SciCodePile/SciCode-Domain-Code

1"keyword","repo_name","file_path","file_extension","file_size","line_count","content","language"
2"CRISPR","ctSkennerton/crass","TODO.md",".md","1440","27","# TODO3 4## Issues5* Flanking sequences are not called correctly6    * Causes spacers to be called as flankers7* Speed degrades rapidly with the number of patterns identified8    * Probable cause is the singleton finder9* In some circumstances closely related groups are not getting split apart10* The final output coverage of the spacer does not always correspond to the number of sources11* Spacers go missing in the graph from Crass, but they are present if you perform a regular overlap assembly12    * This is not a sequencing error issue as even when searching with mismatches, there is not sign of the spacers13* Spacer strings only get created during the initial pass of the graph building.  However, spacer objects can also be made from the p-graph14    * This means that spacers may exist in the graph, but not in the output sequences.  Maybe the cause of the above issue15* If a slave DR is a perfect palindrome of the master DR the offset will be undefined16    17 18## Wanted Features19* Multi-threading the search algorithms20* Using paired read information in the search algorithms21* Ability to run Crass on genomes or assembled contigs22    * Output a gff3 formatted file23* Screen for known eukaryotic microsatellites for datasets that may be host contaminated24 25## Improvements26* Use read information better when building the graph27* Allow for multiple DR types to be in a single sequence. Very important if Crass is to work on genomes 28","Markdown"
29"CRISPR","ctSkennerton/crass","autogen.sh",".sh","49146","1599","#!/bin/sh30#                        a u t o g e n . s h31#32# Copyright (c) 2005-2011 United States Government as represented by33# the U.S. Army Research Laboratory.34#35# Redistribution and use in source and binary forms, with or without36# modification, are permitted provided that the following conditions37# are met:38#39# 1. Redistributions of source code must retain the above copyright40# notice, this list of conditions and the following disclaimer.41#42# 2. Redistributions in binary form must reproduce the above43# copyright notice, this list of conditions and the following44# disclaimer in the documentation and/or other materials provided45# with the distribution.46#47# 3. The name of the author may not be used to endorse or promote48# products derived from this software without specific prior written49# permission.50#51# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS52# OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED53# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE54# ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY55# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL56# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE57# GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS58# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,59# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING60# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS61# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.62#63###64#65# Script for automatically preparing the sources for compilation by66# performing the myriad of necessary steps.  The script attempts to67# detect proper version support, and outputs warnings about particular68# systems that have autotool peculiarities.69#70# Basically, if everything is set up and installed correctly, the71# script will validate that minimum versions of the GNU Build System72# tools are installed, account for several common configuration73# issues, and then simply run autoreconf for you.74#75# If autoreconf fails, which can happen for many valid configurations,76# this script proceeds to run manual preparation steps effectively77# providing a POSIX shell script (mostly complete) reimplementation of78# autoreconf.79#80# The AUTORECONF, AUTOCONF, AUTOMAKE, LIBTOOLIZE, ACLOCAL, AUTOHEADER81# environment variables and corresponding _OPTIONS variables (e.g.82# AUTORECONF_OPTIONS) may be used to override the default automatic83# detection behaviors.  