diff --git a/DESCRIPTION b/DESCRIPTION index 7ee5ad4..f1b69b7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: surveyvoi Type: Package -Version: 1.0.3.11 +Version: 1.0.4 Title: Survey Value of Information Description: Decision support tool for prioritizing sites for ecological surveys based on their potential to improve plans for conserving @@ -75,11 +75,11 @@ LazyData: true Language: en-US SystemRequirements: C++11, - JAGS (>= 4.3.0), + JAGS (>= 4.3.0) (optional), + fftw3 (>= 3.3), gmp (>= 6.2.1), gmpxx (>= 6.2.1), - mpfr (>= 4.1.0), - pkg-config (>= 0.29.2), + mpfr (>= 3.0.0), autoconf (>= 2.69), automake (>= 1.16.5) URL: https://prioritizr.github.io/surveyvoi/ diff --git a/Makefile b/Makefile index f354d18..5b58d27 100644 --- a/Makefile +++ b/Makefile @@ -72,6 +72,10 @@ wbcheck: R --slave -e "devtools::check_win_devel()" cp -Rf doc inst/ +maccheck: + R --slave -e "devtools::check_mac_release()" + cp -Rf doc inst/ + urlcheck: R --slave -e "devtools::document();urlchecker::url_check()" diff --git a/NEWS.md b/NEWS.md index e7c1edf..f744181 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,12 @@ +# surveyvoi 1.0.4 + +- CRAN release. + +# surveyvoi 1.0.3.12 + +- Update CRAN comments document and remove pkg-config from system requirements. +- Fix compiler warning thrown during installation. + # surveyvoi 1.0.3.11 - Update `simulate_site_data()` function to remove RandomFields package diff --git a/README.md b/README.md index fab73de..61c5070 100644 --- a/README.md +++ b/README.md @@ -86,7 +86,7 @@ Please cite the *surveyvoi R* package when using it in publications. To cite the developmental version, please use: > Hanson JO, Chadès I, Hudgins EJ, Bennett J (2022). surveyvoi: Survey -> Value of Information. R package version 1.0.3.10. Available at +> Value of Information. R package version 1.0.4. Available at > . ## Usage diff --git a/configure b/configure index edc5b3b..f223ec9 100755 --- a/configure +++ b/configure @@ -1,11 +1,12 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.69 for surveyvoi see.DESCRIPTION. +# Generated by GNU Autoconf 2.71 for surveyvoi see.DESCRIPTION. # # Report bugs to . # # -# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc. +# Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation, +# Inc. # # # This configure script is free software; the Free Software Foundation @@ -16,14 +17,16 @@ # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : +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 +else $as_nop case `(set -o) 2>/dev/null` in #( *posix*) : set -o posix ;; #( @@ -33,46 +36,46 @@ esac fi + +# Reset variables that may have inherited troublesome values from +# the environment. + +# IFS needs to be set, to space, tab, and newline, in precisely that order. +# (If _AS_PATH_WALK were called with IFS unset, it would have the +# side effect of setting IFS to empty, thus disabling word splitting.) +# Quoting is to prevent editors from complaining about space-tab. as_nl=' ' export as_nl -# Printing a long string crashes Solaris 7 /usr/bin/printf. -as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' -as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo -as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo -# Prefer a ksh shell builtin over an external printf program on Solaris, -# but without wasting forks for bash or zsh. -if test -z "$BASH_VERSION$ZSH_VERSION" \ - && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then - as_echo='print -r --' - as_echo_n='print -rn --' -elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then - as_echo='printf %s\n' - as_echo_n='printf %s' -else - if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then - as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' - as_echo_n='/usr/ucb/echo -n' - else - as_echo_body='eval expr "X$1" : "X\\(.*\\)"' - as_echo_n_body='eval - arg=$1; - case $arg in #( - *"$as_nl"*) - expr "X$arg" : "X\\(.*\\)$as_nl"; - arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; - esac; - expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" - ' - export as_echo_n_body - as_echo_n='sh -c $as_echo_n_body as_echo' - fi - export as_echo_body - as_echo='sh -c $as_echo_body as_echo' -fi +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 $as_var || : +done + +# Ensure that fds 0, 1, and 2 are open. +if (exec 3>&0) 2>/dev/null; then :; else exec 0&1) 2>/dev/null; then :; else exec 1>/dev/null; fi +if (exec 3>&2) ; then :; else exec 2>/dev/null; fi # The user is always right. -if test "${PATH_SEPARATOR+set}" != set; then +if ${PATH_SEPARATOR+false} :; then PATH_SEPARATOR=: (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || @@ -81,13 +84,6 @@ if test "${PATH_SEPARATOR+set}" != set; then fi -# IFS -# We need space, tab and new line, in precisely that order. Quoting is -# there to prevent editors from complaining about space-tab. -# (If _AS_PATH_WALK were called with IFS unset, it would disable word -# splitting by setting IFS to empty value.) -IFS=" "" $as_nl" - # Find who we are. Look in the path if we contain no directory separator. as_myself= case $0 in #(( @@ -96,8 +92,12 @@ case $0 in #(( for as_dir in $PATH do IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break + 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 @@ -109,30 +109,10 @@ if test "x$as_myself" = x; then as_myself=$0 fi if test ! -f "$as_myself"; then - $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 + printf "%s\n" "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 exit 1 fi -# Unset variables that we do not need and which cause bugs (e.g. in -# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" -# suppresses any "Segmentation fault" message there. '((' could -# trigger a bug in pdksh 5.2.14. -for as_var in BASH_ENV ENV MAIL MAILPATH -do eval test x\${$as_var+set} = xset \ - && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : -done -PS1='$ ' -PS2='> ' -PS4='+ ' - -# NLS nuisances. -LC_ALL=C -export LC_ALL -LANGUAGE=C -export LANGUAGE - -# CDPATH. -(unset CDPATH) >/dev/null 2>&1 && unset CDPATH # Use a proper internal environment variable to ensure we don't fall # into an infinite loop, continuously re-executing ourselves. @@ -154,20 +134,22 @@ esac exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"} # Admittedly, this is quite paranoid, since all the known shells bail # out after a failed `exec'. -$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2 -as_fn_exit 255 +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="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; 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 +else \$as_nop case \`(set -o) 2>/dev/null\` in #( *posix*) : set -o posix ;; #( @@ -187,41 +169,52 @@ 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 : +if ( set x; as_fn_ret_success y && test x = \"\$1\" ) +then : -else +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 "$as_required") 2>/dev/null; then : + if (eval "$as_required") 2>/dev/null +then : as_have_required=yes -else +else $as_nop as_have_required=no fi - if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then : + if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null +then : -else +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=$as_save_IFS - test -z "$as_dir" && as_dir=. + 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/$as_base + as_shell=$as_dir$as_base if { test -f "$as_shell" || test -f "$as_shell.exe"; } && - { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then : + as_run=a "$as_shell" -c "$as_bourne_compatible""$as_required" 2>/dev/null +then : CONFIG_SHELL=$as_shell as_have_required=yes - if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then : + if as_run=a "$as_shell" -c "$as_bourne_compatible""$as_suggested" 2>/dev/null +then : break 2 fi fi @@ -229,14 +222,21 @@ fi esac as_found=false done -$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } && - { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then : - CONFIG_SHELL=$SHELL as_have_required=yes -fi; } IFS=$as_save_IFS +if $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 : + 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 @@ -254,18 +254,19 @@ esac exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"} # Admittedly, this is quite paranoid, since all the known shells bail # out after a failed `exec'. -$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2 +printf "%s\n" "$0: could not re-execute with $CONFIG_SHELL" >&2 exit 255 fi - if test x$as_have_required = xno; then : - $as_echo "$0: This script requires a shell more modern than all" - $as_echo "$0: the shells that I found on your system." - if test x${ZSH_VERSION+set} = xset ; then - $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should" - $as_echo "$0: be upgraded to zsh 4.3.4 or later." + if test x$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 - $as_echo "$0: Please tell bug-autoconf@gnu.org and + printf "%s\n" "$0: Please tell bug-autoconf@gnu.org and $0: https://github.com/prioritizr/surveyvoi/issues about $0: your system, including any error possibly output before $0: this message. Then install a modern shell, or manually @@ -293,6 +294,7 @@ as_fn_unset () } as_unset=as_fn_unset + # as_fn_set_status STATUS # ----------------------- # Set $? to STATUS, without forking. @@ -310,6 +312,14 @@ as_fn_exit () 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 # ------------- @@ -324,7 +334,7 @@ as_fn_mkdir_p () as_dirs= while :; do case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *\'*) as_qdir=`printf "%s\n" "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( *) as_qdir=$as_dir;; esac as_dirs="'$as_qdir' $as_dirs" @@ -333,7 +343,7 @@ $as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$as_dir" : 'X\(//\)[^/]' \| \ X"$as_dir" : 'X\(//\)$' \| \ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | +printf "%s\n" X"$as_dir" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q @@ -372,12 +382,13 @@ as_fn_executable_p () # 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 : +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 +else $as_nop as_fn_append () { eval $1=\$$1\$2 @@ -389,18 +400,27 @@ fi # as_fn_append # 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 $(()) and expr. -if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null +then : eval 'as_fn_arith () { as_val=$(( $* )) }' -else +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] # ---------------------------------------- @@ -412,9 +432,9 @@ as_fn_error () as_status=$1; test $as_status -eq 0 && as_status=1 if test "$4"; then as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack - $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 + printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 fi - $as_echo "$as_me: error: $2" >&2 + printf "%s\n" "$as_me: error: $2" >&2 as_fn_exit $as_status } # as_fn_error @@ -441,7 +461,7 @@ as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ X"$0" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X/"$0" | +printf "%s\n" X/"$0" | sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/ q @@ -485,7 +505,7 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits s/-\n.