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config.status
executable file
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config.status
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#! /bin/bash
# Generated by configure.
# Run this file to recreate the current configuration.
# Compiler output produced by configure, useful for debugging
# configure, is in config.log if it exists.
debug=false
ac_cs_recheck=false
ac_cs_silent=false
SHELL=${CONFIG_SHELL-/bin/bash}
export SHELL
## -------------------- ##
## M4sh Initialization. ##
## -------------------- ##
# Be more Bourne compatible
DUALCASE=1; export DUALCASE # for MKS sh
if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
emulate sh
NULLCMD=:
# Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
# is contrary to our usage. Disable this feature.
alias -g '${1+"$@"}'='"$@"'
setopt NO_GLOB_SUBST
else
case `(set -o) 2>/dev/null` in #(
*posix*) :
set -o posix ;; #(
*) :
;;
esac
fi
as_nl='
'
export as_nl
# Printing a long string crashes Solaris 7 /usr/bin/printf.
as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
# Prefer a ksh shell builtin over an external printf program on Solaris,
# but without wasting forks for bash or zsh.
if test -z "$BASH_VERSION$ZSH_VERSION" \
&& (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
as_echo='print -r --'
as_echo_n='print -rn --'
elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
as_echo='printf %s\n'
as_echo_n='printf %s'
else
if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
as_echo_n='/usr/ucb/echo -n'
else
as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
as_echo_n_body='eval
arg=$1;
case $arg in #(
*"$as_nl"*)
expr "X$arg" : "X\\(.*\\)$as_nl";
arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
esac;
expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
'
export as_echo_n_body
as_echo_n='sh -c $as_echo_n_body as_echo'
fi
export as_echo_body
as_echo='sh -c $as_echo_body as_echo'
fi
# The user is always right.
if test "${PATH_SEPARATOR+set}" != set; then
PATH_SEPARATOR=:
(PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
(PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
PATH_SEPARATOR=';'
}
fi
# IFS
# We need space, tab and new line, in precisely that order. Quoting is
# there to prevent editors from complaining about space-tab.
# (If _AS_PATH_WALK were called with IFS unset, it would disable word
# splitting by setting IFS to empty value.)
IFS=" "" $as_nl"
# Find who we are. Look in the path if we contain no directory separator.
as_myself=
case $0 in #((
*[\\/]* ) as_myself=$0 ;;
*) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
done
IFS=$as_save_IFS
;;
esac
# We did not find ourselves, most probably we were run as `sh COMMAND'
# in which case we are not to be found in the path.
if test "x$as_myself" = x; then
as_myself=$0
fi
if test ! -f "$as_myself"; then
$as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
exit 1
fi
# Unset variables that we do not need and which cause bugs (e.g. in
# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
# suppresses any "Segmentation fault" message there. '((' could
# trigger a bug in pdksh 5.2.14.
for as_var in BASH_ENV ENV MAIL MAILPATH
do eval test x\${$as_var+set} = xset \
&& ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
done
PS1='$ '
PS2='> '
PS4='+ '
# NLS nuisances.
LC_ALL=C
export LC_ALL
LANGUAGE=C
export LANGUAGE
# CDPATH.
(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
# as_fn_error STATUS ERROR [LINENO LOG_FD]
# ----------------------------------------
# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
# script with STATUS, using 1 if that was 0.
as_fn_error ()
{
as_status=$1; test $as_status -eq 0 && as_status=1
if test "$4"; then
as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
$as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
fi
$as_echo "$as_me: error: $2" >&2
as_fn_exit $as_status
} # as_fn_error
# as_fn_set_status STATUS
# -----------------------
# Set $? to STATUS, without forking.
as_fn_set_status ()
{
return $1
} # as_fn_set_status
# as_fn_exit STATUS
# -----------------
# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
as_fn_exit ()
{
set +e
as_fn_set_status $1
exit $1
} # as_fn_exit
# as_fn_unset VAR
# ---------------
# Portably unset VAR.
as_fn_unset ()
{
{ eval $1=; unset $1;}
}
as_unset=as_fn_unset
# as_fn_append VAR VALUE
# ----------------------
# Append the text in VALUE to the end of the definition contained in VAR. Take
# advantage of any shell optimizations that allow amortized linear growth over
# repeated appends, instead of the typical quadratic growth present in naive
# implementations.
if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
eval 'as_fn_append ()
{
eval $1+=\$2
}'
else
as_fn_append ()