Similarly the _VERSION variables will override84# the minimum required version numbers.85#86# Examples:87#88#   To obtain help on usage:89#     ./autogen.sh --help90#91#   To obtain verbose output:92#     ./autogen.sh --verbose93#94#   To skip autoreconf and prepare manually:95#     AUTORECONF=false ./autogen.sh96#97#   To verbosely try running with an older (unsupported) autoconf:98#     AUTOCONF_VERSION=2.50 ./autogen.sh --verbose99#100# Author:101#   Christopher Sean Morrison <morrison@brlcad.org>102#103# Patches:104#   Sebastian Pipping <sebastian@pipping.org>105#   Tom Browder <tbrowder2@users.sourceforge.net>106#107######################################################################108 109# set to minimum acceptable version of autoconf110if [ ""x$AUTOCONF_VERSION"" = ""x"" ] ; then111    AUTOCONF_VERSION=2.52112fi113# set to minimum acceptable version of automake114if [ ""x$AUTOMAKE_VERSION"" = ""x"" ] ; then115    AUTOMAKE_VERSION=1.6.0116fi117# set to minimum acceptable version of libtool118if [ ""x$LIBTOOL_VERSION"" = ""x"" ] ; then119    LIBTOOL_VERSION=1.4.2120fi121 122 123##################124# ident function #125##################126ident ( ) {127    # extract copyright from header128    __copyright=""`grep Copyright $AUTOGEN_SH | head -${HEAD_N}1 | awk '{print $4}'`""129    if [ ""x$__copyright"" = ""x"" ] ; then130	__copyright=""`date +%Y`""131    fi132 133    # extract version from CVS Id string134    __id=""$Id$""135    __version=""`echo $__id | sed 's/.*\([0-9][0-9][0-9][0-9]\)[-\/]\([0-9][0-9]\)[-\/]\([0-9][0-9]\).*/\1\2\3/'`""136    if [ ""x$__version"" = ""x"" ] ; then137	__version=""""138    fi139 140    echo ""autogen.sh build preparation script by Christopher Sean Morrison""141    echo ""  + config.guess download patch by Sebastian Pipping (2008-12-03)""142    echo ""revised 3-clause BSD-style license, copyright (c) $__copyright""143    echo ""script version $__version, ISO/IEC 9945 POSIX shell script""144}145 146 147##################148# USAGE FUNCTION #149##################150usage ( ) {151    echo ""Usage: $AUTOGEN_SH [-h|--help] [-v|--verbose] [-q|--quiet] [-d|--download] [--version]""152    echo ""    --help      Help on $NAME_OF_AUTOGEN usage""153    echo ""    --verbose   Verbose progress output""154    echo ""    --quiet     Quiet suppressed progress output""155    echo ""    --download  Download the latest config.guess from gnulib""156    echo ""    --version   Only perform GNU Build System version checks""157    echo158    echo ""Description: This script will validate that minimum versions of the""159    echo ""GNU Build System tools are installed and then run autoreconf for you.""160    echo ""Should autoreconf fail, manual preparation steps will be run""161    echo ""potentially accounting for several common preparation issues.  The""162 163    echo ""AUTORECONF, AUTOCONF, AUTOMAKE, LIBTOOLIZE, ACLOCAL, AUTOHEADER,""164    echo ""PROJECT, & CONFIGURE environment variables and corresponding _OPTIONS""165    echo ""variables (e.g. AUTORECONF_OPTIONS) may be used to override the""166    echo ""default automatic detection behavior.""167    echo168 169    ident170 171    return 0172}173 174 175##########################176# VERSION_ERROR FUNCTION #177##########################178version_error ( ) {179    if [ ""x$1"" = ""x"" ] ; then180	echo ""INTERNAL ERROR: version_error was not provided a version""181	exit 1182    fi183    if [ ""x$2"" = ""x"" ] ; then184	echo ""INTERNAL ERROR: version_error was not provided an application name""185	exit 1186    fi187    $ECHO188    $ECHO ""ERROR:  To prepare the ${PROJECT} build system from scratch,""189    $ECHO ""        at least version $1 of $2 must be installed.""190    $ECHO191    $ECHO ""$NAME_OF_AUTOGEN does not need to be run on the same machine that will""192    $ECHO ""run configure or make.  Either the GNU Autotools will need to be installed""193    $ECHO ""or upgraded on this system, or $NAME_OF_AUTOGEN must be run on the source""194    $ECHO ""code on another system and then transferred to here. -- Cheers!""195    $ECHO196}197 198##########################199# VERSION_CHECK FUNCTION #200##########################201version_check ( ) {202    if [ ""x$1"" = ""x"" ] ; then203	echo ""INTERNAL ERROR: version_check was not provided a minimum version""204	exit 1205    fi206    _min=""$1""207    if [ ""x$2"" = ""x"" ] ; then208	echo ""INTERNAL ERROR: version check was not provided a comparison version""209	exit 1210    fi211    _cur=""$2""212 213    # needed to handle versions like 1.10 and 1.4-p6214    _min=""`echo ${_min}. | sed 's/[^0-9]/./g' | sed 's/\.\././g'`""215    _cur=""`echo ${_cur}. | sed 's/[^0-9]/./g' | sed 's/\.\././g'`""216 217    _min_major=""`echo $_min | cut -d. -f1`""218    _min_minor=""`echo $_min | cut -d. -f2`""219    _min_patch=""`echo $_min | cut -d. -f3`""220 221    _cur_major=""`echo $_cur | cut -d. -f1`""222    _cur_minor=""`echo $_cur | cut -d. -f2`""223    _cur_patch=""`echo $_cur | cut -d. -f3`""224 225    if [ ""x$_min_major"" = ""x"" ] ; then226	_min_major=0227    fi228    if [ ""x$_min_minor"" = ""x"" ] ; then229	_min_minor=0230    fi231    if [ ""x$_min_patch"" = ""x"" ] ; then232	_min_patch=0233    fi234    if [ ""x$_cur_minor"" = ""x"" ] ; then235	_cur_major=0236    fi237    if [ ""x$_cur_minor"" = ""x"" ] ; then238	_cur_minor=0239    fi240    if [ ""x$_cur_patch"" = ""x"" ] ; then241	_cur_patch=0242    fi243 244    $VERBOSE_ECHO ""Checking if ${_cur_major}.${_cur_minor}.${_cur_patch} is greater than ${_min_major}.${_min_minor}.