*// ' >$as_me.lineno && chmod +x "$as_me.lineno" || - { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; } + { printf "%s\n" "$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 $CONFIG_SHELL, we're ensured to have # already done that, so ensure we don't try to do so again and fall @@ -499,6 +519,10 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits 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*) @@ -512,6 +536,13 @@ case `echo -n x` in #((((( 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 @@ -703,8 +734,6 @@ do *) ac_optarg=yes ;; esac - # Accept the important Cygnus configure options, so we can diagnose typos. - case $ac_dashdash$ac_option in --) ac_dashdash=yes ;; @@ -745,9 +774,9 @@ do ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid feature name: $ac_useropt" + as_fn_error $? "invalid feature name: \`$ac_useropt'" ac_useropt_orig=$ac_useropt - ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in *" "enable_$ac_useropt" @@ -771,9 +800,9 @@ do 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" + as_fn_error $? "invalid feature name: \`$ac_useropt'" ac_useropt_orig=$ac_useropt - ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in *" "enable_$ac_useropt" @@ -984,9 +1013,9 @@ do 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" + as_fn_error $? "invalid package name: \`$ac_useropt'" ac_useropt_orig=$ac_useropt - ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in *" "with_$ac_useropt" @@ -1000,9 +1029,9 @@ do 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" + as_fn_error $? "invalid package name: \`$ac_useropt'" ac_useropt_orig=$ac_useropt - ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` + ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in *" "with_$ac_useropt" @@ -1046,9 +1075,9 @@ Try \`$0 --help' for more information" *) # FIXME: should be removed in autoconf 3.0. - $as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2 + printf "%s\n" "$as_me: WARNING: you should use --build, --host, --target" >&2 expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null && - $as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2 + printf "%s\n" "$as_me: WARNING: invalid host type: $ac_option" >&2 : "${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}" ;; @@ -1064,7 +1093,7 @@ if test -n "$ac_unrecognized_opts"; then case $enable_option_checking in no) ;; fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;; - *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;; + *) printf "%s\n" "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;; esac fi @@ -1128,7 +1157,7 @@ $as_expr X"$as_myself" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$as_myself" : 'X\(//\)[^/]' \| \ X"$as_myself" : 'X\(//\)$' \| \ X"$as_myself" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_myself" | +printf "%s\n" X"$as_myself" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q @@ -1267,9 +1296,9 @@ if test "$ac_init_help" = "recursive"; then case "$ac_dir" in .) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;; *) - ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'` + ac_dir_suffix=/`printf "%s\n" "$ac_dir" | sed 's|^\.[\\/]||'` # A ".." for each directory in $ac_dir_suffix. - ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'` + ac_top_builddir_sub=`printf "%s\n" "$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/ ;; @@ -1297,7 +1326,8 @@ esac ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix cd "$ac_dir" || { ac_status=$?; continue; } - # Check for guested configure. + # 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 @@ -1305,7 +1335,7 @@ ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix echo && $SHELL "$ac_srcdir/configure" --help=recursive else - $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2 + printf "%s\n" "$as_me: WARNING: no configuration information is in $ac_dir" >&2 fi || ac_status=$? cd "$ac_pwd" || { ac_status=$?; break; } done @@ -1315,9 +1345,9 @@ test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF surveyvoi configure see.DESCRIPTION -generated by GNU Autoconf 2.69 +generated by GNU Autoconf 2.71 -Copyright (C) 2012 Free Software Foundation, Inc. +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 @@ -1327,14 +1357,34 @@ 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 surveyvoi $as_me see.DESCRIPTION, which was -generated by GNU Autoconf 2.69. Invocation command line was +generated by GNU Autoconf 2.71. Invocation command line was - $ $0 $@ + $ $0$ac_configure_args_raw _ACEOF exec 5>>config.log @@ -1367,8 +1417,12 @@ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - $as_echo "PATH: $as_dir" + case $as_dir in #((( + '') as_dir=./ ;; + */) ;; + *) as_dir=$as_dir/ ;; + esac + printf "%s\n" "PATH: $as_dir" done IFS=$as_save_IFS @@ -1403,7 +1457,7 @@ do | -silent | --silent | --silen | --sile | --sil) continue ;; *\'*) - ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; + ac_arg=`printf "%s\n" "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; esac case $ac_pass in 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;; @@ -1438,11 +1492,13 @@ done # 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 - $as_echo "## ---------------- ## + printf "%s\n" "## ---------------- ## ## Cache variables. ## ## ---------------- ##" echo @@ -1453,8 +1509,8 @@ trap 'exit_status=$? case $ac_val in #( *${as_nl}*) case $ac_var in #( - *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 -$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; + *_cv_*) { printf "%s\n" "$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) ;; #( @@ -1478,7 +1534,7 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; ) echo - $as_echo "## ----------------- ## + printf "%s\n" "## ----------------- ## ## Output variables. ## ## ----------------- ##" echo @@ -1486,14 +1542,14 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; do eval ac_val=\$$ac_var case $ac_val in - *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; + *\'\''*) ac_val=`printf "%s\n" "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; esac - $as_echo "$ac_var='\''$ac_val'\''" + printf "%s\n" "$ac_var='\''$ac_val'\''" done | sort echo if test -n "$ac_subst_files"; then - $as_echo "## ------------------- ## + printf "%s\n" "## ------------------- ## ## File substitutions. ## ## ------------------- ##" echo @@ -1501,15 +1557,15 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; do eval ac_val=\$$ac_var case $ac_val in - *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; + *\'\''*) ac_val=`printf "%s\n" "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;; esac - $as_echo "$ac_var='\''$ac_val'\''" + printf "%s\n" "$ac_var='\''$ac_val'\''" done | sort echo fi if test -s confdefs.h; then - $as_echo "## ----------- ## + printf "%s\n" "## ----------- ## ## confdefs.h. ## ## ----------- ##" echo @@ -1517,8 +1573,8 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; echo fi test "$ac_signal" != 0 && - $as_echo "$as_me: caught signal $ac_signal" - $as_echo "$as_me: exit $exit_status" + printf "%s\n" "$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$$* $ac_clean_files && @@ -1532,63 +1588,48 @@ ac_signal=0 # confdefs.h avoids OS command line length limits that DEFS can exceed. rm -f -r conftest* confdefs.h -$as_echo "/* confdefs.h */" > confdefs.h +printf "%s\n" "/* confdefs.h */" > confdefs.h # Predefined preprocessor variables. -cat >>confdefs.h <<_ACEOF -#define PACKAGE_NAME "$PACKAGE_NAME" -_ACEOF +printf "%s\n" "#define PACKAGE_NAME \"$PACKAGE_NAME\"" >>confdefs.h -cat >>confdefs.h <<_ACEOF -#define PACKAGE_TARNAME "$PACKAGE_TARNAME" -_ACEOF +printf "%s\n" "#define PACKAGE_TARNAME \"$PACKAGE_TARNAME\"" >>confdefs.h -cat >>confdefs.h <<_ACEOF -#define PACKAGE_VERSION "$PACKAGE_VERSION" -_ACEOF +printf "%s\n" "#define PACKAGE_VERSION \"$PACKAGE_VERSION\"" >>confdefs.h -cat >>confdefs.h <<_ACEOF -#define PACKAGE_STRING "$PACKAGE_STRING" -_ACEOF +printf "%s\n" "#define PACKAGE_STRING \"$PACKAGE_STRING\"" >>confdefs.h -cat >>confdefs.h <<_ACEOF -#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" -_ACEOF +printf "%s\n" "#define PACKAGE_BUGREPORT \"$PACKAGE_BUGREPORT\"" >>confdefs.h -cat >>confdefs.h <<_ACEOF -#define PACKAGE_URL "$PACKAGE_URL" -_ACEOF +printf "%s\n" "#define PACKAGE_URL \"$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. -ac_site_file1=NONE -ac_site_file2=NONE if test -n "$CONFIG_SITE"; then - # We do not want a PATH search for config.site. - case $CONFIG_SITE in #(( - -*) ac_site_file1=./$CONFIG_SITE;; - */*) ac_site_file1=$CONFIG_SITE;; - *) ac_site_file1=./$CONFIG_SITE;; - esac + ac_site_files="$CONFIG_SITE" elif test "x$prefix" != xNONE; then - ac_site_file1=$prefix/share/config.site - ac_site_file2=$prefix/etc/config.site + ac_site_files="$prefix/share/config.site $prefix/etc/config.site" else - ac_site_file1=$ac_default_prefix/share/config.site - ac_site_file2=$ac_default_prefix/etc/config.site + ac_site_files="$ac_default_prefix/share/config.site $ac_default_prefix/etc/config.site" fi -for ac_site_file in "$ac_site_file1" "$ac_site_file2" + +for ac_site_file in $ac_site_files do - test "x$ac_site_file" = xNONE && continue - if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5 -$as_echo "$as_me: loading site script $ac_site_file" >&6;} + 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" \ - || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 -$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} + || { { 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 @@ -1598,16 +1639,16 @@ 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 - { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5 -$as_echo "$as_me: loading cache $cache_file" >&6;} + { printf "%s\n" "$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 - { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5 -$as_echo "$as_me: creating cache $cache_file" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5 +printf "%s\n" "$as_me: creating cache $cache_file" >&6;} >$cache_file fi @@ -1621,12 +1662,12 @@ for ac_var in $ac_precious_vars; do eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 -$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} + { 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) - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 -$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} + { 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=: ;; ,);; *) @@ -1635,24 +1676,24 @@ $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} 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 - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 -$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} + { 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 - { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 -$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} + { 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 - { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 -$as_echo "$as_me: former value: \`$ac_old_val'" >&2;} - { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 -$as_echo "$as_me: current value: \`$ac_new_val'" >&2;} + { 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=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;; + *\'*) 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 @@ -1662,11 +1703,12 @@ $as_echo "$as_me: current value: \`$ac_new_val'" >&2;} fi done if $ac_cache_corrupted; then - { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 -$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} - { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 -$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;} - as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 + { 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. ## @@ -1701,17 +1743,17 @@ MPFR_TEST_HEADER="" # Preliminary processing ## print status message -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if R found" >&5 -$as_echo_n "checking if R found... " >&6; } +{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking if R found" >&5 +printf %s "checking if R found... " >&6; } ## ensure C++ is set up as R expects : ${R_HOME=`R RHOME`} if test -z "${R_HOME}"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -$as_echo "no" >&6; } + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 +printf "%s\n" "no" >&6; } as_fn_error $? "Could not determine R_HOME." "$LINENO" 5 fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -$as_echo "yes" >&6; } +{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +printf "%s\n" "yes" >&6; } ## verify suitable R version RBIN="${R_HOME}/bin/R" @@ -1722,13 +1764,13 @@ RVER_MINOR=`echo ${RVER} | cut -f2 -d"."