{
eval $1=\$$1\$2
}
fi # as_fn_append
# as_fn_arith ARG...
# ------------------
# Perform arithmetic evaluation on the ARGs, and store the result in the
# global $as_val. Take advantage of shells that can avoid forks. The arguments
# must be portable across $(()) and expr.
if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
eval 'as_fn_arith ()
{
as_val=$(( $* ))
}'
else
as_fn_arith ()
{
as_val=`expr "$@" || test $? -eq 1`
}
fi # as_fn_arith
if expr a : '\(a\)' >/dev/null 2>&1 &&
test "X`expr 00001 : '.*\(...\)'`" = X001; then
as_expr=expr
else
as_expr=false
fi
if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
as_basename=basename
else
as_basename=false
fi
if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
as_dirname=dirname
else
as_dirname=false
fi
as_me=`$as_basename -- "$0" ||
$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
X"$0" : 'X\(//\)$' \| \
X"$0" : 'X\(/\)' \| . 2>/dev/null ||
$as_echo X/"$0" |
sed '/^.*\/\([^/][^/]*\)\/*$/{
s//\1/
q
}
/^X\/\(\/\/\)$/{
s//\1/
q
}
/^X\/\(\/\).*/{
s//\1/
q
}
s/.*/./; q'`
# Avoid depending upon Character Ranges.
as_cr_letters='abcdefghijklmnopqrstuvwxyz'
as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
as_cr_Letters=$as_cr_letters$as_cr_LETTERS
as_cr_digits='0123456789'
as_cr_alnum=$as_cr_Letters$as_cr_digits
ECHO_C= ECHO_N= ECHO_T=
case `echo -n x` in #(((((
-n*)
case `echo 'xy\c'` in
*c*) ECHO_T=' ';; # ECHO_T is single tab character.
xy) ECHO_C='\c';;
*) echo `echo ksh88 bug on AIX 6.1` > /dev/null
ECHO_T=' ';;
esac;;
*)
ECHO_N='-n';;
esac
rm -f conf$$ conf$$.exe conf$$.file
if test -d conf$$.dir; then
rm -f conf$$.dir/conf$$.file
else
rm -f conf$$.dir
mkdir conf$$.dir 2>/dev/null
fi
if (echo >conf$$.file) 2>/dev/null; then
if ln -s conf$$.file conf$$ 2>/dev/null; then
as_ln_s='ln -s'
# ... but there are two gotchas:
# 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
# 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
# In both cases, we have to default to `cp -pR'.
ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
as_ln_s='cp -pR'
elif ln conf$$.file conf$$ 2>/dev/null; then
as_ln_s=ln
else
as_ln_s='cp -pR'
fi
else
as_ln_s='cp -pR'
fi
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null
# as_fn_mkdir_p
# -------------
# Create "$as_dir" as a directory, including parents if necessary.
as_fn_mkdir_p ()
{
case $as_dir in #(
-*) as_dir=./$as_dir;;
esac
test -d "$as_dir" || eval $as_mkdir_p || {
as_dirs=
while :; do
case $as_dir in #(
*\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
*) as_qdir=$as_dir;;
esac
as_dirs="'$as_qdir' $as_dirs"
as_dir=`$as_dirname -- "$as_dir" ||
$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
X"$as_dir" : 'X\(//\)[^/]' \| \
X"$as_dir" : 'X\(//\)$' \| \
X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
$as_echo X"$as_dir" |
sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
s//\1/
q
}
/^X\(\/\/\)[^/].*/{
s//\1/
q
}
/^X\(\/\/\)$/{
s//\1/
q
}
/^X\(\/\).*/{
s//\1/
q
}
s/.*/./; q'`
test -d "$as_dir" && break
done
test -z "$as_dirs" || eval "mkdir $as_dirs"
} || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
} # as_fn_mkdir_p
if mkdir -p . 2>/dev/null; then
as_mkdir_p='mkdir -p "$as_dir"'
else
test -d ./-p && rmdir ./-p
as_mkdir_p=false
fi
# as_fn_executable_p FILE
# -----------------------
# Test if FILE is an executable regular file.
as_fn_executable_p ()
{
test -f "$1" && test -x "$1"
} # as_fn_executable_p
as_test_x='test -x'