${_min_patch}""245 246    if [ $_min_major -lt $_cur_major ] ; then247	return 0248    elif [ $_min_major -eq $_cur_major ] ; then249	if [ $_min_minor -lt $_cur_minor ] ; then250	    return 0251	elif [ $_min_minor -eq $_cur_minor ] ; then252	    if [ $_min_patch -lt $_cur_patch ] ; then253		return 0254	    elif [ $_min_patch -eq $_cur_patch ] ; then255		return 0256	    fi257	fi258    fi259    return 1260}261 262 263######################################264# LOCATE_CONFIGURE_TEMPLATE FUNCTION #265######################################266locate_configure_template ( ) {267    _pwd=""`pwd`""268    if test -f ""./configure.ac"" ; then269	echo ""./configure.ac""270    elif test -f ""./configure.in"" ; then271	echo ""./configure.in""272    elif test -f ""$_pwd/configure.ac"" ; then273	echo ""$_pwd/configure.ac""274    elif test -f ""$_pwd/configure.in"" ; then275	echo ""$_pwd/configure.in""276    elif test -f ""$PATH_TO_AUTOGEN/configure.ac"" ; then277	echo ""$PATH_TO_AUTOGEN/configure.ac""278    elif test -f ""$PATH_TO_AUTOGEN/configure.in"" ; then279	echo ""$PATH_TO_AUTOGEN/configure.in""280    fi281}282 283 284##################285# argument check #286##################287ARGS=""$*""288PATH_TO_AUTOGEN=""`dirname $0`""289NAME_OF_AUTOGEN=""`basename $0`""290AUTOGEN_SH=""$PATH_TO_AUTOGEN/$NAME_OF_AUTOGEN""291 292LIBTOOL_M4=""${PATH_TO_AUTOGEN}/misc/libtool.m4""293 294if [ ""x$HELP"" = ""x"" ] ; then295    HELP=no296fi297if [ ""x$QUIET"" = ""x"" ] ; then298    QUIET=no299fi300if [ ""x$VERBOSE"" = ""x"" ] ; then301    VERBOSE=no302fi303if [ ""x$VERSION_ONLY"" = ""x"" ] ; then304    VERSION_ONLY=no305fi306if [ ""x$DOWNLOAD"" = ""x"" ] ; then307    DOWNLOAD=no308fi309if [ ""x$AUTORECONF_OPTIONS"" = ""x"" ] ; then310    AUTORECONF_OPTIONS=""-i -f""311fi312if [ ""x$AUTOCONF_OPTIONS"" = ""x"" ] ; then313    AUTOCONF_OPTIONS=""-f""314fi315if [ ""x$AUTOMAKE_OPTIONS"" = ""x"" ] ; then316    AUTOMAKE_OPTIONS=""-a -c -f""317fi318ALT_AUTOMAKE_OPTIONS=""-a -c""319if [ ""x$LIBTOOLIZE_OPTIONS"" = ""x"" ] ; then320    LIBTOOLIZE_OPTIONS=""--automake -c -f""321fi322ALT_LIBTOOLIZE_OPTIONS=""--automake --copy --force""323if [ ""x$ACLOCAL_OPTIONS"" = ""x"" ] ; then324    ACLOCAL_OPTIONS=""""325fi326if [ ""x$AUTOHEADER_OPTIONS"" = ""x"" ] ; then327    AUTOHEADER_OPTIONS=""""328fi329if [ ""x$CONFIG_GUESS_URL"" = ""x"" ] ; then330    CONFIG_GUESS_URL=""http://git.savannah.gnu.org/gitweb/?p=gnulib.git;a=blob_plain;f=build-aux/config.guess;hb=HEAD""331fi332for arg in $ARGS ; do333    case ""x$arg"" in334	x--help) HELP=yes ;;335	x-[hH]) HELP=yes ;;336	x--quiet) QUIET=yes ;;337	x-[qQ]) QUIET=yes ;;338	x--verbose) VERBOSE=yes ;;339	x-[dD]) DOWNLOAD=yes ;;340	x--download) DOWNLOAD=yes ;;341	x-[vV]) VERBOSE=yes ;;342	x--version) VERSION_ONLY=yes ;;343	*)344	    echo ""Unknown option: $arg""345	    echo346	    usage347	    exit 1348	    ;;349    esac350done351 352 353#####################354# environment check #355#####################356 357# sanity check before recursions potentially begin358if [ ! -f ""$AUTOGEN_SH"" ] ; then359    if test -f ./autogen.sh ; then360	PATH_TO_AUTOGEN="".""361	NAME_OF_AUTOGEN=""autogen.sh""362	AUTOGEN_SH=""$PATH_TO_AUTOGEN/$NAME_OF_AUTOGEN""363    else364	echo ""INTERNAL ERROR: $AUTOGEN_SH does not exist""365	exit 1366    fi367fi368 369# force locale setting to C so things like date output as expected370LC_ALL=C371 372# commands that this script expects373for __cmd in echo head tail pwd ; do374    echo ""test"" > /dev/null 2>&1 | $__cmd > /dev/null 2>&1375    if [ $? != 0 ] ; then376	echo ""INTERNAL ERROR: '${__cmd}' command is required""377	exit 2378    fi379done380echo ""test"" | grep ""test"" > /dev/null 2>&1381if test ! x$? = x0 ; then382    echo ""INTERNAL ERROR: grep command is required""383    exit 1384fi385echo ""test"" | sed ""s/test/test/"" > /dev/null 2>&1386if test ! x$? = x0 ; then387    echo ""INTERNAL ERROR: sed command is required""388    exit 1389fi390 391 392# determine the behavior of echo393case `echo ""testing\c""; echo 1,2,3`,`echo -n testing; echo 1,2,3` in394    *c*,-n*) ECHO_N= ECHO_C='395' ECHO_T='	' ;;396    *c*,*  ) ECHO_N=-n ECHO_C= ECHO_T= ;;397    *)       ECHO_N= ECHO_C='\c' ECHO_T= ;;398esac399 400# determine the behavior of head401case ""x`echo 'head' | head -n 1 2>&1`"" in402    *xhead*) HEAD_N=""n "" ;;403    *) HEAD_N="""" ;;404esac405 406# determine the behavior of tail407case ""x`echo 'tail' | tail -n 1 2>&1`"" in408    *xtail*) TAIL_N=""n "" ;;409    *) TAIL_N="""" ;;410esac411 412VERBOSE_ECHO=:413ECHO=:414if [ ""x$QUIET"" = ""xyes"" ] ; then415    if [ ""x$VERBOSE"" = ""xyes"" ] ; then416	echo ""Verbose output quelled by quiet option.  Further output disabled.""417    fi418else419    ECHO=echo420    if [ ""x$VERBOSE"" = ""xyes"" ] ; then421	echo ""Verbose output enabled""422	VERBOSE_ECHO=echo423    fi424fi425 426 427# allow a recursive run to disable further recursions428if [ ""x$RUN_RECURSIVE"" = ""x"" ] ; then429    RUN_RECURSIVE=yes430fi431 432 433################################################434# check for help arg and bypass version checks #435################################################436if [ ""x`echo $ARGS | sed 's/.