` RVER_PATCH=`echo ${RVER} | cut -f3 -d"."` if test $RVER_MAJOR = "development"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: R version: development" >&5 -$as_echo "$as_me: R version: development" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: R version: development" >&5 +printf "%s\n" "$as_me: R version: development" >&6;} CXX11=`"${RBIN}" CMD config CXX11` CXX11STD=`"${RBIN}" CMD config CXX11STD` else - { $as_echo "$as_me:${as_lineno-$LINENO}: R version: ${RVER_MAJOR}.${RVER_MINOR}.${RVER_PATCH}" >&5 -$as_echo "$as_me: R version: ${RVER_MAJOR}.${RVER_MINOR}.${RVER_PATCH}" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: R version: ${RVER_MAJOR}.${RVER_MINOR}.${RVER_PATCH}" >&5 +printf "%s\n" "$as_me: R version: ${RVER_MAJOR}.${RVER_MINOR}.${RVER_PATCH}" >&6;} if test $RVER_MAJOR -lt 4; then as_fn_error $? "surveyvoi is not compatible with R versions before 4.0.0" "$LINENO" 5 else @@ -1750,11 +1792,12 @@ fi # Extract the first word of "pkg-config", so it can be a program name with args. set dummy pkg-config; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -$as_echo_n "checking for $ac_word... " >&6; } -if ${ac_cv_prog_PKGCONFIG+:} false; then : - $as_echo_n "(cached) " >&6 -else +{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +printf %s "checking for $ac_word... " >&6; } +if test ${ac_cv_prog_PKGCONFIG+y} +then : + printf %s "(cached) " >&6 +else $as_nop if test -n "$PKGCONFIG"; then ac_cv_prog_PKGCONFIG="$PKGCONFIG" # Let the user override the test. else @@ -1762,11 +1805,15 @@ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. + 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 + if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then ac_cv_prog_PKGCONFIG="yes" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5 break 2 fi done @@ -1777,11 +1824,11 @@ fi fi PKGCONFIG=$ac_cv_prog_PKGCONFIG if test -n "$PKGCONFIG"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PKGCONFIG" >&5 -$as_echo "$PKGCONFIG" >&6; } + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $PKGCONFIG" >&5 +printf "%s\n" "$PKGCONFIG" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -$as_echo "no" >&6; } + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 +printf "%s\n" "no" >&6; } fi @@ -1819,15 +1866,15 @@ CPPFLAGS="${PKG_CPPFLAGS}" LIBS="${PKG_LIBS}" ## display compiler flags -{ $as_echo "$as_me:${as_lineno-$LINENO}: Package PKG_CPPFLAGS: ${CPPFLAGS}" >&5 -$as_echo "$as_me: Package PKG_CPPFLAGS: ${CPPFLAGS}" >&6;} -{ $as_echo "$as_me:${as_lineno-$LINENO}: Package PKG_LIBS: ${LIBS}" >&5 -$as_echo "$as_me: Package PKG_LIBS: ${LIBS}" >&6;} +{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: Package PKG_CPPFLAGS: ${CPPFLAGS}" >&5 +printf "%s\n" "$as_me: Package PKG_CPPFLAGS: ${CPPFLAGS}" >&6;} +{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: Package PKG_LIBS: ${LIBS}" >&5 +printf "%s\n" "$as_me: Package PKG_LIBS: ${LIBS}" >&6;} # Verify GMP settings work ## display message -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if ${GMP_NAME} compiles" >&5 -$as_echo_n "checking if ${GMP_NAME} compiles... " >&6; } +{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking if ${GMP_NAME} compiles" >&5 +printf %s "checking if ${GMP_NAME} compiles... " >&6; } ## try compiling file with settings cat > gmp_test.cpp <<_EOCONF @@ -1845,32 +1892,32 @@ _EOCONF ${CXX} ${CPPFLAGS} -o gmp_test gmp_test.cpp ${LIBS} 2> errors.txt if test `echo $?` -ne 0 ; then gmp_ok=no - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -$as_echo "no" >&6; } + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 +printf "%s\n" "no" >&6; } else gmp_ok=yes - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -$as_echo "yes" >&6; } + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +printf "%s\n" "yes" >&6; } fi ## throw error if needed if test x"${gmp_ok}" == x"no"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: Configuration failed because ${GMP_NAME} was not found. Try installing:" >&5 -$as_echo "$as_me: Configuration failed because ${GMP_NAME} was not found. Try installing:" >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: * deb: ${GMP_DEB_NAME} (Debian, Ubuntu)" >&5 -$as_echo "$as_me: * deb: ${GMP_DEB_NAME} (Debian, Ubuntu)" >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: * rpm: ${GMP_RPM_NAME} (Fedora, EPEL)" >&5 -$as_echo "$as_me: * rpm: ${GMP_RPM_NAME} (Fedora, EPEL)" >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: * brew: ${GMP_BREW_NAME} (Mac OSX)" >&5 -$as_echo "$as_me: * brew: ${GMP_BREW_NAME} (Mac OSX)" >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: " >&5 -$as_echo "$as_me: " >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: If ${GMP_NAME} is already installed, check that 'pkg-config' is in" >&5 -$as_echo "$as_me: If ${GMP_NAME} is already installed, check that 'pkg-config' is in" >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: your PATH and PKG_CONFIG_PATH contains a ${GMP_CONFIG_NAME}.pc file." >&5 -$as_echo "$as_me: your PATH and PKG_CONFIG_PATH contains a ${GMP_CONFIG_NAME}.pc file." >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: " >&5 -$as_echo "$as_me: " >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: Configuration failed because ${GMP_NAME} was not found. Try installing:" >&5 +printf "%s\n" "$as_me: Configuration failed because ${GMP_NAME} was not found. Try installing:" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: * deb: ${GMP_DEB_NAME} (Debian, Ubuntu)" >&5 +printf "%s\n" "$as_me: * deb: ${GMP_DEB_NAME} (Debian, Ubuntu)" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: * rpm: ${GMP_RPM_NAME} (Fedora, EPEL)" >&5 +printf "%s\n" "$as_me: * rpm: ${GMP_RPM_NAME} (Fedora, EPEL)" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: * brew: ${GMP_BREW_NAME} (Mac OSX)" >&5 +printf "%s\n" "$as_me: * brew: ${GMP_BREW_NAME} (Mac OSX)" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: " >&5 +printf "%s\n" "$as_me: " >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: If ${GMP_NAME} is already installed, check that 'pkg-config' is in" >&5 +printf "%s\n" "$as_me: If ${GMP_NAME} is already installed, check that 'pkg-config' is in" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: your PATH and PKG_CONFIG_PATH contains a ${GMP_CONFIG_NAME}.pc file." >&5 +printf "%s\n" "$as_me: your PATH and PKG_CONFIG_PATH contains a ${GMP_CONFIG_NAME}.pc file." >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: " >&5 +printf "%s\n" "$as_me: " >&6;} as_fn_error $? "ERROR: Installation failed" "$LINENO" 5 fi @@ -1879,8 +1926,8 @@ rm -f gmp_test errors.txt gmp_test.cpp # Verify MFPR settings work ## display message -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if ${MPFR_NAME} compiles" >&5 -$as_echo_n "checking if ${MPFR_NAME} compiles... " >&6; } +{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking if ${MPFR_NAME} compiles" >&5 +printf %s "checking if ${MPFR_NAME} compiles... " >&6; } ## try compiling file with settings cat > mpfr_test.cpp <<_EOCONF @@ -1897,32 +1944,32 @@ _EOCONF ${CXX} ${CPPFLAGS} -o mpfr_test mpfr_test.cpp ${LIBS} 2> errors.txt if test `echo $?` -ne 0 ; then mpfr_ok=no - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -$as_echo "no" >&6; } + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5 +printf "%s\n" "no" >&6; } else mpfr_ok=yes - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -$as_echo "yes" >&6; } + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +printf "%s\n" "yes" >&6; } fi ## throw error if needed if test x"${mpfr_ok}" == x"no"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: Configuration failed because ${MPFR_NAME} was not found. Try installing:" >&5 -$as_echo "$as_me: Configuration failed because ${MPFR_NAME} was not found. Try installing:" >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: * deb: ${MPFR_DEB_NAME} (Debian, Ubuntu)" >&5 -$as_echo "$as_me: * deb: ${MPFR_DEB_NAME} (Debian, Ubuntu)" >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: * rpm: ${MPFR_RPM_NAME} (Fedora, EPEL)" >&5 -$as_echo "$as_me: * rpm: ${MPFR_RPM_NAME} (Fedora, EPEL)" >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: * brew: ${MPFR_BREW_NAME} (Mac OSX)" >&5 -$as_echo "$as_me: * brew: ${MPFR_BREW_NAME} (Mac OSX)" >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: " >&5 -$as_echo "$as_me: " >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: If ${MPFR_NAME} is already installed, check that 'pkg-config' is in" >&5 -$as_echo "$as_me: If ${MPFR_NAME} is already installed, check that 'pkg-config' is in" >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: your PATH and PKG_CONFIG_PATH contains a ${MPFR_CONFIG_NAME}.pc file." >&5 -$as_echo "$as_me: your PATH and PKG_CONFIG_PATH contains a ${MPFR_CONFIG_NAME}.pc file." >&6;} - { $as_echo "$as_me:${as_lineno-$LINENO}: " >&5 -$as_echo "$as_me: " >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: Configuration failed because ${MPFR_NAME} was not found. Try installing:" >&5 +printf "%s\n" "$as_me: Configuration failed because ${MPFR_NAME} was not found. Try installing:" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: * deb: ${MPFR_DEB_NAME} (Debian, Ubuntu)" >&5 +printf "%s\n" "$as_me: * deb: ${MPFR_DEB_NAME} (Debian, Ubuntu)" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: * rpm: ${MPFR_RPM_NAME} (Fedora, EPEL)" >&5 +printf "%s\n" "$as_me: * rpm: ${MPFR_RPM_NAME} (Fedora, EPEL)" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: * brew: ${MPFR_BREW_NAME} (Mac OSX)" >&5 +printf "%s\n" "$as_me: * brew: ${MPFR_BREW_NAME} (Mac OSX)" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: " >&5 +printf "%s\n" "$as_me: " >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: If ${MPFR_NAME} is already installed, check that 'pkg-config' is in" >&5 +printf "%s\n" "$as_me: If ${MPFR_NAME} is already installed, check that 'pkg-config' is in" >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: your PATH and PKG_CONFIG_PATH contains a ${MPFR_CONFIG_NAME}.pc file." >&5 +printf "%s\n" "$as_me: your PATH and PKG_CONFIG_PATH contains a ${MPFR_CONFIG_NAME}.pc file." >&6;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: " >&5 +printf "%s\n" "$as_me: " >&6;} as_fn_error $? "ERROR: Installation failed" "$LINENO" 5 fi @@ -1939,8 +1986,8 @@ ac_config_files="$ac_config_files src/Makevars" # print