vector for year i
+ // gsl_matrix_get_row(candidate_vector, theta_hat, year);
+
+ gsl_vector_view curr_theta_hat = gsl_matrix_row(theta_hat, year);
+ // Iterate over each obs date in year i summing up SSE with each i
+ double vi_sim = 0;
+ for (size_t obs_i = 0; obs_i < year_i_obs.vector.size; ++obs_i) {
+ // Calculate the VI for obs_i with year_i parameter vector
+ double doy_i = gsl_vector_get(&year_i_doy.vector, obs_i);
+ vi_sim = vi_double_logistic(doy_i, &curr_theta_hat.vector);
+
+ double indv_obs = gsl_vector_get(&year_i_obs.vector, obs_i);
+
+ sse_sim += gsl_pow_2(indv_obs - vi_sim);
+ }
+ }
+
+ // 2. Draw global sigma from gamma distribution
+ double sigma_tmp;
+ double sigma_gamma_a, sigma_gamma_b;
+
+ sigma_gamma_a = TS_Data->n_obs / 2.0 + 0.1;
+ sigma_gamma_b = sse_sim / 2.0 + 0.1;
+
+ sigma_tmp = gsl_ran_gamma(RNG_ptr, sigma_gamma_a, 1 / sigma_gamma_b);
+
+ sigma = 1 / sqrtl(sigma_tmp);
+ }
+
+ /* FILE *out_f = fopen("./data/test.dat", "wb"); */
+ /* gsl_matrix_fwrite(out_f, metropolis_hastings_matrix); */
+ /* fclose(out_f); */
+ return theta_hat;
+}
A src/sampler.h => src/sampler.h +8 -0
@@ 0,0 1,8 @@
+#ifndef SAMPLER_H_
+#define SAMPLER_H_
+
+#include "blsp_data.h"
+gsl_matrix *blsp_sampler(BLSP_Data_t *TS_Data, double *theta_mean, double *theta_sd,
+ double sigma, size_t iterations, size_t burn);
+
+#endif
D src/sampler1.c => src/sampler1.c +0 -479
@@ 1,479 0,0 @@
-//#define DEBUG
-#include "common.h"
-#include "ts_data.h"
-#include <stdio.h>
-
-#define GSL_RNG_SEED 1
-#define W 0.9950249 // w <- nyear / (nyear + m) # coeff for post norm
-
-#define M_LN_SQRT_2PI 0.918938533204672741780329736406
-#define N_PARAMETER 7
-
-// GENERAL FUNKS **************************************************************
-
-/*
- * Double logistic function with greendown parameter (Elmore et al., 2012)
- */
-double vi_double_logistic(double doy, gsl_vector *parameter_vector) {
-
- double m1_l = gsl_cdf_logistic_P(gsl_vector_get(parameter_vector, 0), 1);
- double m7_l = gsl_cdf_logistic_P(gsl_vector_get(parameter_vector, 6), 1);
-
- double term1, // (m2 - m7 * t)
- term2, // 1 / (1 + e^((m3 - t) / m4))
- term3; // 1 / (1 + e^((m5 - t) / m6))
- int status = 0;
-
- gsl_sf_result_e10 term2_exp;
- gsl_sf_result_e10 term3_exp;
- term1 = gsl_vector_get(parameter_vector, 1) - m7_l * doy;
-
- gsl_sf_exp_e10_e((gsl_vector_get(parameter_vector, 2) - doy) /
- gsl_vector_get(parameter_vector, 3),
- &term2_exp);
- term2 = (1 / (1 + term2_exp.val));
-
- gsl_sf_exp_e10_e((gsl_vector_get(parameter_vector, 4) - doy) /
- gsl_vector_get(parameter_vector, 5),
- &term3_exp);
-
- term3 = (1 / (1 + term3_exp.val));
-
- return m1_l + term1 * (term2 - term3);
-}
-
-/*
- * Safely compute /log/ probabilty from normal distribution.
- * Adapated from dnorm.c & dnorm4() from R Core.