*[hH][eE][lL][pP].*/help/'`"" = ""xhelp"" ] ; then437    HELP=yes438fi439if [ ""x$HELP"" = ""xyes"" ] ; then440    usage441    $ECHO ""---""442    $ECHO ""Help was requested.  No preparation or configuration will be performed.""443    exit 0444fi445 446 447#######################448# set up signal traps #449#######################450untrap_abnormal ( ) {451    for sig in 1 2 13 15; do452	trap - $sig453    done454}455 456# do this cleanup whenever we exit.457trap '458    # start from the root459    if test -d ""$START_PATH"" ; then460	cd ""$START_PATH""461    fi462 463    # restore/delete backup files464    if test ""x$PFC_INIT"" = ""x1"" ; then465	recursive_restore466    fi467' 0468 469# trap SIGHUP (1), SIGINT (2), SIGPIPE (13), SIGTERM (15)470for sig in 1 2 13 15; do471    trap '472	$ECHO """"473	$ECHO ""Aborting $NAME_OF_AUTOGEN: caught signal '$sig'""474 475	# start from the root476	if test -d ""$START_PATH"" ; then477	    cd ""$START_PATH""478	fi479 480	# clean up on abnormal exit481	$VERBOSE_ECHO ""rm -rf autom4te.cache""482	rm -rf autom4te.cache483 484	if test -f ""acinclude.m4.$$.backup"" ; then485	    $VERBOSE_ECHO ""cat acinclude.m4.$$.backup > acinclude.m4""486	    chmod u+w acinclude.m4487	    cat acinclude.m4.$$.backup > acinclude.m4488 489	    $VERBOSE_ECHO ""rm -f acinclude.m4.$$.backup""490	    rm -f acinclude.m4.$$.backup491        fi492 493	{ (exit 1); exit 1; }494' $sig495done496 497 498#############################499# look for a configure file #500#############################501if [ ""x$CONFIGURE"" = ""x"" ] ; then502    CONFIGURE=""`locate_configure_template`""503    if [ ! ""x$CONFIGURE"" = ""x"" ] ; then504	$VERBOSE_ECHO ""Found a configure template: $CONFIGURE""505    fi506else507    $ECHO ""Using CONFIGURE environment variable override: $CONFIGURE""508fi509if [ ""x$CONFIGURE"" = ""x"" ] ; then510    if [ ""x$VERSION_ONLY"" = ""xyes"" ] ; then511	CONFIGURE=/dev/null512    else513	$ECHO514	$ECHO ""A configure.ac or configure.in file could not be located implying""515	$ECHO ""that the GNU Build System is at least not used in this directory.  In""516	$ECHO ""any case, there is nothing to do here without one of those files.""517	$ECHO518	$ECHO ""ERROR: No configure.in or configure.ac file found in `pwd`""519	exit 1520    fi521fi522 523####################524# get project name #525####################526if [ ""x$PROJECT"" = ""x"" ] ; then527    PROJECT=""`grep AC_INIT $CONFIGURE | grep -v '.*#.*AC_INIT' | tail -${TAIL_N}1 | sed 's/^[ 	]*AC_INIT(\([^,)]*\).*/\1/' | sed 's/.*\[\(.*\)\].*/\1/'`""528    if [ ""x$PROJECT"" = ""xAC_INIT"" ] ; then529	# projects might be using the older/deprecated arg-less AC_INIT .. look for AM_INIT_AUTOMAKE instead530	PROJECT=""`grep AM_INIT_AUTOMAKE $CONFIGURE | grep -v '.*#.*AM_INIT_AUTOMAKE' | tail -${TAIL_N}1 | sed 's/^[ 	]*AM_INIT_AUTOMAKE(\([^,)]*\).*/\1/' | sed 's/.*\[\(.*\)\].*/\1/'`""531    fi532    if [ ""x$PROJECT"" = ""xAM_INIT_AUTOMAKE"" ] ; then533	PROJECT=""project""534    fi535    if [ ""x$PROJECT"" = ""x"" ] ; then536	PROJECT=""project""537    fi538else539    $ECHO ""Using PROJECT environment variable override: $PROJECT""540fi541$ECHO ""Preparing the $PROJECT build system...please wait""542$ECHO543 544 545########################546# check for autoreconf #547########################548HAVE_AUTORECONF=no549if [ ""x$AUTORECONF"" = ""x"" ] ; then550    for AUTORECONF in autoreconf ; do551	$VERBOSE_ECHO ""Checking autoreconf version: $AUTORECONF --version""552	$AUTORECONF --version > /dev/null 2>&1553	if [ $? = 0 ] ; then554	    HAVE_AUTORECONF=yes555	    break556	fi557    done558else559    HAVE_AUTORECONF=yes560    $ECHO ""Using AUTORECONF environment variable override: $AUTORECONF""561fi562 563 564##########################565# autoconf version check #566##########################567_acfound=no568if [ ""x$AUTOCONF"" = ""x"" ] ; then569    for AUTOCONF in autoconf ; do570	$VERBOSE_ECHO ""Checking autoconf version: $AUTOCONF --version""571	$AUTOCONF --version > /dev/null 2>&1572	if [ $? = 0 ] ; then573	    _acfound=yes574	    break575	fi576    done577else578    _acfound=yes579    $ECHO ""Using AUTOCONF environment variable override: $AUTOCONF""580fi581 582_report_error=no583if [ ! ""x$_acfound"" = ""xyes"" ] ; then584    $ECHO ""ERROR:  Unable to locate GNU Autoconf.""585    _report_error=yes586else587    _version=""`$AUTOCONF --version | head -${HEAD_N}1 | sed 's/[^0-9]*\([0-9\.][0-9\.]