message indicating success -{ $as_echo "$as_me:${as_lineno-$LINENO}: configuration successful!" >&5 -$as_echo "$as_me: configuration successful!" >&6;} +{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: configuration successful!" >&5 +printf "%s\n" "$as_me: configuration successful!" >&6;} ## finish cat >confcache <<\_ACEOF @@ -1970,8 +2017,8 @@ _ACEOF case $ac_val in #( *${as_nl}*) case $ac_var in #( - *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 -$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; + *_cv_*) { printf "%s\n" "$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) ;; #( @@ -2001,15 +2048,15 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; /^ac_cv_env_/b end t clear :clear - s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/ + 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 - { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5 -$as_echo "$as_me: updating cache $cache_file" >&6;} + { printf "%s\n" "$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 @@ -2023,8 +2070,8 @@ $as_echo "$as_me: updating cache $cache_file" >&6;} fi fi else - { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5 -$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;} + { printf "%s\n" "$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 @@ -2077,7 +2124,7 @@ 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$//' - ac_i=`$as_echo "$ac_i" | sed "$ac_script"` + 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" @@ -2093,8 +2140,8 @@ LTLIBOBJS=$ac_ltlibobjs ac_write_fail=0 ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files $CONFIG_STATUS" -{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5 -$as_echo "$as_me: creating $CONFIG_STATUS" >&6;} +{ printf "%s\n" "$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 #! $SHELL @@ -2117,14 +2164,16 @@ cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1 # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : +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 +else $as_nop case `(set -o) 2>/dev/null` in #( *posix*) : set -o posix ;; #( @@ -2134,46 +2183,46 @@ esac fi + +# Reset variables that may have inherited troublesome values from +# the environment. + +# IFS needs to be set, to space, tab, and newline, in precisely that order. +# (If _AS_PATH_WALK were called with IFS unset, it would have the +# side effect of setting IFS to empty, thus disabling word splitting.) +# Quoting is to prevent editors from complaining about space-tab. as_nl=' ' export as_nl -# Printing a long string crashes Solaris 7 /usr/bin/printf. -as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' -as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo -as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo -# Prefer a ksh shell builtin over an external printf program on Solaris, -# but without wasting forks for bash or zsh. -if test -z "$BASH_VERSION$ZSH_VERSION" \ - && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then - as_echo='print -r --' - as_echo_n='print -rn --' -elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then - as_echo='printf %s\n' - as_echo_n='printf %s' -else - if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then - as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' - as_echo_n='/usr/ucb/echo -n' - else - as_echo_body='eval expr "X$1" : "X\\(.*\\)"' - as_echo_n_body='eval - arg=$1; - case $arg in #( - *"$as_nl"*) - expr "X$arg" : "X\\(.*\\)$as_nl"; - arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; - esac; - expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" - ' - export as_echo_n_body - as_echo_n='sh -c $as_echo_n_body as_echo' - fi - export as_echo_body - as_echo='sh -c $as_echo_body as_echo' -fi +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 $as_var || : +done + +# Ensure that fds 0, 1, and 2 are open. +if (exec 3>&0) 2>/dev/null; then :; else exec 0&1) 2>/dev/null; then :; else exec 1>/dev/null; fi +if (exec 3>&2) ; then :; else exec 2>/dev/null; fi # The user is always right. -if test "${PATH_SEPARATOR+set}" != set; then +if ${PATH_SEPARATOR+false} :; then PATH_SEPARATOR=: (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || @@ -2182,13 +2231,6 @@ if test "${PATH_SEPARATOR+set}" != set; then fi -# IFS -# We need space, tab and new line, in precisely that order. Quoting is -# there to prevent editors from complaining about space-tab. -# (If _AS_PATH_WALK were called with IFS unset, it would disable word -# splitting by setting IFS to empty value.) -IFS=" "" $as_nl" - # Find who we are. Look in the path if we contain no directory separator. as_myself= case $0 in #(( @@ -2197,8 +2239,12 @@ case $0 in #(( for as_dir in $PATH do IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break + 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 @@ -2210,30 +2256,10 @@ if test "x$as_myself" = x; then as_myself=$0 fi if test ! -f "$as_myself"; then - $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 + printf "%s\n" "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 exit 1 fi -# Unset variables that we do not need and which cause bugs (e.g. in -# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" -# suppresses any "Segmentation fault" message there. '((' could -# trigger a bug in pdksh 5.2.14. -for as_var in BASH_ENV ENV MAIL MAILPATH -do eval test x\${$as_var+set} = xset \ - && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : -done -PS1='$ ' -PS2='> ' -PS4='+ ' - -# NLS nuisances. -LC_ALL=C -export LC_ALL -LANGUAGE=C -export LANGUAGE - -# CDPATH. -(unset CDPATH) >/dev/null 2>&1 && unset CDPATH # as_fn_error STATUS ERROR [LINENO LOG_FD] @@ -2246,13 +2272,14 @@ as_fn_error () as_status=$1; test $as_status -eq 0 && as_status=1 if test "$4"; then as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack - $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 + printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 fi - $as_echo "$as_me: error: $2" >&2 + printf "%s\n" "$as_me: error: $2" >&2 as_fn_exit $as_status } # as_fn_error + # as_fn_set_status STATUS # ----------------------- # Set $? to STATUS, without forking. @@ -2279,18 +2306,20 @@ 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 : +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 +else $as_nop as_fn_append () { eval $1=\$$1\$2 @@ -2302,12 +2331,13 @@ fi # as_fn_append # 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 $(()) and expr. -if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null +then : eval 'as_fn_arith () { as_val=$(( $* )) }' -else +else $as_nop as_fn_arith () { as_val=`expr "$@" || test $? -eq 1` @@ -2338,7 +2368,7 @@ as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ X"$0" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X/"$0" | +printf "%s\n" X/"$0" | sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/ q @@ -2360,6 +2390,10 @@ as_cr_Letters=$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*) @@ -2373,6 +2407,12 @@ case `echo -n x` in #((((( 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 @@ -2414,7 +2454,7 @@ as_fn_mkdir_p () as_dirs= while :; do case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *\'*) as_qdir=`printf "%s\n" "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( *) as_qdir=$as_dir;; esac as_dirs="'$as_qdir' $as_dirs" @@ -2423,7 +2463,7 @@ $as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$as_dir" : 'X\(//\)[^/]' \| \ X"$as_dir" : 'X\(//\)$' \| \ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | +printf "%s\n" X"$as_dir" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q @@ -2486,7 +2526,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # values after options handling. ac_log=" This file was extended by surveyvoi $as_me see.DESCRIPTION, which was -generated by GNU Autoconf 2.69. Invocation command line was +generated by GNU Autoconf 2.71. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS @@ -2535,14 +2575,16 @@ $config_files Report bugs to ." _ACEOF +ac_cs_config=`printf "%s\n" "$ac_configure_args" | sed "$ac_safe_unquote"` +ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\''/g"` cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 -ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" +ac_cs_config='$ac_cs_config_escaped' ac_cs_version="\\ surveyvoi config.status see.DESCRIPTION -configured by $0, generated by GNU Autoconf 2.69, +configured by $0, generated by GNU Autoconf 2.71, with options \\"\$ac_cs_config\\" -Copyright (C) 2012 Free Software Foundation, Inc. +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." @@ -2579,21 +2621,21 @@ do -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r) ac_cs_recheck=: ;; --version | --versio | --versi | --vers | --ver | --ve | --v | -V ) - $as_echo "$ac_cs_version"; exit ;; + printf "%s\n" "$ac_cs_version"; exit ;; --config | --confi | --conf | --con | --co | --c ) - $as_echo "$ac_cs_config"; exit ;; + printf "%s\n" "$ac_cs_config"; exit ;; --debug | --debu | --deb | --de | --d | -d ) debug=: ;; --file | --fil | --fi | --f ) $ac_shift case $ac_optarg in - *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; + *\'*) ac_optarg=`printf "%s\n" "$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 ) - $as_echo "$ac_cs_usage"; exit ;; + printf "%s\n" "$ac_cs_usage"; exit ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ | -silent | --silent | --silen | --sile | --sil | --si | --s) ac_cs_silent=: ;; @@ -2621,7 +2663,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 if \$ac_cs_recheck; then set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion shift - \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6 + \printf "%s\n" "running CONFIG_SHELL=$SHELL \$*" >&6 CONFIG_SHELL='$SHELL' export CONFIG_SHELL exec "\$@" @@ -2635,7 +2677,7 @@ exec 5>>config.log sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX ## Running $as_me. ## _ASBOX - $as_echo "$ac_log" + printf "%s\n" "$ac_log" } >&5 _ACEOF @@ -2660,7 +2702,7 @@ done # 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+set}" = set || CONFIG_FILES=$config_files + test ${CONFIG_FILES+y} || CONFIG_FILES=$config_files fi # Have a temporary directory for convenience. Make it in the build tree @@ -2888,7 +2930,7 @@ do esac || as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;; esac - case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; 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 @@ -2896,17 +2938,17 @@ do # use $as_me), people would be surprised to read: # /* config.h. Generated by config.status. */ configure_input='Generated from '` - $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g' + printf "%s\n" "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g' `' by configure.' if test x"$ac_file" != x-; then configure_input="$ac_file. $configure_input" - { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5 -$as_echo "$as_me: creating $ac_file" >&6;} + { printf "%s\n" "$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 $configure_input in #( *\&* | *\|* | *\\* ) - ac_sed_conf_input=`$as_echo "$configure_input" | + ac_sed_conf_input=`printf "%s\n" "$configure_input" | sed 's/[\\\\&|]/\\\\&/g'`;; #( *) ac_sed_conf_input=$configure_input;; esac @@ -2923,7 +2965,7 @@ $as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ X"$ac_file" : 'X\(//\)[^/]' \| \ X"$ac_file" : 'X\(//\)$' \| \ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$ac_file" | +printf "%s\n" X"$ac_file" | sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/ q @@ -2947,9 +2989,9 @@ $as_echo X"$ac_file" | case "$ac_dir" in .) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;; *) - ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'` + ac_dir_suffix=/`printf "%s\n" "$ac_dir" | sed 's|^\.[\\/]||'` # A ".." for each directory in $ac_dir_suffix. - ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'` + ac_top_builddir_sub=`printf "%s\n" "$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/ ;; @@ -3002,8 +3044,8 @@ ac_sed_dataroot=' case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in *datarootdir*) ac_datarootdir_seen=yes;; *@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*) - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 -$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;} + { printf "%s\n" "$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=' @@ -3045,9 +3087,9 @@ 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"; } && - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined" >&5 -$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' +printf "%s\n" "$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" @@ -3094,7 +3136,8 @@ if test "$no_create" != yes; then $ac_cs_success || as_fn_exit 1 fi if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 -$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} + { printf "%s\n" "$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 + diff --git a/cran-comments.md b/cran-comments.md index 91eb495..1274c67 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,6 +1,6 @@ Dear CRAN volunteers, -Thank you very much for reviewing this submission. I recognize that there were many issues with the previous submission of this package (back in May 2021), and I apologize for my carelessness. I am extremely grateful to CRAN volunteers for providing advice on addressing these issues. I have verified that the package passes CRAN package checks on both the Win-Builder and macOS platforms, along with several other environments using GitHub Actions and Docker (see Test environments below). I have also aimed to verify that the system requirements for this package are available on CRAN's check servers, and provide links to relevant files/documentation that indicate the presence of these requirements on CRAN's servers (see System requirements below). +Thank you very much for reviewing this submission. I recognize that there were many issues with the previous submission of this package (back in May 2021), and I apologize for my carelessness. I am extremely grateful to CRAN volunteers for providing such detailed advice on addressing these issues. I have verified that the package passes CRAN package checks on both the Win-Builder and macOS platforms, along with several other environments using GitHub Actions and Docker (see Test environments below). I have also aimed to verify that the system requirements for this package are available on CRAN's check servers, and provide details indicating the presence of these requirements on CRAN's servers (see System requirements below). Cheers, @@ -22,6 +22,10 @@ Jeff # Notes +* Requires non-standard build of gmp (undeclared and unchecked). + + **This message appears when testing the package on WinBuilder. My understanding is that this message is displayed because the package uses the RWinLib infrastructure to obtain a version of gmp with the C++ bindings available (see https://github.com/rwinlib/gmp). Although the standard Windows Rtools build-chain does provide such C++ bindings (see https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-gmp/PKGBUILD), WinBuilder has a manually installed version of gmp -- which overrides the version of gmp distributed with Rtools -- that does not provide the C++ bindings (indicated by https://win-builder.r-project.org/GPLcompliance/). As such, a non-standard build of gmp is used when compiling the package on WinBuilder (i.e., the gmp build obtained from the RWinLib infrastructure).** + * checking installed package size ... NOTE installed size is 14.4Mb sub-directories of 1Mb or more: @@ -36,21 +40,27 @@ Jeff # System requirements -The package has system requirements. Some of these requirements are mandatory -- and are required for successful installation -- and others are optional. To help ensure that these requirements are available on CRAN systems, I have checked that they are available under the Windows and macOS toolchains (i.e., [RTools](https://cran.r-project.org/bin/windows/Rtools/rtools40.html) and [macOS recipes](https://github.com/R-macos/recipes), respectively) and the rcheckserver Debian meta-package used by CRAN's Debian server. Below, I have provided information on whether each requirement is optional or mandatory, as well as a link indicating the requirement is available on CRAN's Debian, Windows, and macOS systems. +The package has system requirements. Some of these requirements are mandatory -- and are required for successful installation -- and others are optional. To ensure that all mandatory requirements are available on CRAN systems, I have checked the software installed on CRAN's various systems. Briefly, this information was obtained from the [Windows](https://github.com/r-windows/rtools-packages) and [macOS](https://github.com/R-macos/recipes) toolchains; the [rcheckserver Debian meta-package](https://statmath.wu.ac.at/AASC/debian/dists/stable/main/binary-amd64/Packages), and correspondence with CRAN volunteers. + +Below, I have provided a markdown table detailing whether each system requirement is optional or mandatory under various operating systems. I have also included details and URLs verifying the availability of mandatory system requirements on CRAN's systems. + +| Software | Debian | Fedora | Windows | macOS | +|:--------|:---------:|:--------:|:------:|:------:| +| JAGS (>= 4.3.0) | Optional | Optional |Optional | Optional | +| fftw3 (>= 3.3) | Mandatory (1) | Mandatory (1) | Mandatory (1) | Mandatory (1) | +| gmp (>= 6.2.1) | Mandatory (2) | Mandatory (3) | [Mandatory](https://statmath.wu.ac.at/AASC/debian/dists/stable/main/binary-amd64/Packages) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-gmp/PKGBUILD) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-gmp/PKGBUILD) | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/gmp) | +| gmpxx (>= 6.2.1) | [Mandatory (2)](https://statmath.wu.ac.at/AASC/debian/dists/stable/main/binary-amd64/Packages) | Mandatory (3) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-gmp/PKGBUILD) | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/gmp) | +| mpfr (>= 4.1.0) | [Mandatory (4)](https://statmath.wu.ac.at/AASC/debian/dists/stable/main/binary-amd64/Packages) | Mandatory (4) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-mpfr/PKGBUILD) | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/mpfr) | +| autoconf (>= 2.69) | Optional | Optional | Optional | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/autoconf) | +| automake (>= 1.16.5) | Optional | Optional | Optional | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/automake) | + +(1) This requirement is available on all of CRAN's servers because the PoissonBinomial R package relies on the fftw3 library as a system requirement and this package passes checks on all systems (see https://cran.r-project.org/package=PoissonBinomial). -| Software | Debian | Windows | macOS | -|:--------|:---------:|:--------:|:------:| -| JAGS (>= 4.3.0) | Optional |Optional | Optional | -| gmp (>= 6.2.1) | [Mandatory (1)](https://statmath.wu.ac.at/AASC/debian/dists/stable/main/binary-amd64/Packages) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-gmp/PKGBUILD) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-gmp/PKGBUILD) | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/gmp) | -| gmpxx (>= 6.2.1) | [Mandatory (1)](https://statmath.wu.ac.at/AASC/debian/dists/stable/main/binary-amd64/Packages) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-gmp/PKGBUILD) | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/gmp) | -| mpfr (>= 4.1.0) | [Mandatory (2)](https://statmath.wu.ac.at/AASC/debian/dists/stable/main/binary-amd64/Packages) | [Mandatory](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-mpfr/PKGBUILD) | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/mpfr) | -| pkgconfig (>= 0.29.2) | Optional | [Optional](https://github.com/r-windows/rtools-packages/blob/master/mingw-w64-mpfr/PKGBUILD) | [Optional](https://github.com/R-macos/recipes/blob/master/recipes/pkgconfig) | -| autoconf (>= 2.69) | Optional | Optional | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/autoconf) | -| automake (>= 1.16.5) | Optinal | Optional | [Mandatory](https://github.com/R-macos/recipes/blob/master/recipes/automake) | +(2) This requirement is available on CRAN's Debian server(s) because it is available via the Debian libgmp3-dev package, and this package is a dependency of the rcheckserver Debian meta-package. -(1) This system requirement is available on CRAN's Debian server because it is available via the Debian libgmp3-dev package, and this package is a dependency of the rcheckserver Debian meta-package. +(3) This requirement is available on CRAN's Fedora server(s) because Prof. Brian Ripely checked that that the gmp-devel RPM is available on each machine (i.e., https://fedora.pkgs.org/35/fedora-x86_64/gmp-devel-6.2.0-7.fc35.i686.rpm.html) (Prof Brian Ripley, personal communication, August 25, 2022). -(2) This requirement is available on CRAN's Debian server because it is available via the Debian libmpfr-dev package, and this package is a dependency of the rcheckserver Debian meta-package. +(4) This requirement is available on all of CRAN's servers because the Rmpfr R package relies on the mpfr library as a system requirement and this package passes checks on all systems (see https://cran.r-project.org/package=Rmpfr). # Downstream dependencies @@ -75,4 +85,4 @@ from the published 'recipes' at https://github.com/R-macos/recipes). * Please always add all authors, contributors and copyright holders in the Authors@R field with the appropriate roles. e.g.: Free Software Foundation, Inc. Please explain in the submission comments what you did about this issue. - **This comment was raised on a previous submission wherein the Free Software Foundation was listed as a copyright holder. I had previously listed the foundation as a copyright holder because the package contained a header file copied from the gmp library. Since the package now uses the RWinLib infrastructure to handle gmpxx dependencies (https://github.com/rwinlib/gmp), the header file has been removed from package and the Free Software Foundation removed as a copyright holder.** + **This comment was raised on a previous submission wherein the Free Software Foundation was listed as a copyright holder. Previously, the foundation was listed a copyright holder because the package contained a header file from the gmp library to help ensure that dependencies were available. Since the dependencies should now all be available on CRAN's systems, the header file has been removed and, as such, the foundation has been removed as a copyright holder.** diff --git a/docs/404.html b/docs/404.html index 2feb9c6..aa24777 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ surveyvoi - 1.0.3.11 + 1.0.4 @@ -91,7 +91,7 @@