- */
-double log_norm(double x, double mu, double sigma) {
- double xx;
- xx = (x - mu) / sigma;
- xx = fabs(xx);
- return -(M_LN_SQRT_2PI + 0.5 * xx * xx + gsl_sf_log(sigma));
-}
-
-// MAIN ***********************************************************************
-int main(int argc, char const *argv[]) {
-
- // Parameters taken from simulated data in R
- double theta_mean[N_PARAMETER] = {-1.998392, 0.960355, 120.702350, 9.263498,
- 288.853856, 9.166685, -6.592421};
- double theta_sd[N_PARAMETER] = {0.07057906, 0.05609551, 1.08944966,
- 0.88183154, 1.55979462, 1.20727157,
- 0.19881890};
-
- // Copy over theta mean and theta standard deviation to GSL_Vectors
- // Could also just create a GSL array view to the two arrays but would rather
- // just copy the data for now
- gsl_vector *theta_sd_view = gsl_vector_calloc(N_PARAMETER);
- gsl_vector *theta_mean_view = gsl_vector_calloc(N_PARAMETER);
- for (size_t i = 0; i < N_PARAMETER; ++i) {
- gsl_vector_set(theta_mean_view, i, theta_mean[i]);
- gsl_vector_set(theta_sd_view, i, theta_sd[i]);
- }
-
- // Set up RNG
- const gsl_rng_type *RNG_t;
- gsl_rng *RNG_ptr;
- // Create random number generator
- gsl_rng_env_setup();
- RNG_t = gsl_rng_taus;
- RNG_ptr = gsl_rng_alloc(RNG_t);
- gsl_rng_set(RNG_ptr, 1);
-
- // We simulated 20 years and 334 obs
- size_t num_years = 20, num_obs = 334, curr_yr_id = 0;
- double prior_strength = 0.1; // used when updating MCMC
-
- // GSL vectors to store data
- gsl_vector *doy_vector = gsl_vector_alloc(num_obs);
- gsl_vector *y_vector = gsl_vector_alloc(num_obs);
- gsl_vector *yr_id_vector = gsl_vector_alloc(num_years);
-
- plog("Reading data");
- // Read in test data. GLS will throw error if file not found
- FILE *file_doy = fopen("./data/doy_full.dat", "r");
- gsl_vector_fscanf(file_doy, doy_vector);
- fclose(file_doy);
-
- FILE *file_y = fopen("./data/y_full.dat", "r");
- gsl_vector_fscanf(file_y, y_vector);
- fclose(file_y);
-
- FILE *file_yr_id = fopen("./data/year_idx.dat", "r");
- gsl_vector_fscanf(file_y, yr_id_vector);
- fclose(file_yr_id);
-
- // Store our initial state. This is used in the sampler but *does not change*
- gsl_vector *initial_theta_hat = gsl_vector_alloc(N_PARAMETER);
- gsl_vector_memcpy(initial_theta_hat, theta_mean_view);
-
- // Allocate structure to hold data allowing us to slice data by year
- TS_Data_t *TS_Data = TS_Data_alloc(num_years, num_obs);
-
- // Change pointer to the needed vectors
- TS_Data->obs = y_vector;
- TS_Data->doy = doy_vector;
-
- // Set up the year_idx vector. Important to note that we iterate from one so
- // that we make sure the year indexing values start from 0.
- // See ts_data.h for more info
- plog("Set up year idx");
- for (size_t i = 1; i < TS_Data->n_years +1; ++i) {
- gsl_vector_set(TS_Data->year_idx, i,
- gsl_vector_get(TS_Data->year_idx, i - 1) +
- gsl_vector_get(yr_id_vector, i - 1));
- }
-
-
-
- // Initialize matrix of parameter means.
- // The parameter vector state for each year is updated in this matrix,
- // and the global mean and stddev are updated using the values stored here
- // as well.
- plog("initializing theta hat");
- gsl_matrix *theta_hat = gsl_matrix_alloc(num_years, N_PARAMETER);
- for (size_t j = 0; j < num_years; ++j) {
- gsl_matrix_set_row(theta_hat, j, theta_mean_view);
- }
-
- double sigma = 0.08040725;
-
- // INITIAL LOG LIKELIHOOD ***************************************************
- // Initial Log likelihood at the current value of theta for each year.