*\)/\1/'`""588    if [ ""x$_version"" = ""x"" ] ; then589	_version=""0.0.0""590    fi591    $ECHO ""Found GNU Autoconf version $_version""592    version_check ""$AUTOCONF_VERSION"" ""$_version""593    if [ $? -ne 0 ] ; then594	_report_error=yes595    fi596fi597if [ ""x$_report_error"" = ""xyes"" ] ; then598    version_error ""$AUTOCONF_VERSION"" ""GNU Autoconf""599    exit 1600fi601 602 603##########################604# automake version check #605##########################606_amfound=no607if [ ""x$AUTOMAKE"" = ""x"" ] ; then608    for AUTOMAKE in automake ; do609	$VERBOSE_ECHO ""Checking automake version: $AUTOMAKE --version""610	$AUTOMAKE --version > /dev/null 2>&1611	if [ $? = 0 ] ; then612	    _amfound=yes613	    break614	fi615    done616else617    _amfound=yes618    $ECHO ""Using AUTOMAKE environment variable override: $AUTOMAKE""619fi620 621 622_report_error=no623if [ ! ""x$_amfound"" = ""xyes"" ] ; then624    $ECHO625    $ECHO ""ERROR: Unable to locate GNU Automake.""626    _report_error=yes627else628    _version=""`$AUTOMAKE --version | head -${HEAD_N}1 | sed 's/[^0-9]*\([0-9\.][0-9\.]*\)/\1/'`""629    if [ ""x$_version"" = ""x"" ] ; then630	_version=""0.0.0""631    fi632    $ECHO ""Found GNU Automake version $_version""633    version_check ""$AUTOMAKE_VERSION"" ""$_version""634    if [ $? -ne 0 ] ; then635	_report_error=yes636    fi637fi638if [ ""x$_report_error"" = ""xyes"" ] ; then639    version_error ""$AUTOMAKE_VERSION"" ""GNU Automake""640    exit 1641fi642 643 644########################645# check for libtoolize #646########################647HAVE_LIBTOOLIZE=yes648HAVE_ALT_LIBTOOLIZE=no649_ltfound=no650if [ ""x$LIBTOOLIZE"" = ""x"" ] ; then651    LIBTOOLIZE=libtoolize652    $VERBOSE_ECHO ""Checking libtoolize version: $LIBTOOLIZE --version""653    $LIBTOOLIZE --version > /dev/null 2>&1654    if [ ! $? = 0 ] ; then655	HAVE_LIBTOOLIZE=no656	$ECHO657	if [ ""x$HAVE_AUTORECONF"" = ""xno"" ] ; then658	    $ECHO ""Warning:  libtoolize does not appear to be available.""659	else660	    $ECHO ""Warning:  libtoolize does not appear to be available.  This means that""661	    $ECHO ""the automatic build preparation via autoreconf will probably not work.""662	    $ECHO ""Preparing the build by running each step individually, however, should""663	    $ECHO ""work and will be done automatically for you if autoreconf fails.""664	fi665 666	# look for some alternates667	for tool in glibtoolize libtoolize15 libtoolize14 libtoolize13 ; do668	    $VERBOSE_ECHO ""Checking libtoolize alternate: $tool --version""669	    _glibtoolize=""`$tool --version > /dev/null 2>&1`""670	    if [ $? = 0 ] ; then671		$VERBOSE_ECHO ""Found $tool --version""672		_glti=""`which $tool`""673		if [ ""x$_glti"" = ""x"" ] ; then674		    $VERBOSE_ECHO ""Cannot find $tool with which""675		    continue;676		fi677		if test ! -f ""$_glti"" ; then678		    $VERBOSE_ECHO ""Cannot use $tool, $_glti is not a file""679		    continue;680		fi681		_gltidir=""`dirname $_glti`""682		if [ ""x$_gltidir"" = ""x"" ] ; then683		    $VERBOSE_ECHO ""Cannot find $tool path with dirname of $_glti""684		    continue;685		fi686		if test ! -d ""$_gltidir"" ; then687		    $VERBOSE_ECHO ""Cannot use $tool, $_gltidir is not a directory""688		    continue;689		fi690		HAVE_ALT_LIBTOOLIZE=yes691		LIBTOOLIZE=""$tool""692		$ECHO693		$ECHO ""Fortunately, $tool was found which means that your system may simply""694		$ECHO ""have a non-standard or incomplete GNU Autotools install.  If you have""695		$ECHO ""sufficient system access, it may be possible to quell this warning by""696		$ECHO ""running:""697		$ECHO698		sudo -V > /dev/null 2>&1699		if [ $? = 0 ] ; then700		    $ECHO ""   sudo ln -s $_glti $_gltidir/libtoolize""701		    $ECHO702		else703		    $ECHO ""   ln -s $_glti $_gltidir/libtoolize""704		    $ECHO705		    $ECHO ""Run that as root or with proper permissions to the $_gltidir directory""706		    $ECHO707		fi708		_ltfound=yes709		break710	    fi711	done712    else713	_ltfound=yes714    fi715else716    _ltfound=yes717    $ECHO ""Using LIBTOOLIZE environment variable override: $LIBTOOLIZE""718fi719 720 721############################722# libtoolize version check #723############################724_report_error=no725if [ ! ""x$_ltfound"" = ""xyes"" ] ; then726    $ECHO727    $ECHO ""ERROR: Unable to locate GNU Libtool.""728    _report_error=yes729else730    _version=""`$LIBTOOLIZE --version | head -${HEAD_N}1 | sed 's/[^0-9]*\([0-9\.][0-9\.]