Page not found (404)

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/articles/index.html b/docs/articles/index.html index b11fa9c..41a9f14 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.11 + 1.0.4 @@ -65,7 +65,7 @@

All vignettes

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/articles/surveyvoi.html b/docs/articles/surveyvoi.html index 8197157..1a181d6 100644 --- a/docs/articles/surveyvoi.html +++ b/docs/articles/surveyvoi.html @@ -33,7 +33,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -72,7 +72,7 @@

surveyvoi: Survey Value of Information

Jeffrey O. Hanson

-

2022-07-23

+

2022-08-26

Source: vignettes/surveyvoi.Rmd @@ -151,8 +151,7 @@

Simulate data## 8 (0.590849 0.748232) ## 9 (0.373888 0.150227) ## 10 (0.141298 0.307626) -## # … with 20 more rows -## # ℹ Use `print(n = ...)` to see more rows +## # … with 20 more rows
 # plot the spatial location of the sites
 ggplot(site_data) +
@@ -304,8 +303,7 @@ 

Modeling probability of occupancy## 8 0.565847 ## 9 0.452463 ## 10 0.565847 -## # … with 20 more rows -## # ℹ Use `print(n = ...)` to see more rows

+## # … with 20 more rows
 site_data$p1 <- xgb_predictions$f1
diff --git a/docs/authors.html b/docs/authors.html index e3dfb0c..195bbef 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.11 + 1.0.4
@@ -78,13 +78,13 @@

Citation

Hanson JO, Chadès I, Hudgins EJ, Bennett JR (2022). surveyvoi: Survey Value of Information. -R package version 1.0.3.11, https://prioritizr.github.io/surveyvoi/. +R package version 1.0.4, https://prioritizr.github.io/surveyvoi/.