-
- // Initialize empty (zeroed) vector to hold log likelihoods
- gsl_vector *current_log_like = gsl_vector_calloc(num_years);
-
- // Iterate over each year
-
- plog("Computing initial log likelihoods");
- for (size_t year = 0; year < num_years; ++year) {
- // Variable to store summed log likelihood for each year
- double year_i_log_likelihood = 0;
- // Get value vectors for year i
-
- gsl_vector_view year_i_obs = TS_Data_get_year_obs(TS_Data, year);
- gsl_vector_view year_i_doy = TS_Data_get_year_doy(TS_Data, year);
-
- // Get parameter vector for year i
- gsl_vector_view curr_theta_hat = gsl_matrix_row(theta_hat, year);
-
- // Iterate over each obs in year
- double vi_sim = 0;
- double ll_draw = 0;
-
- for (size_t obs_i = 0; obs_i < year_i_obs.vector.size; ++obs_i) {
- // Compute simulated VI
- double doy_i = gsl_vector_get(&year_i_doy.vector, obs_i);
- vi_sim = vi_double_logistic(doy_i, &curr_theta_hat.vector);
-
- // Draw logp(x)
- double vi_true = gsl_vector_get(&year_i_obs.vector, obs_i);
- ll_draw = log_norm(vi_true, vi_sim, sigma);
-
- // Sum up log likelihood
- year_i_log_likelihood += ll_draw;
- }
-
- // Set log likelihood
- gsl_vector_set(current_log_like, year, year_i_log_likelihood);
- }
-
- plog("Initializing metropolis hastings acceptence and attempt grids");
- // Set up matrix for attempts and for acceptences for metropolis hastings
- gsl_matrix *attempts = gsl_matrix_alloc(num_years, N_PARAMETER);
- gsl_matrix_set_all(attempts, 0.1);
-
- gsl_matrix *acceptences = gsl_matrix_alloc(num_years, N_PARAMETER);
- gsl_matrix_set_all(acceptences, 0.1);
-
- // Set up metropolis hastings grid and initialize
- // This stores the current standard deviation for sampling a specific
- // parameter in a specific year.
- plog("Initializing metropolis hastings sampling grid");
- gsl_matrix *mh_matrix = gsl_matrix_alloc(num_years, N_PARAMETER);
- for (size_t j = 0; j < num_years; ++j) {
- gsl_matrix_set_row(mh_matrix, j, theta_sd_view);
- }
- gsl_matrix_scale(mh_matrix, 5.0);
-
- unsigned int iterations = 7000;
- unsigned int burn = 2000;
-
- // NOTE: Right now we are not keeping track each parameter draw.
- // I am diagnosing the sampler based off the final SD and mean grids.
- // gsl_matrix *parameter_tracker =
- // gsl_matrix_calloc(num_years * 7000, N_PARAMETER);
- // gsl_matrix *parameter_tracker_1 = gsl_matrix_calloc(num_years,
- // N_PARAMETER);
-
- // Initialize a vector to hold a /copy/ of the current year's vector so that
- // we can update the years parameter vector with the current parameters draw
- // without overwriting the value in the original theta_hat matrix until we
- // decide to accept the candidate draw.
- gsl_vector *candidate_theta_hat_vector =
- gsl_vector_calloc(N_PARAMETER); // Candidate vector
-
- // **** BEGIN ***************************************************************
- plog("Starting sampler");
- for (size_t iter = 0; iter < iterations; ++iter) {
- for (size_t year = 0; year < TS_Data->n_years; ++year) {
- // Create vector views for the data in the current year
- gsl_vector_view year_i_obs = TS_Data_get_year_obs(TS_Data, year);
- gsl_vector_view year_i_doy = TS_Data_get_year_doy(TS_Data, year);
- gsl_vector_view theta_hat_year = gsl_matrix_row(theta_hat, year);
-
- for (size_t param = 0; param < N_PARAMETER; ++param) {
-
- plog("ITER: %lu\t | YEAR: %lu\t | PARAM: %lu", iter, year, param);
-
- // attempts ++