*\)/\1/'`""731    if [ ""x$_version"" = ""x"" ] ; then732	_version=""0.0.0""733    fi734    $ECHO ""Found GNU Libtool version $_version""735    version_check ""$LIBTOOL_VERSION"" ""$_version""736    if [ $? -ne 0 ] ; then737	_report_error=yes738    fi739fi740if [ ""x$_report_error"" = ""xyes"" ] ; then741    version_error ""$LIBTOOL_VERSION"" ""GNU Libtool""742    exit 1743fi744 745 746#####################747# check for aclocal #748#####################749if [ ""x$ACLOCAL"" = ""x"" ] ; then750    for ACLOCAL in aclocal ; do751	$VERBOSE_ECHO ""Checking aclocal version: $ACLOCAL --version""752	$ACLOCAL --version > /dev/null 2>&1753	if [ $? = 0 ] ; then754	    break755	fi756    done757else758    $ECHO ""Using ACLOCAL environment variable override: $ACLOCAL""759fi760 761 762########################763# check for autoheader #764########################765if [ ""x$AUTOHEADER"" = ""x"" ] ; then766    for AUTOHEADER in autoheader ; do767	$VERBOSE_ECHO ""Checking autoheader version: $AUTOHEADER --version""768	$AUTOHEADER --version > /dev/null 2>&1769	if [ $? = 0 ] ; then770	    break771	fi772    done773else774    $ECHO ""Using AUTOHEADER environment variable override: $AUTOHEADER""775fi776 777 778#########################779# check if version only #780#########################781$VERBOSE_ECHO ""Checking whether to only output version information""782if [ ""x$VERSION_ONLY"" = ""xyes"" ] ; then783    $ECHO784    ident785    $ECHO ""---""786    $ECHO ""Version requested.  No preparation or configuration will be performed.""787    exit 0788fi789 790 791#################################792# PROTECT_FROM_CLOBBER FUNCTION #793#################################794protect_from_clobber ( ) {795    PFC_INIT=1796 797    # protect COPYING & INSTALL from overwrite by automake.  the798    # automake force option will (inappropriately) ignore the existing799    # contents of a COPYING and/or INSTALL files (depending on the800    # version) instead of just forcing *missing* files like it does801    # for AUTHORS, NEWS, and README. this is broken but extremely802    # prevalent behavior, so we protect against it by keeping a backup803    # of the file that can later be restored.804 805    for file in COPYING INSTALL ; do806	if test -f ${file} ; then807	    if test -f ${file}.$$.protect_from_automake.backup ; then808		$VERBOSE_ECHO ""Already backed up ${file} in `pwd`""809	    else810		$VERBOSE_ECHO ""Backing up ${file} in `pwd`""811		$VERBOSE_ECHO ""cp -p ${file} ${file}.$$.protect_from_automake.backup""812		cp -p ${file} ${file}.$$.protect_from_automake.backup813	    fi814	fi815    done816}817 818 819##############################820# RECURSIVE_PROTECT FUNCTION #821##############################822recursive_protect ( ) {823 824    # for projects using recursive configure, run the build825    # preparation steps for the subdirectories.  this function assumes826    # START_PATH was set to pwd before recursion begins so that827    # relative paths work.828 829    # git 'r done, protect COPYING and INSTALL from being clobbered830    protect_from_clobber831 832    if test -d autom4te.cache ; then833	$VERBOSE_ECHO ""Found an autom4te.cache directory, deleting it""834	$VERBOSE_ECHO ""rm -rf autom4te.cache""835	rm -rf autom4te.cache836    fi837 838    # find configure template839    _configure=""`locate_configure_template`""840    if [ ""x$_configure"" = ""x"" ] ; then841	return842    fi843    # $VERBOSE_ECHO ""Looking for configure template found `pwd`/$_configure""844 845    # look for subdirs846    # $VERBOSE_ECHO ""Looking for subdirs in `pwd`""847    _det_config_subdirs=""`grep AC_CONFIG_SUBDIRS $_configure | grep -v '.*#.*AC_CONFIG_SUBDIRS' | sed 's/^[ 	]*AC_CONFIG_SUBDIRS(\(.*\)).*/\1/' | sed 's/.*\[\(.*\)\].*/\1/'`""848    CHECK_DIRS=""""849    for dir in $_det_config_subdirs ; do850	if test -d ""`pwd`/$dir"" ; then851	    CHECK_DIRS=""$CHECK_DIRS \""`pwd`/$dir\""""852	fi853    done854 855    # process subdirs856    if [ ! ""x$CHECK_DIRS"" = ""x"" ] ; then857	$VERBOSE_ECHO ""Recursively scanning the following directories:""858	$VERBOSE_ECHO ""  $CHECK_DIRS""859	for dir in $CHECK_DIRS ; do860	    $VERBOSE_ECHO ""Protecting files from automake in $dir""861	    cd ""$START_PATH""862	    eval ""cd $dir""863 864	    # recursively git 'r done865	    recursive_protect866	done867    fi868} # end of recursive_protect869 870 871#############################872# RESTORE_CLOBBERED FUNCION #873#############################874restore_clobbered ( ) {875 876    # The automake (and autoreconf by extension) -f/--force-missing877    # option may overwrite COPYING and INSTALL even if they do exist.878    # Here we restore the files if necessary.879 880    spacer=no881 882    for file in COPYING INSTALL ; do883	if test -f ${file}.$$.protect_from_automake.backup ; then884	    if test -f ${file} ; then885	    # compare entire content, restore if needed886	    if test ""x`cat ${file}`"" != ""x`cat ${file}.$$.protect_from_automake.backup`"" ; then887		if test ""x$spacer"" = ""xno"" ; then888		    $VERBOSE_ECHO889		    spacer=yes890		fi891		# restore the backup892		$VERBOSE_ECHO ""Restoring ${file} from backup (automake -f likely clobbered it)""893		$VERBOSE_ECHO ""rm -f ${file}""894		rm -f ${file}895		$VERBOSE_ECHO ""mv ${file}.$$.protect_from_automake.backup ${file}""896		mv ${file}.$$.protect_from_automake.backup ${file}897	    fi # check contents898	    elif test -f ${file}.$$.protect_from_automake.backup ; then899		$VERBOSE_ECHO ""mv ${file}.$$.protect_from_automake.backup ${file}""900		mv ${file}.