@Manual{,
   title = {surveyvoi: Survey Value of Information},
   author = {Jeffrey O Hanson and Iadine Chadès and Emma J Hudgins and Joseph R Bennett},
   year = {2022},
-  note = {R package version 1.0.3.11},
+  note = {R package version 1.0.4},
   url = {https://prioritizr.github.io/surveyvoi/},
 }
@@ -99,7 +99,7 @@

Citation

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/index.html b/docs/index.html index c6b3b54..7e17d03 100644 --- a/docs/index.html +++ b/docs/index.html @@ -46,7 +46,7 @@ surveyvoi - 1.0.3.11 + 1.0.4 @@ -126,7 +126,7 @@

macOS

Citation

Please cite the surveyvoi R package when using it in publications. To cite the developmental version, please use:

-

Hanson JO, Chadès I, Hudgins EJ, Bennett J (2022). surveyvoi: Survey Value of Information. R package version 1.0.3.10. Available at https://github.com/prioritizr/surveyvoi.

+

Hanson JO, Chadès I, Hudgins EJ, Bennett J (2022). surveyvoi: Survey Value of Information. R package version 1.0.4. Available at https://github.com/prioritizr/surveyvoi.

Usage @@ -351,7 +351,7 @@

Dev status

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/news/index.html b/docs/news/index.html index 75fc7de..2cc22c9 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.11 + 1.0.4
@@ -50,6 +50,14 @@

Changelog

Source: NEWS.md +
+ +
  • CRAN release.
+
+ +
  • Update CRAN comments document and remove pkg-config from system requirements.
  • +
  • Fix compiler warning thrown during installation.
  • +
@@ -144,7 +152,7 @@

Examples

#> 6 3.35 48.9 1 0.667 0.333 3 3 3 -1.18 0.557 0.896 0.998 #> # … with 2 more variables: p3 <dbl>, geometry <POINT>, and abbreviated variable #> # names ¹​survey_cost, ²​management_cost -#> # ℹ Use `colnames()` to see all variable names # load example feature data data(sim_features) @@ -357,7 +356,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/approx_near_optimal_survey_scheme.html b/docs/reference/approx_near_optimal_survey_scheme.html index 7214516..1a652c7 100644 --- a/docs/reference/approx_near_optimal_survey_scheme.html +++ b/docs/reference/approx_near_optimal_survey_scheme.html @@ -20,7 +20,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -368,7 +368,6 @@

Examples

#> 6 3.35 48.9 1 0.667 0.333 3 3 3 -1.18 0.557 0.896 0.998 #> # … with 2 more variables: p3 <dbl>, geometry <POINT>, and abbreviated variable #> # names ¹​survey_cost, ²​management_cost -#> # ℹ Use `colnames()` to see all variable names # load example feature data data(sim_features) @@ -420,7 +419,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/approx_optimal_survey_scheme.html b/docs/reference/approx_optimal_survey_scheme.html index b4947b0..e335f6e 100644 --- a/docs/reference/approx_optimal_survey_scheme.html +++ b/docs/reference/approx_optimal_survey_scheme.html @@ -19,7 +19,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -347,7 +347,6 @@

Examples

#> 6 3.35 48.9 1 0.667 0.333 3 3 3 -1.18 0.557 0.896 0.998 #> # … with 2 more variables: p3 <dbl>, geometry <POINT>, and abbreviated variable #> # names ¹​survey_cost, ²​management_cost -#> # ℹ Use `colnames()` to see all variable names # load example feature data data(sim_features) @@ -425,7 +424,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/env_div_survey_scheme.html b/docs/reference/env_div_survey_scheme.html index e3df34a..0c33404 100644 --- a/docs/reference/env_div_survey_scheme.html +++ b/docs/reference/env_div_survey_scheme.html @@ -18,7 +18,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -222,7 +222,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/evdci.html b/docs/reference/evdci.html index 30b931d..44e2b6a 100644 --- a/docs/reference/evdci.html +++ b/docs/reference/evdci.html @@ -20,7 +20,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -254,7 +254,6 @@

Examples

#> 6 3.35 48.9 1 0.667 0.333 3 3 3 -1.18 0.557 0.896 0.998 #> # … with 2 more variables: p3 <dbl>, geometry <POINT>, and abbreviated variable #> # names ¹​survey_cost, ²​management_cost -#> # ℹ Use `colnames()` to see all variable names # load example feature data data(sim_features) @@ -297,7 +296,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/evdsi.html b/docs/reference/evdsi.html index 8cca7a8..ab8a068 100644 --- a/docs/reference/evdsi.html +++ b/docs/reference/evdsi.html @@ -20,7 +20,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -284,7 +284,6 @@

Examples

#> 6 3.35 48.9 1 0.667 0.333 3 3 3 -1.18 0.557 0.896 0.998 #> # … with 2 more variables: p3 <dbl>, geometry <POINT>, and abbreviated variable #> # names ¹​survey_cost, ²​management_cost -#> # ℹ Use `colnames()` to see all variable names # load example feature data data(sim_features) @@ -333,7 +332,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/feasible_survey_schemes.html b/docs/reference/feasible_survey_schemes.html index b1a1c58..8ed4ebf 100644 --- a/docs/reference/feasible_survey_schemes.html +++ b/docs/reference/feasible_survey_schemes.html @@ -18,7 +18,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -188,7 +188,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/fit_hglm_occupancy_models.html b/docs/reference/fit_hglm_occupancy_models.html index d087000..0c3a1e1 100644 --- a/docs/reference/fit_hglm_occupancy_models.html +++ b/docs/reference/fit_hglm_occupancy_models.html @@ -23,7 +23,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -739,7 +739,6 @@

Examples

#> 9 1.72e- 6 0.999 #> 10 8.00e- 3 0.953 #> # … with 20 more rows -#> # ℹ Use `print(n = ...)` to see more rows # print model performance print(results$performance, width = Inf) @@ -775,7 +774,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/fit_xgb_occupancy_models.html b/docs/reference/fit_xgb_occupancy_models.html index 6d14db0..4a2fd78 100644 --- a/docs/reference/fit_xgb_occupancy_models.html +++ b/docs/reference/fit_xgb_occupancy_models.html @@ -19,7 +19,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -371,7 +371,6 @@

Examples

#> 9 0.450 0.547 #> 10 0.459 0.549 #> # … with 20 more rows -#> # ℹ Use `print(n = ...)` to see more rows # print model performance print(results$performance, width = Inf) @@ -407,7 +406,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/geo_cov_survey_scheme.html b/docs/reference/geo_cov_survey_scheme.html index dcf7a50..de367d5 100644 --- a/docs/reference/geo_cov_survey_scheme.html +++ b/docs/reference/geo_cov_survey_scheme.html @@ -18,7 +18,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -203,7 +203,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 7a7fb01..a462010 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.11 + 1.0.4 @@ -166,7 +166,7 @@

Miscellaneous function -

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/n_states.html b/docs/reference/n_states.html index 93e5102..a71cbec 100644 --- a/docs/reference/n_states.html +++ b/docs/reference/n_states.html @@ -18,7 +18,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -98,7 +98,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/optimal_survey_scheme.html b/docs/reference/optimal_survey_scheme.html index 2ee46f4..b0fd569 100644 --- a/docs/reference/optimal_survey_scheme.html +++ b/docs/reference/optimal_survey_scheme.html @@ -19,7 +19,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -322,7 +322,6 @@