as_executable_p=as_fn_executable_p
# Sed expression to map a string onto a valid CPP name.
as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
# Sed expression to map a string onto a valid variable name.
as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
exec 6>&1
## ----------------------------------- ##
## Main body of $CONFIG_STATUS script. ##
## ----------------------------------- ##
# Save the log message, to keep $0 and so on meaningful, and to
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by orparapp $as_me 0.1.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
CONFIG_HEADERS = $CONFIG_HEADERS
CONFIG_LINKS = $CONFIG_LINKS
CONFIG_COMMANDS = $CONFIG_COMMANDS
$ $0 $@
on `(hostname || uname -n) 2>/dev/null | sed 1q`
"
# Files that config.status was made for.
config_files=" docs/Doxyfile docs/Makefile Makefile src/Makefile src/consensus/Makefile src/seqana/Makefile src/seqana/cdna/Makefile src/seqana/fasta/Makefile src/seqana/seqsep/Makefile src/seqconv/Makefile src/bionj/Makefile src/test/Makefile"
config_headers=" config.h"
config_commands=" depfiles libtool"
ac_cs_usage="\
\`$as_me' instantiates files and other configuration actions
from templates according to the current configuration. Unless the files
and actions are specified as TAGs, all are instantiated by default.
Usage: $0 [OPTION]... [TAG]...
-h, --help print this help, then exit
-V, --version print version number and configuration settings, then exit
--config print configuration, then exit
-q, --quiet, --silent
do not print progress messages
-d, --debug don't remove temporary files
--recheck update $as_me by reconfiguring in the same conditions
--file=FILE[:TEMPLATE]
instantiate the configuration file FILE
--header=FILE[:TEMPLATE]
instantiate the configuration header FILE
Configuration files:
$config_files
Configuration headers:
$config_headers
Configuration commands:
$config_commands
Report bugs to <[email protected]>."
ac_cs_config=""
ac_cs_version="\
orparapp config.status 0.1.0
configured by ./configure, generated by GNU Autoconf 2.69,
with options \"$ac_cs_config\"
Copyright (C) 2012 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it."
ac_pwd='/home/kzhou/coding/orparapp'
srcdir='.'
INSTALL='/usr/bin/install -c'
MKDIR_P='/bin/mkdir -p'
AWK='mawk'
test -n "$AWK" || AWK=awk
# The default lists apply if the user does not specify any file.
ac_need_defaults=:
while test $# != 0
do
case $1 in
--*=?*)
ac_option=`expr "X$1" : 'X\([^=]*\)='`
ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
ac_shift=:
;;
--*=)
ac_option=`expr "X$1" : 'X\([^=]*\)='`
ac_optarg=
ac_shift=:
;;
*)
ac_option=$1
ac_optarg=$2
ac_shift=shift
;;
esac
case $ac_option in
# Handling of the options.
-recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
ac_cs_recheck=: ;;
--version | --versio | --versi | --vers | --ver | --ve | --v | -V )
$as_echo "$ac_cs_version"; exit ;;
--config | --confi | --conf | --con | --co | --c )
$as_echo "$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"` ;;
'') as_fn_error $? "missing file argument" ;;
esac
as_fn_append CONFIG_FILES " '$ac_optarg'"
ac_need_defaults=false;;
--header | --heade | --head | --hea )
$ac_shift
case $ac_optarg in
*\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
esac
as_fn_append CONFIG_HEADERS " '$ac_optarg'"
ac_need_defaults=false;;
--he | --h)
# Conflict between --help and --header
as_fn_error $? "ambiguous option: \`$1'
Try \`$0 --help' for more information.";;
--help | --hel | -h )
$as_echo "$ac_cs_usage"; exit ;;
-q | -quiet | --quiet | --quie | --qui | --qu | --q \
| -silent | --silent | --silen | --sile | --sil | --si | --s)
ac_cs_silent=: ;;
# This is an error.
-*) as_fn_error $? "unrecognized option: \`$1'
Try \`$0 --help' for more information." ;;
*) as_fn_append ac_config_targets " $1"
ac_need_defaults=false ;;
esac
shift
done
ac_configure_extra_args=
if $ac_cs_silent; then
exec 6>/dev/null
ac_configure_extra_args="$ac_configure_extra_args --silent"
fi
if $ac_cs_recheck; then
set X /bin/bash './configure' $ac_configure_extra_args --no-create --no-recursion
shift
$as_echo "running CONFIG_SHELL=/bin/bash $*" >&6
CONFIG_SHELL='/bin/bash'
export CONFIG_SHELL
exec "$@"
fi
exec 5>>config.log
{
echo
sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
## Running $as_me. ##
_ASBOX
$as_echo "$ac_log"
} >&5
#
# INIT-COMMANDS
#
AMDEP_TRUE="" ac_aux_dir="."