- gsl_matrix_set(attempts, year, param,
- gsl_matrix_get(attempts, year, param) + 1);
-
- // memcopy so we can change the current parameter without setting it in
- // the original
- // Get current years parameter vector
- // gsl_vector_view candidate_theta = gsl_matrix_row(theta_hat, year);
- // gsl_vector_memcpy(candidate_vector, &candidate_theta.vector);
- // gsl_matrix_get_row(candidate_theta_hat_vector, theta_hat, year);
- gsl_vector_memcpy(candidate_theta_hat_vector, &theta_hat_year.vector);
-
- double cc_sd = gsl_matrix_get(mh_matrix, year, param); // Current stddev
- double cc_mn = gsl_matrix_get(theta_hat, year, param); // current mean
-
- // Draw a candidate for parameter
- double candidate_draw = gsl_ran_gaussian(RNG_ptr, cc_sd) + cc_mn;
- gsl_vector_set(candidate_theta_hat_vector, param, candidate_draw);
-
- // Compute the candidate log likelihood for year
- double vi_sim = 0;
- double ll_draw = 0;
- double candidate_year_i_log_likelihood = 0;
- for (size_t obs_i = 0; obs_i < year_i_obs.vector.size; ++obs_i) {
- // Compute simulated VI
- double doy_i = gsl_vector_get(&year_i_doy.vector, obs_i);
- vi_sim = vi_double_logistic(doy_i, candidate_theta_hat_vector);
-
- // Draw logp(x)
- double vi_true = gsl_vector_get(&year_i_obs.vector, obs_i);
- ll_draw = log_norm(vi_true, vi_sim, sigma);
-
- // Sum up log likelihood
- candidate_year_i_log_likelihood += ll_draw;
- }
-
- // Get the global mean and stddev for current parameter
- double theta_mn_j, theta_sd_j;
- theta_mn_j = gsl_vector_get(theta_mean_view, param);
- theta_sd_j = gsl_vector_get(theta_sd_view, param);
-
- // Compute values to compute accetence ratio
- double theta_i = gsl_matrix_get(theta_hat, year, param);
- double log_1 = log_norm(candidate_draw, theta_mn_j, theta_sd_j);
- double log_2 = log_norm(theta_i, theta_mn_j, theta_sd_j);
-
- double cur_ll = gsl_vector_get(current_log_like, year);
- double ll_dif = candidate_year_i_log_likelihood - cur_ll;
-
- // Compute acceptance ratio
- double R = ll_dif + log_1 - log_2;
-
- // Decide to accept or reject
- double ttt = gsl_ran_flat(RNG_ptr, 0, 1); // TODO: change shit variable
- // name
- double l_ttt = logl(ttt);
- // double ttt = logf((rand()/(double)(RAND_MAX)) * 2 - 1);
-
- // int status = gsl_fcmp(R, gsl_sf_log(gsl_ran_flat(r, 0, 1)),
- // 0.000001f);
- // if (status > 0) {
- if (l_ttt < R) { // Update values for current parameter
- double c_a = gsl_matrix_get(acceptences, year, param);
-
- gsl_matrix_set(theta_hat, year, param, candidate_draw);
- gsl_vector_set(current_log_like, year,
- candidate_year_i_log_likelihood);
- gsl_matrix_set(acceptences, year, param, c_a + 1);
- }
-
- // Tune metropolis hastings sampler
- if (iter < burn) {
- double attempt_cnt = gsl_matrix_get(attempts, year, param);
- double acceptence_cnt = gsl_matrix_get(acceptences, year, param);
-
- // Tune every 50 iterations
- if (attempt_cnt > 50) {
- double curr_mh = gsl_matrix_get(mh_matrix, year, param);
- // NOTE: mh_matrix is not converging correctly
-
- // If acceptence rate is low, tighten stddev
- if (acceptence_cnt / attempt_cnt < 0.2) {
- gsl_matrix_set(mh_matrix, year, param, 0.8 * curr_mh);
- }
-
- // If acceptence rate is high, expand sttdev
- if (acceptence_cnt / attempt_cnt > 0.6) {
- gsl_matrix_set(mh_matrix, year, param, 1.2 * curr_mh);
- }
-
- // Reset the attempt and acceptence value for current parameter
- gsl_matrix_set(acceptences, year, param, 0);