Examples

#> 6 3.35 48.9 1 0.667 0.333 3 3 3 -1.18 0.557 0.896 0.998 #> # … with 2 more variables: p3 <dbl>, geometry <POINT>, and abbreviated variable #> # names ¹​survey_cost, ²​management_cost -#> # ℹ Use `colnames()` to see all variable names # load example feature data data(sim_features) @@ -376,7 +375,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/prior_probability_matrix.html b/docs/reference/prior_probability_matrix.html index 07860c2..524ef98 100644 --- a/docs/reference/prior_probability_matrix.html +++ b/docs/reference/prior_probability_matrix.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -181,7 +181,6 @@

Examples

#> 6 3.35 48.9 1 0.667 0.333 3 3 3 -1.18 0.557 0.896 0.998 #> # … with 2 more variables: p3 <dbl>, geometry <POINT>, and abbreviated variable #> # names ¹​survey_cost, ²​management_cost -#> # ℹ Use `colnames()` to see all variable names # load example feature data data(sim_features) @@ -221,7 +220,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/relative_site_richness_scores.html b/docs/reference/relative_site_richness_scores.html index 74373d6..59a273d 100644 --- a/docs/reference/relative_site_richness_scores.html +++ b/docs/reference/relative_site_richness_scores.html @@ -20,7 +20,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -161,7 +161,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/relative_site_uncertainty_scores.html b/docs/reference/relative_site_uncertainty_scores.html index 39dea3e..120eee2 100644 --- a/docs/reference/relative_site_uncertainty_scores.html +++ b/docs/reference/relative_site_uncertainty_scores.html @@ -21,7 +21,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -167,7 +167,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/sim_data.html b/docs/reference/sim_data.html index fd0f921..8441734 100644 --- a/docs/reference/sim_data.html +++ b/docs/reference/sim_data.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -169,7 +169,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/simulate_feature_data.html b/docs/reference/simulate_feature_data.html index e4b8dc0..3b43164 100644 --- a/docs/reference/simulate_feature_data.html +++ b/docs/reference/simulate_feature_data.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -157,7 +157,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/simulate_site_data.html b/docs/reference/simulate_site_data.html index 41a42e3..213107f 100644 --- a/docs/reference/simulate_site_data.html +++ b/docs/reference/simulate_site_data.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -225,7 +225,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/surveyvoi.html b/docs/reference/surveyvoi.html index 3df77a8..522e660 100644 --- a/docs/reference/surveyvoi.html +++ b/docs/reference/surveyvoi.html @@ -28,7 +28,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -106,7 +106,7 @@

See also

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/weighted_survey_scheme.html b/docs/reference/weighted_survey_scheme.html index 4e53a93..17c64bd 100644 --- a/docs/reference/weighted_survey_scheme.html +++ b/docs/reference/weighted_survey_scheme.html @@ -18,7 +18,7 @@ surveyvoi - 1.0.3.10 + 1.0.4 @@ -207,7 +207,7 @@

Examples

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/inst/doc/surveyvoi.html b/inst/doc/surveyvoi.html index b4251ff..1c66a1c 100644 --- a/inst/doc/surveyvoi.html +++ b/inst/doc/surveyvoi.html @@ -12,7 +12,7 @@ - + surveyvoi: Survey Value of Information @@ -110,13 +110,20 @@ for (var i = 0; i < sheets.length; i++) { if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue; try { var rules = sheets[i].cssRules; } catch (e) { continue; } - for (var j = 0; j < rules.length; j++) { + var j = 0; + while (j < rules.length) { var rule = rules[j]; // check if there is a div.sourceCode rule - if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") continue; + if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") { + j++; + continue; + } var style = rule.style.cssText; // check if color or background-color is set - if (rule.style.color === '' && rule.style.backgroundColor === '') continue; + if (rule.style.color === '' && rule.style.backgroundColor === '') { + j++; + continue; + } // replace div.sourceCode by a pre.sourceCode rule sheets[i].deleteRule(j); sheets[i].insertRule('pre.sourceCode{' + style + '}', j); @@ -164,7 +171,7 @@

surveyvoi: Survey Value of Information

Jeffrey O. Hanson

-

2022-07-23

+

2022-08-26

@@ -247,8 +254,7 @@

Simulate data

## 8 (0.590849 0.748232) ## 9 (0.373888 0.150227) ## 10 (0.141298 0.307626) -## # … with 20 more rows -## # ℹ Use `print(n = ...)` to see more rows +## # … with 20 more rows
# plot the spatial location of the sites
 ggplot(site_data) +
   geom_sf() +
@@ -389,8 +395,7 @@ 

Modeling probability of occupancy

## 8 0.565847 ## 9 0.452463 ## 10 0.565847 -## # … with 20 more rows -## # ℹ Use `print(n = ...)` to see more rows
+## # … with 20 more rows
site_data$p1 <- xgb_predictions$f1
# plot site-level estimated occupancy probabilities
 site_data %>%
diff --git a/src/rcpp_model_performance.cpp b/src/rcpp_model_performance.cpp
index ff8d5e2..8cc1a22 100644
--- a/src/rcpp_model_performance.cpp
+++ b/src/rcpp_model_performance.cpp
@@ -24,11 +24,11 @@ void model_sensitivity_and_specificity(
   double total_negative = static_cast(w.sum()) - total_positive;
   double true_positive = static_cast(
     (w.array() *
-    ((yhat.array() >= 0.5f) * (y.array() >= 0.5f)).cast()).sum()
+    ((yhat.array() >= 0.5f) && (y.array() >= 0.5f)).cast()).sum()
   );
   double true_negative = static_cast(
     (w.array() *
-     ((yhat.array() < 0.5f) * (y.array() < 0.5f)).cast()).sum()
+     ((yhat.array() < 0.5f) && (y.array() < 0.5f)).cast()).sum()
   );
   double false_negative = total_positive - true_positive;
   double false_positive = total_negative - true_negative;
diff --git a/tests/testthat/helper_skip_functions.R b/tests/testthat/helper_skip_functions.R
new file mode 100644
index 0000000..e25f039
--- /dev/null
+++ b/tests/testthat/helper_skip_functions.R
@@ -0,0 +1,8 @@
+skip_if_parallel_processing_not_available <- function() {
+  skip_if(
+    (!requireNamespace("surveyvoi", quietly = TRUE) &&
+      !identical(.Platform$OS.type, "unix")) ||
+    (!"surveyvoi" %in% rownames(installed.packages())),
+    message = "parallel processing not available"
+  )
+}
diff --git a/tests/testthat/test_approx_near_optimal_survey_scheme.R b/tests/testthat/test_approx_near_optimal_survey_scheme.R
index 5a52b93..83a50b8 100644
--- a/tests/testthat/test_approx_near_optimal_survey_scheme.R
+++ b/tests/testthat/test_approx_near_optimal_survey_scheme.R
@@ -217,9 +217,7 @@ test_that("consistent results", {
 test_that("consistent results (multiple threads)", {
   skip_on_cran()
   skip_on_os("windows")
-  # skip if using PSOCK cluster and package not installed
-  skip_if(!requireNamespace("surveyvoi") &&
-          !identical(.Platform$OS.type, "unix"))
+  skip_if_parallel_processing_not_available()
   # seeds
   set.seed(505)
   # data
diff --git a/tests/testthat/test_cluster.R b/tests/testthat/test_cluster.R
index 4bad4e7..e9c1594 100644
--- a/tests/testthat/test_cluster.R
+++ b/tests/testthat/test_cluster.R
@@ -3,6 +3,7 @@ context("cluster")
 test_that("FORK", {
   skip_on_cran()
   skip_on_os("windows")
+  skip_if_parallel_processing_not_available()
   # data
   x <- seq_len(3)
   f <- function(z) {
@@ -21,6 +22,7 @@ test_that("FORK", {
 
 test_that("PSOCK", {
   skip_on_cran()
+  skip_if_parallel_processing_not_available()
   # data
   x <- seq_len(3)
   f <- function(z) {
diff --git a/tests/testthat/test_fit_hglm_occupancy_models.R b/tests/testthat/test_fit_hglm_occupancy_models.R
index 5dcc740..c80c977 100644
--- a/tests/testthat/test_fit_hglm_occupancy_models.R
+++ b/tests/testthat/test_fit_hglm_occupancy_models.R
@@ -150,9 +150,7 @@ test_that("multiple species (sparse, multiple threads)", {
   skip_on_cran()
   skip_on_os("windows")
   skip_if_not(suppressWarnings(is_jags_installed()))
-  # skip if using PSOCK cluster and package not installed
-  skip_if(!requireNamespace("surveyvoi") &&
-          !identical(.Platform$OS.type, "unix"))
+  skip_if_parallel_processing_not_available()
   # data
   set.seed(123)
   n_pu <- 2000