# The HP-UX ksh and POSIX shell print the target directory to stdout
# if CDPATH is set.
(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
sed_quote_subst='s/\(["`$\\]\)/\\\1/g'
double_quote_subst='s/\(["`\\]\)/\\\1/g'
delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
macro_version='2.4.6'
macro_revision='2.4.6'
enable_shared='yes'
enable_static='yes'
pic_mode='default'
enable_fast_install='yes'
shared_archive_member_spec=''
SHELL='/bin/bash'
ECHO='printf %s\n'
PATH_SEPARATOR=':'
host_alias=''
host='x86_64-pc-linux-gnu'
host_os='linux-gnu'
build_alias=''
build='x86_64-pc-linux-gnu'
build_os='linux-gnu'
SED='/bin/sed'
Xsed='/bin/sed -e 1s/^X//'
GREP='/bin/grep'
EGREP='/bin/grep -E'
FGREP='/bin/grep -F'
LD='/usr/bin/ld -m elf_x86_64'
NM='/usr/bin/nm -B'
LN_S='ln -s'
max_cmd_len='1572864'
ac_objext='o'
exeext=''
lt_unset='unset'
lt_SP2NL='tr \040 \012'
lt_NL2SP='tr \015\012 \040\040'
lt_cv_to_host_file_cmd='func_convert_file_noop'
lt_cv_to_tool_file_cmd='func_convert_file_noop'
reload_flag=' -r'
reload_cmds='$LD$reload_flag -o $output$reload_objs'
OBJDUMP='objdump'
deplibs_check_method='pass_all'
file_magic_cmd='$MAGIC_CMD'
file_magic_glob=''
want_nocaseglob='no'
DLLTOOL='false'
sharedlib_from_linklib_cmd='printf %s\n'
AR='ar'
AR_FLAGS='cru'
archiver_list_spec='@'
STRIP='strip'
RANLIB='ranlib'
old_postinstall_cmds='chmod 644 $oldlib~$RANLIB $tool_oldlib'
old_postuninstall_cmds=''
old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs~$RANLIB $tool_oldlib'
lock_old_archive_extraction='no'
CC='gcc'
CFLAGS='-g -O2'
compiler='g++'
GCC='yes'
lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'' | sed '\''/ __gnu_lto/d'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
lt_cv_sys_global_symbol_to_import=''
lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \(.*\) .*$/ {"\1", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/ {"\1", (void *) \&\1},/p'\'''
lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \(.*\) .*$/ {"\1", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(lib.*\)$/ {"\1", (void *) \&\1},/p'\'' -e '\''s/^[ABCDGIRSTW][ABCDGIRSTW]* .* \(.*\)$/ {"lib\1", (void *) \&\1},/p'\'''
lt_cv_nm_interface='BSD nm'
nm_file_list_spec='@'
lt_sysroot=''
lt_cv_truncate_bin='/bin/dd bs=4096 count=1'
objdir='.libs'
MAGIC_CMD='file'
lt_prog_compiler_no_builtin_flag=' -fno-builtin'
lt_prog_compiler_pic=' -fPIC -DPIC'
lt_prog_compiler_wl='-Wl,'
lt_prog_compiler_static='-static'
lt_cv_prog_compiler_c_o='yes'
need_locks='no'
MANIFEST_TOOL=':'
DSYMUTIL=''
NMEDIT=''
LIPO=''
OTOOL=''
OTOOL64=''
libext='a'
shrext_cmds='.so'
extract_expsyms_cmds=''
archive_cmds_need_lc='no'
enable_shared_with_static_runtimes='no'
export_dynamic_flag_spec='$wl--export-dynamic'
whole_archive_flag_spec='$wl--whole-archive$convenience $wl--no-whole-archive'
compiler_needs_object='no'
old_archive_from_new_cmds=''
old_archive_from_expsyms_cmds=''
archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags $wl-soname $wl$soname -o $lib'
archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~
cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
echo "local: *; };" >> $output_objdir/$libname.ver~
$CC -shared $pic_flag $libobjs $deplibs $compiler_flags $wl-soname $wl$soname $wl-version-script $wl$output_objdir/$libname.ver -o $lib'
module_cmds=''
module_expsym_cmds=''
with_gnu_ld='yes'
allow_undefined_flag=''
no_undefined_flag=''
hardcode_libdir_flag_spec='$wl-rpath $wl$libdir'
hardcode_libdir_separator=''
hardcode_direct='no'
hardcode_direct_absolute='no'
hardcode_minus_L='no'
hardcode_shlibpath_var='unsupported'
hardcode_automatic='no'
inherit_rpath='no'
link_all_deplibs='no'
always_export_symbols='no'