- gsl_matrix_set(attempts, year, param, 0);
- }
- }
- } // END metropolis hastings for parameter vector
-
- // NOTE: When storing parameters, here is where to do it
- // printf("%lu %lu ", iter, year);
- // for (size_t i = 0; i < N_PARAMETER; ++i) printf("%f ", gsl_matrix_get(theta_hat, year, i));
- // printf("\n");
-
- } // END year loop
-
- // **** GIBBS *************************************************************
- // Sample for global mean and stddev
-
- // THETA MEAN *************************************************************
- // Update the vector storing global mean for each parameter
- // theta_mn <- rnorm(npar, w * colMeans(theta_hat) + (1 - w) * mu,
- // theta_sd / sqrt((nyear + m)))
- //
- // NOTE: When refactoring, see if it's faster to use BLAS to calculate
- // column means instead of iterating fully over each column:
- // gsl_blas_dgemv(CblasTrans, 1.0 / theta_hat->size1, theta_hat,
- // scale_vector, 0.0, col_means);
-
- for (size_t p = 0; p < N_PARAMETER; ++p) {
- double column_mean = 0, column_sum = 0;
- double theta_mn_mu = 0, theta_mn_sig = 0;
- double theta_mean_p = 0;
-
- // calculate column mean for parameter p
- for (size_t year = 0; year < TS_Data->n_years; ++year) {
- double th_p = gsl_matrix_get(theta_hat, year, p);
- column_sum += th_p;
- }
- column_mean = column_sum / TS_Data->n_years;
-
- // calculate mu parameter for distribution
- theta_mn_mu =
- W * column_mean + (1 - W) * gsl_vector_get(initial_theta_hat, p);
-
- // calculate sigma parameter for distribution
- theta_mn_sig =
- gsl_vector_get(theta_sd_view, p) / sqrtl((num_years + 0.1));
-
- // Pull draw
- theta_mean_p = gsl_ran_gaussian(RNG_ptr, theta_mn_sig);
- // Apply mean transformation
- theta_mean_p += theta_mn_mu;
-
- // Set theta_mn[p]
- gsl_vector_set(theta_mean_view, p, theta_mean_p);
- } // END THETA MEAN UPDATE
-
- // THETA STDDEV ***********************************************************
- // Update the vector storing global stddev for each parameter
- // 1. Calculate SSE
- // 2. Draw new stddev from gamma dist
-
- for (size_t p = 0; p < N_PARAMETER; ++p) {
- // 1. SSE for parameter p
- double xi = 0, xj = 0, stddev_sse = 0;
- double sse_i = 0;
- double sse_2 = 0;
- for (size_t year = 0; year < TS_Data->n_years; ++year) {
- xi = gsl_matrix_get(theta_hat, year, p);
- xj = gsl_vector_get(theta_mean_view, p); // move this out (future)
- sse_i = xi - xj;
- sse_2 = gsl_pow_2(sse_i);
-
- stddev_sse += sse_2;
- }
-
- // 2. Draw new stddev from gamma dist
- double gamma_a = 0, gamma_b = 0, theta_stddev_p = 0;
- // Compute parameters
- gamma_a = num_years / 2.0 + 0.1;
- gamma_b = stddev_sse / 2.0 + 0.1;
-
- // Draw sample
- theta_stddev_p = gsl_ran_gamma(RNG_ptr, gamma_a, 1.0 / gamma_b);
-
-
- // intermediate variable for debugging
- double theta_stddev_p_final = 1 / sqrtl(theta_stddev_p);
-
- gsl_vector_set(theta_sd_view, p, theta_stddev_p_final);
- } // END THETA STDDEV UPDATE
-
- // GLOBAL STDDEV **********************************************************
- // update overall standard dev (noise)
- double sse_sim = 0;
- for (size_t year = 0; year < TS_Data->n_years; ++year) {
- // 1. Calculate VI SSE for each year and add to SSE
-
- // Get value vectors for year i
- gsl_vector_view year_i_obs = TS_Data_get_year_obs(TS_Data, year);
- gsl_vector_view year_i_doy = TS_Data_get_year_doy(TS_Data, year);
-
- // We use the scale vector as a temporary place to memcpy our parameter