$$.protect_from_automake.backup ${file}901	    fi # -f ${file}902	903	    # just in case904	    $VERBOSE_ECHO ""rm -f ${file}.$$.protect_from_automake.backup""905	    rm -f ${file}.$$.protect_from_automake.backup906	fi # -f ${file}.$$.protect_from_automake.backup907    done908 909    CONFIGURE=""`locate_configure_template`""910    if [ ""x$CONFIGURE"" = ""x"" ] ; then911	return912    fi913 914    _aux_dir=""`grep AC_CONFIG_AUX_DIR $CONFIGURE | grep -v '.*#.*AC_CONFIG_AUX_DIR' | tail -${TAIL_N}1 | sed 's/^[ 	]*AC_CONFIG_AUX_DIR(\(.*\)).*/\1/' | sed 's/.*\[\(.*\)\].*/\1/'`""915    if test ! -d ""$_aux_dir"" ; then916	_aux_dir=.917    fi918 919    for file in config.guess config.sub ltmain.sh ; do920	if test -f ""${_aux_dir}/${file}"" ; then921	    $VERBOSE_ECHO ""rm -f \""${_aux_dir}/${file}.backup\""""922	    rm -f ""${_aux_dir}/${file}.backup""923	fi924    done925} # end of restore_clobbered926 927 928##############################929# RECURSIVE_RESTORE FUNCTION #930##############################931recursive_restore ( ) {932 933    # restore COPYING and INSTALL from backup if they were clobbered934    # for each directory recursively.935 936    # git 'r undone937    restore_clobbered938 939    # find configure template940    _configure=""`locate_configure_template`""941    if [ ""x$_configure"" = ""x"" ] ; then942	return943    fi944 945    # look for subdirs946    _det_config_subdirs=""`grep AC_CONFIG_SUBDIRS $_configure | grep -v '.*#.*AC_CONFIG_SUBDIRS' | sed 's/^[ 	]*AC_CONFIG_SUBDIRS(\(.*\)).*/\1/' | sed 's/.*\[\(.*\)\].*/\1/'`""947    CHECK_DIRS=""""948    for dir in $_det_config_subdirs ; do949	if test -d ""`pwd`/$dir"" ; then950	    CHECK_DIRS=""$CHECK_DIRS \""`pwd`/$dir\""""951	fi952    done953 954    # process subdirs955    if [ ! ""x$CHECK_DIRS"" = ""x"" ] ; then956	$VERBOSE_ECHO ""Recursively scanning the following directories:""957	$VERBOSE_ECHO ""  $CHECK_DIRS""958	for dir in $CHECK_DIRS ; do959	    $VERBOSE_ECHO ""Checking files for automake damage in $dir""960	    cd ""$START_PATH""961	    eval ""cd $dir""962 963	    # recursively git 'r undone964	    recursive_restore965	done966    fi967} # end of recursive_restore968 969 970#######################971# INITIALIZE FUNCTION #972#######################973initialize ( ) {974 975    # this routine performs a variety of directory-specific976    # initializations.  some are sanity checks, some are preventive,977    # and some are necessary setup detection.978    #979    # this function sets:980    #   CONFIGURE981    #   SEARCH_DIRS982    #   CONFIG_SUBDIRS983 984    ##################################985    # check for a configure template #986    ##################################987    CONFIGURE=""`locate_configure_template`""988    if [ ""x$CONFIGURE"" = ""x"" ] ; then989	$ECHO990	$ECHO ""A configure.ac or configure.in file could not be located implying""991	$ECHO ""that the GNU Build System is at least not used in this directory.  In""992	$ECHO ""any case, there is nothing to do here without one of those files.""993	$ECHO994	$ECHO ""ERROR: No configure.in or configure.ac file found in `pwd`""995	exit 1996    fi997 998    #####################999    # detect an aux dir #1000    #####################1001    _aux_dir=""`grep AC_CONFIG_AUX_DIR $CONFIGURE | grep -v '.*#.*AC_CONFIG_AUX_DIR' | tail -${TAIL_N}1 | sed 's/^[ 	]*AC_CONFIG_AUX_DIR(\(.*\)).*/\1/' | sed 's/.*\[\(.*\)\].*/\1/'`""1002    if test ! -d ""$_aux_dir"" ; then1003	_aux_dir=.1004    else1005	$VERBOSE_ECHO ""Detected auxillary directory: $_aux_dir""1006    fi1007 1008    ################################1009    # detect a recursive configure #1010    ################################1011    CONFIG_SUBDIRS=""""1012    _det_config_subdirs=""`grep AC_CONFIG_SUBDIRS $CONFIGURE | grep -v '.*#.*AC_CONFIG_SUBDIRS' | sed 's/^[ 	]*AC_CONFIG_SUBDIRS(\(.*\)).*/\1/' | sed 's/.*\[\(.*\)\].*/\1/'`""1013    for dir in $_det_config_subdirs ; do1014	if test -d ""`pwd`/$dir"" ; then1015	    $VERBOSE_ECHO ""Detected recursive configure directory: `pwd`/$dir""1016	    CONFIG_SUBDIRS=""$CONFIG_SUBDIRS `pwd`/$dir""1017	fi1018    done1019 1020    ###########################################################1021    # make sure certain required files exist for GNU projects #1022    ###########################################################1023    _marker_found=""""1024    _marker_found_message_intro='Detected non-GNU marker ""'1025    _marker_found_message_mid='"" in '1026    for marker in foreign cygnus ; do1027	_marker_found_message=${_marker_found_message_intro}${marker}${_marker_found_message_mid}1028	_marker_found=""`grep 'AM_INIT_AUTOMAKE.*'${marker} $CONFIGURE`""1029	if [ ! ""x$_marker_found"" = ""x"" ] ; then1030	    $VERBOSE_ECHO ""${_marker_found_message}`basename \""$CONFIGURE\""`""1031	    break1032	fi1033	__makefile=`dirname \""$CONFIGURE\""/Makefile.am`1034	if test -f ""$__makefile"" ; then1035	    _marker_found=""`grep 'AUTOMAKE_OPTIONS.