export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
exclude_expsyms='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
include_expsyms=''
prelink_cmds=''
postlink_cmds=''
file_list_spec=''
variables_saved_for_relink='PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH'
need_lib_prefix='no'
need_version='no'
version_type='linux'
runpath_var='LD_RUN_PATH'
shlibpath_var='LD_LIBRARY_PATH'
shlibpath_overrides_runpath='no'
libname_spec='lib$name'
library_names_spec='$libname$release$shared_ext$versuffix $libname$release$shared_ext$major $libname$shared_ext'
soname_spec='$libname$release$shared_ext$major'
install_override_mode=''
postinstall_cmds=''
postuninstall_cmds=''
finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
finish_eval=''
hardcode_into_libs='yes'
sys_lib_search_path_spec='/usr/lib/gcc/x86_64-linux-gnu/5 /usr/lib/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib '
configure_time_dlsearch_path='/lib /usr/lib /usr/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/mesa-egl /usr/lib/x86_64-linux-gnu/mesa '
configure_time_lt_sys_library_path=''
hardcode_action='immediate'
enable_dlopen='unknown'
enable_dlopen_self='unknown'
enable_dlopen_self_static='unknown'
old_striplib='strip --strip-debug'
striplib='strip --strip-unneeded'
compiler_lib_search_dirs=''
predep_objects=''
postdep_objects=''
predeps=''
postdeps=''
compiler_lib_search_path=''
LD_CXX='/usr/bin/ld -m elf_x86_64'
reload_flag_CXX=' -r'
reload_cmds_CXX='$LD$reload_flag -o $output$reload_objs'
old_archive_cmds_CXX='$AR $AR_FLAGS $oldlib$oldobjs~$RANLIB $tool_oldlib'
compiler_CXX='g++'
GCC_CXX='yes'
lt_prog_compiler_no_builtin_flag_CXX=' -fno-builtin'
lt_prog_compiler_pic_CXX=' -fPIC -DPIC'
lt_prog_compiler_wl_CXX='-Wl,'
lt_prog_compiler_static_CXX='-static'
lt_cv_prog_compiler_c_o_CXX='yes'
archive_cmds_need_lc_CXX='no'
enable_shared_with_static_runtimes_CXX='no'
export_dynamic_flag_spec_CXX='$wl--export-dynamic'
whole_archive_flag_spec_CXX='$wl--whole-archive$convenience $wl--no-whole-archive'
compiler_needs_object_CXX='no'
old_archive_from_new_cmds_CXX=''
old_archive_from_expsyms_cmds_CXX=''
archive_cmds_CXX='$CC $pic_flag -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags $wl-soname $wl$soname -o $lib'
archive_expsym_cmds_CXX='$CC $pic_flag -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags $wl-soname $wl$soname $wl-retain-symbols-file $wl$export_symbols -o $lib'
module_cmds_CXX=''
module_expsym_cmds_CXX=''
with_gnu_ld_CXX='yes'
allow_undefined_flag_CXX=''
no_undefined_flag_CXX=''
hardcode_libdir_flag_spec_CXX='$wl-rpath $wl$libdir'
hardcode_libdir_separator_CXX=''
hardcode_direct_CXX='no'
hardcode_direct_absolute_CXX='no'
hardcode_minus_L_CXX='no'
hardcode_shlibpath_var_CXX='unsupported'
hardcode_automatic_CXX='no'
inherit_rpath_CXX='no'
link_all_deplibs_CXX='no'
always_export_symbols_CXX='no'
export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
exclude_expsyms_CXX='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
include_expsyms_CXX=''
prelink_cmds_CXX=''
postlink_cmds_CXX=''
file_list_spec_CXX=''
hardcode_action_CXX='immediate'
compiler_lib_search_dirs_CXX='/usr/lib/gcc/x86_64-linux-gnu/5 /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu /usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /usr/lib/gcc/x86_64-linux-gnu/5/../../..'
predep_objects_CXX='/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/5/crtbeginS.o'
postdep_objects_CXX='/usr/lib/gcc/x86_64-linux-gnu/5/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crtn.o'
predeps_CXX=''
postdeps_CXX='-lstdc++ -lm -lgcc_s -lc -lgcc_s'
compiler_lib_search_path_CXX='-L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/5/../../..'