- // vector for year i
- // gsl_matrix_get_row(candidate_vector, theta_hat, year);
-
- gsl_vector_view curr_theta_hat = gsl_matrix_row(theta_hat, year);
- // Iterate over each obs date in year i summing up SSE with each i
- double vi_sim = 0;
- for (size_t obs_i = 0; obs_i < year_i_obs.vector.size; ++obs_i) {
- // Calculate the VI for obs_i with year_i parameter vector
- double doy_i = gsl_vector_get(&year_i_doy.vector, obs_i);
- vi_sim = vi_double_logistic(doy_i, &curr_theta_hat.vector);
-
- double indv_obs = gsl_vector_get(&year_i_obs.vector, obs_i);
-
- sse_sim += gsl_pow_2(indv_obs - vi_sim);
- }
- }
-
- // 2. Draw global sigma from gamma distribution
- double sigma_tmp;
- double sigma_gamma_a, sigma_gamma_b;
-
- sigma_gamma_a = TS_Data->n_obs / 2.0 + 0.1;
- sigma_gamma_b = sse_sim / 2.0 + 0.1;
-
- sigma_tmp = gsl_ran_gamma(RNG_ptr, sigma_gamma_a, 1 / sigma_gamma_b);
-
- sigma = 1 / sqrtl(sigma_tmp);
-
- } // END iter loop
-
- FILE *out_f = fopen("./data/test.dat", "wb");
- // gsl_matrix_fprintf(out_f, theta_hat, "%f");
- gsl_matrix_fwrite(out_f, mh_matrix);
- fclose(out_f);
-
-
- TS_Data_free(TS_Data);
- // these are freed by TS_Data_free currently
- // gsl_vector_free(doy_vector);
- // gsl_vector_free(y_vector);
- // gsl_vector_free(yr_id_vector);
-
- gsl_vector_free(theta_mean_view);
- gsl_vector_free(theta_sd_view);
- gsl_vector_free(initial_theta_hat);
- gsl_vector_free(current_log_like);
- gsl_vector_free(candidate_theta_hat_vector);
-
- gsl_matrix_free(theta_hat);
- gsl_matrix_free(attempts);
- gsl_matrix_free(acceptences);
- gsl_matrix_free(mh_matrix);
-
-
- return 0;
-}
D src/ts_data.c => src/ts_data.c +0 -68
@@ 1,68 0,0 @@
-#include "ts_data.h"
-#include <stdio.h>
-#include <stdlib.h>
-
-TS_Data_t *TS_Data_alloc(size_t n_years, size_t n_obs) {
- TS_Data_t *TS_Data = malloc(sizeof(TS_Data_t));
- if (TS_Data == NULL) {
- printf("Couldn't allocate memory for TS_Data\n");
- exit(EXIT_FAILURE);
- }
-
- TS_Data->n_years = n_years;
- TS_Data->n_obs = n_obs;
-
-
- // right now we are overidding these externally so we just wont allocate them
- // TS_Data->obs = gsl_vector_calloc(n_obs);
- // TS_Data->doy = gsl_vector_calloc(n_obs);
- TS_Data->year_idx = gsl_vector_calloc(n_years + 1);
-
- return TS_Data;
-}
-
-
-void TS_Data_free(TS_Data_t* TS_Data) {
- free(TS_Data->obs);
- free(TS_Data->doy);
- free(TS_Data->year_idx);
- free(TS_Data);
-}
-
-unsigned int TS_Data_get_year(TS_Data_t *TS_Data, size_t i) {
- return gsl_vector_get(TS_Data->year_idx, i);
-}
-
-
-double TS_Data_get_doy(TS_Data_t *TS_Data, size_t i) {
- return gsl_vector_get(TS_Data->doy, i);
-}
-
-gsl_vector_view TS_Data_get_year_doy(TS_Data_t *TS_Data, size_t year_idx) {
- size_t idx_s, idx_e;
-
- if (year_idx > (TS_Data->n_years) - 1)
- exit(EXIT_FAILURE); // TODO: Add message
-
- idx_s = TS_Data_get_year(TS_Data, year_idx);
- idx_e = TS_Data_get_year(TS_Data, year_idx + 1);
-
- return gsl_vector_subvector(TS_Data->doy, idx_s, idx_e - idx_s);
-}
-
-double TS_Data_get_obs(TS_Data_t *TS_Data, size_t i) {
- return gsl_vector_get(TS_Data->obs, i);
-}
-
-gsl_vector_view TS_Data_get_year_obs(TS_Data_t *TS_Data, size_t year_idx) {
- size_t idx_s, idx_e;
-
- if (year_idx > (TS_Data->n_years) - 1)
- exit(EXIT_FAILURE); // TODO: Add message
-
- idx_s = TS_Data_get_year(TS_Data, year_idx);
- idx_e = TS_Data_get_year(TS_Data, year_idx + 1);
-
- return gsl_vector_subvector(TS_Data->obs, idx_s, idx_e - idx_s);
-}
-