LTCC='gcc'
LTCFLAGS='-g -O2'
compiler='gcc'
# A function that is used when there is no print builtin or printf.
func_fallback_echo ()
{
eval 'cat <<_LTECHO_EOF
$1
_LTECHO_EOF'
}
# Quote evaled strings.
for var in SHELL ECHO PATH_SEPARATOR SED GREP EGREP FGREP LD NM LN_S lt_SP2NL lt_NL2SP reload_flag OBJDUMP deplibs_check_method file_magic_cmd file_magic_glob want_nocaseglob DLLTOOL sharedlib_from_linklib_cmd AR AR_FLAGS archiver_list_spec STRIP RANLIB CC CFLAGS compiler lt_cv_sys_global_symbol_pipe lt_cv_sys_global_symbol_to_cdecl lt_cv_sys_global_symbol_to_import lt_cv_sys_global_symbol_to_c_name_address lt_cv_sys_global_symbol_to_c_name_address_lib_prefix lt_cv_nm_interface nm_file_list_spec lt_cv_truncate_bin lt_prog_compiler_no_builtin_flag lt_prog_compiler_pic lt_prog_compiler_wl lt_prog_compiler_static lt_cv_prog_compiler_c_o need_locks MANIFEST_TOOL DSYMUTIL NMEDIT LIPO OTOOL OTOOL64 shrext_cmds export_dynamic_flag_spec whole_archive_flag_spec compiler_needs_object with_gnu_ld allow_undefined_flag no_undefined_flag hardcode_libdir_flag_spec hardcode_libdir_separator exclude_expsyms include_expsyms file_list_spec variables_saved_for_relink libname_spec library_names_spec soname_spec install_override_mode finish_eval old_striplib striplib compiler_lib_search_dirs predep_objects postdep_objects predeps postdeps compiler_lib_search_path LD_CXX reload_flag_CXX compiler_CXX lt_prog_compiler_no_builtin_flag_CXX lt_prog_compiler_pic_CXX lt_prog_compiler_wl_CXX lt_prog_compiler_static_CXX lt_cv_prog_compiler_c_o_CXX export_dynamic_flag_spec_CXX whole_archive_flag_spec_CXX compiler_needs_object_CXX with_gnu_ld_CXX allow_undefined_flag_CXX no_undefined_flag_CXX hardcode_libdir_flag_spec_CXX hardcode_libdir_separator_CXX exclude_expsyms_CXX include_expsyms_CXX file_list_spec_CXX compiler_lib_search_dirs_CXX predep_objects_CXX postdep_objects_CXX predeps_CXX postdeps_CXX compiler_lib_search_path_CXX; do
case `eval \\$ECHO \\""\\$$var"\\"` in
*[\\\`\"\$]*)
eval "lt_$var=\\\"\`\$ECHO \"\$$var\" | \$SED \"\$sed_quote_subst\"\`\\\"" ## exclude from sc_prohibit_nested_quotes
;;
*)
eval "lt_$var=\\\"\$$var\\\""
;;
esac
done
# Double-quote double-evaled strings.
for var in reload_cmds old_postinstall_cmds old_postuninstall_cmds old_archive_cmds extract_expsyms_cmds old_archive_from_new_cmds old_archive_from_expsyms_cmds archive_cmds archive_expsym_cmds module_cmds module_expsym_cmds export_symbols_cmds prelink_cmds postlink_cmds postinstall_cmds postuninstall_cmds finish_cmds sys_lib_search_path_spec configure_time_dlsearch_path configure_time_lt_sys_library_path reload_cmds_CXX old_archive_cmds_CXX old_archive_from_new_cmds_CXX old_archive_from_expsyms_cmds_CXX archive_cmds_CXX archive_expsym_cmds_CXX module_cmds_CXX module_expsym_cmds_CXX export_symbols_cmds_CXX prelink_cmds_CXX postlink_cmds_CXX; do
case `eval \\$ECHO \\""\\$$var"\\"` in
*[\\\`\"\$]*)
eval "lt_$var=\\\"\`\$ECHO \"\$$var\" | \$SED -e \"\$double_quote_subst\" -e \"\$sed_quote_subst\" -e \"\$delay_variable_subst\"\`\\\"" ## exclude from sc_prohibit_nested_quotes
;;
*)
eval "lt_$var=\\\"\$$var\\\""
;;
esac
done
ac_aux_dir='.'
# See if we are running on zsh, and set the options that allow our
# commands through without removal of \ escapes INIT.
if test -n "${ZSH_VERSION+set}"; then
setopt NO_GLOB_SUBST
fi
PACKAGE='orparapp'
VERSION='0.1.0'
RM='rm -f'
ofile='libtool'
# Handling of arguments.
for ac_config_target in $ac_config_targets
do
case $ac_config_target in
"config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
"depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
"libtool") CONFIG_COMMANDS="$CONFIG_COMMANDS libtool" ;;
"docs/Doxyfile") CONFIG_FILES="$CONFIG_FILES docs/Doxyfile" ;;
"docs/Makefile") CONFIG_FILES="$CONFIG_FILES docs/Makefile" ;;
"Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
"src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
"src/consensus/Makefile") CONFIG_FILES="$CONFIG_FILES src/consensus/Makefile" ;;
"src/seqana/Makefile") CONFIG_FILES="$CONFIG_FILES src/seqana/Makefile" ;;
"src/seqana/cdna/Makefile") CONFIG_FILES="$CONFIG_FILES src/seqana/cdna/Makefile" ;;
"src/seqana/fasta/Makefile") CONFIG_FILES="$CONFIG_FILES src/seqana/fasta/Makefile" ;;
"src/seqana/seqsep/Makefile") CONFIG_FILES="$CONFIG_FILES src/seqana/seqsep/Makefile" ;;
"src/seqconv/Makefile") CONFIG_FILES="$CONFIG_FILES src/seqconv/Makefile" ;;
"src/bionj/Makefile") CONFIG_FILES="$CONFIG_FILES src/bionj/Makefile" ;;
"src/test/Makefile") CONFIG_FILES="$CONFIG_FILES src/test/Makefile" ;;
*) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
esac
done
# If the user did not use the arguments to specify the items to instantiate,
# then the envvar interface is used. Set only those that are not.
# We use the long form for the default assignment because of an extremely
# bizarre bug on SunOS 4.1.3.
if $ac_need_defaults; then
test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers
test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
fi
# Have a temporary directory for convenience. Make it in the build tree
# simply because there is no reason against having it here, and in addition,
# creating and moving files from /tmp can sometimes cause problems.
# Hook for its removal unless debugging.
# Note that there is a small window in which the directory will not be cleaned:
# after its creation but before its name has been assigned to `$tmp'.
$debug ||
{
tmp= ac_tmp=
trap 'exit_status=$?
: "${ac_tmp:=$tmp}"
{ test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status
' 0
trap 'as_fn_exit 1' 1 2 13 15
}
# Create a (secure) tmp directory for tmp files.
{
tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
test -d "$tmp"
} ||
{
tmp=./conf$$-$RANDOM
(umask 077 && mkdir "$tmp")
} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5
ac_tmp=$tmp
# Set up the scripts for CONFIG_FILES section.
# No need to generate them if there are no CONFIG_FILES.
# This happens for instance with `./config.status config.h'.
if test -n "$CONFIG_FILES"; then
ac_cr=`echo X | tr X '\015'`
# On cygwin, bash can eat \r inside `` if the user requested igncr.
# But we know of no other shell where ac_cr would be empty at this
# point, so we can use a bashism as a fallback.
if test "x$ac_cr" = x; then
eval ac_cr=\$\'\\r\'
fi
ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
ac_cs_awk_cr='\\r'
else
ac_cs_awk_cr=$ac_cr
fi
echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
cat >>"$ac_tmp/subs1.awk" <<\_ACAWK &&
S["am__EXEEXT_FALSE"]=""
S["am__EXEEXT_TRUE"]="#"
S["LTLIBOBJS"]=""
S["LIBOBJS"]=""
S["HAVE_DOXYGEN_FALSE"]="#"
S["HAVE_DOXYGEN_TRUE"]=""
S["PDFLATEX"]="pdflatex"
S["DOT"]="dot"
S["DOXYGEN"]="doxygen"
S["plotter_LDFLAGS"]="-L/usr/local/lib"
S["plotter_CXXFLAGS"]="-I/usr/local/include"
S["plotter_LIBS"]="-lplotter -lXaw -lXmu -lXt -lSM -lICE -lXext -lX11 -lpng -lz -lm"
S["PLOTUTILLIB"]=""
S["PLOTUTILINC"]=""
S["orpara_LDFLAGS"]="-L/usr/local/lib"
S["orpara_CXXFLAGS"]="-I/usr/local/include/orpara"
S["orpara_LIBS"]="-lkemin"
S["ORPARALIB"]=""
S["ORPARAIND"]=""
S["boost_LDFLAGS"]="-L/usr/local/lib"
S["boost_CXXFLAGS"]="-I/usr/local/include/boost"
S["boost_LIBS"]="-lboost_program_options"
S["BOOSTLIB"]=""
S["BOOSTINC"]=""
S["bam_LDFLAGS"]="-L/usr/local/lib/bamtools"
S["bam_CXXFLAGS"]="-I/usr/local/include/bamtools"
S["bam_LIBS"]="-lbamtools"
S["BAMTOOLSLIB"]=""
S["BAMTOOLSINC"]=""
S["gtest_LIBS"]=" -lgtest -lgtest_main -lgmock -lgmock_main -lpthread"
S["gtest_CXXFLAGS"]="-I/usr/local/include -g -O2"
S["gtest_CFLAGS"]="-g -O2 -pthread"
S["GTESTLIB"]=""
S["GTESTINC"]=""
S["PTHREAD_CFLAGS"]="-pthread"
S["PTHREAD_LIBS"]=""
S["PTHREAD_CC"]="gcc"
S["ax_pthread_config"]=""
S["HAVE_CXX11"]="1"
S["CXXCPP"]="g++ -E -std=c++11"
S["am__fastdepCXX_FALSE"]="#"
S["am__fastdepCXX_TRUE"]=""
S["CXXDEPMODE"]="depmode=gcc3"
S["ac_ct_CXX"]="g++"
S["CXXFLAGS"]="-g -O2"
S["CXX"]="g++ -std=c++11"
S["CPP"]="gcc -E"
S["LT_SYS_LIBRARY_PATH"]=""
S["OTOOL64"]=""
S["OTOOL"]=""
S["LIPO"]=""
S["NMEDIT"]=""
S["DSYMUTIL"]=""
S["MANIFEST_TOOL"]=":"
S["RANLIB"]="ranlib"
S["DLLTOOL"]="false"
S["OBJDUMP"]="objdump"
S["LN_S"]="ln -s"
S["NM"]="/usr/bin/nm -B"
S["ac_ct_DUMPBIN"]=""
S["DUMPBIN"]=""
S["LD"]="/usr/bin/ld -m elf_x86_64"
S["FGREP"]="/bin/grep -F"
S["EGREP"]="/bin/grep -E"
S["GREP"]="/bin/grep"
S["SED"]="/bin/sed"
S["host_os"]="linux-gnu"
S["host_vendor"]="pc"
S["host_cpu"]="x86_64"
S["host"]="x86_64-pc-linux-gnu"
S["build_os"]="linux-gnu"
S["build_vendor"]="pc"
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S["build"]="x86_64-pc-linux-gnu"
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S["am__quote"]=""
S["am__include"]="include"
S["DEPDIR"]=".deps"
S["OBJEXT"]="o"
S["EXEEXT"]=""
S["ac_ct_CC"]="gcc"
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S["LDFLAGS"]=""
S["CFLAGS"]="-g -O2"
S["CC"]="gcc"
S["ac_ct_AR"]="ar"
S["AR"]="ar"
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S["AM_V"]="$(V)"
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S["am__tar"]="$${TAR-tar} chof - \"$$tardir\""
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S["INSTALL_STRIP_PROGRAM"]="$(install_sh) -c -s"
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S["install_sh"]="${SHELL} /home/kzhou/coding/orparapp/install-sh"
S["MAKEINFO"]="${SHELL} /home/kzhou/coding/orparapp/missing makeinfo"
S["AUTOHEADER"]="${SHELL} /home/kzhou/coding/orparapp/missing autoheader"
S["AUTOMAKE"]="${SHELL} /home/kzhou/coding/orparapp/missing automake-1.15"
S["AUTOCONF"]="${SHELL} /home/kzhou/coding/orparapp/missing autoconf"
S["ACLOCAL"]="${SHELL} /home/kzhou/coding/orparapp/missing aclocal-1.15"
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S["PACKAGE"]="orparapp"