*'${marker} $__makefile`""1036	    if [ ! ""x$_marker_found"" = ""x"" ] ; then1037		$VERBOSE_ECHO ""${_marker_found_message}${__makefile}""1038		break1039	    fi1040	fi1041    done1042    if [ ""x${_marker_found}"" = ""x"" ] ; then1043	_suggest_foreign=no1044	for file in AUTHORS COPYING ChangeLog INSTALL NEWS README ; do1045	    if [ ! -f $file ] ; then1046		$VERBOSE_ECHO ""Touching ${file} since it does not exist""1047		_suggest_foreign=yes1048		touch $file1049	    fi1050	done1051 1052	if [ ""x${_suggest_foreign}"" = ""xyes"" ] ; then1053	    $ECHO1054	    $ECHO ""Warning: Several files expected of projects that conform to the GNU""1055	    $ECHO ""coding standards were not found.  The files were automatically added""1056	    $ECHO ""for you since you do not have a 'foreign' declaration specified.""1057	    $ECHO1058	    $ECHO ""Consider adding 'foreign' to AM_INIT_AUTOMAKE in `basename \""$CONFIGURE\""`""1059	    __makefile=`dirname \""$CONFIGURE\""/Makefile.am`1060	    if test -f ""$__makefile"" ; then1061		$ECHO ""or to AUTOMAKE_OPTIONS in your top-level Makefile.am file.""1062	    fi1063	    $ECHO1064	fi1065    fi1066 1067    ##################################################1068    # make sure certain generated files do not exist #1069    ##################################################1070    for file in config.guess config.sub ltmain.sh ; do1071	if test -f ""${_aux_dir}/${file}"" ; then1072	    $VERBOSE_ECHO ""mv -f \""${_aux_dir}/${file}\"" \""${_aux_dir}/${file}.backup\""""1073	    mv -f ""${_aux_dir}/${file}"" ""${_aux_dir}/${file}.backup""1074	fi1075    done1076 1077    ############################1078    # search alternate m4 dirs #1079    ############################1080    SEARCH_DIRS=""""1081    for dir in m4 ; do1082	if [ -d $dir ] ; then1083	    $VERBOSE_ECHO ""Found extra aclocal search directory: $dir""1084	    SEARCH_DIRS=""$SEARCH_DIRS -I `pwd`/$dir""1085	fi1086    done1087 1088    ######################################1089    # remove any previous build products #1090    ######################################1091    if test -d autom4te.cache ; then1092	$VERBOSE_ECHO ""Found an autom4te.cache directory, deleting it""1093	$VERBOSE_ECHO ""rm -rf autom4te.cache""1094	rm -rf autom4te.cache1095    fi1096# tcl/tk (and probably others) have a customized aclocal.m4, so can't delete it1097#     if test -f aclocal.m4 ; then1098# 	$VERBOSE_ECHO ""Found an aclocal.m4 file, deleting it""1099# 	$VERBOSE_ECHO ""rm -f aclocal.m4""1100# 	rm -f aclocal.m41101#     fi1102 1103} # end of initialize()1104 1105 1106##############1107# initialize #1108##############1109 1110# stash path1111START_PATH=""`pwd`""1112 1113# Before running autoreconf or manual steps, some prep detection work1114# is necessary or useful.  Only needs to occur once per directory, but1115# does need to traverse the entire subconfigure hierarchy to protect1116# files from being clobbered even by autoreconf.1117recursive_protect1118 1119# start from where we started1120cd ""$START_PATH""1121 1122# get ready to process1123initialize1124 1125 1126#########################################1127# DOWNLOAD_GNULIB_CONFIG_GUESS FUNCTION #1128#########################################1129 1130# TODO - should make sure wget/curl exist and/or work before trying to1131# use them.1132 1133download_gnulib_config_guess () {1134    # abuse gitweb to download gnulib's latest config.guess via HTTP1135    config_guess_temp=""config.guess.$$.download""1136    ret=11137    for __cmd in wget curl fetch ; do1138	$VERBOSE_ECHO ""Checking for command ${__cmd}""1139	${__cmd} --version > /dev/null 2>&11140	ret=$?1141	if [ ! $ret = 0 ] ; then1142	    continue1143        fi1144 1145	__cmd_version=`${__cmd} --version | head -n 1 | sed -e 's/^[^0-9]\+//' -e 's/ .*//'`1146	$VERBOSE_ECHO ""Found ${__cmd} ${__cmd_version}""1147 1148	opts=""""1149	case ${__cmd} in1150	    wget)1151		opts=""-O"" 1152		;;1153	    curl)1154		opts=""-o""1155		;;1156	    fetch)1157		opts=""-t 5 -f""1158		;;1159	esac1160 1161	$VERBOSE_ECHO ""Running $__cmd \""${CONFIG_GUESS_URL}\"" $opts \""${config_guess_temp}\""""1162	eval ""$__cmd \""${CONFIG_GUESS_URL}\"" $opts \""${config_guess_temp}\"""" > /dev/null 2>&11163	if [ $? = 0 ] ; then1164	    mv -f ""${config_guess_temp}"" ${_aux_dir}/config.guess1165	    ret=01166	    break1167	fi1168    done1169 1170    if [ ! $ret = 0 ] ; then1171	$ECHO ""Warning: config.guess download failed from: $CONFIG_GUESS_URL""1172	rm -f ""${config_guess_temp}""1173    fi1174}1175 1176 1177##############################1178# LIBTOOLIZE_NEEDED FUNCTION #1179##############################1180libtoolize_needed () {1181    ret=1 # means no, don't need libtoolize1182    for feature in AC_PROG_LIBTOOL AM_PROG_LIBTOOL LT_INIT ; do1183	$VERBOSE_ECHO ""Searching for $feature in $CONFIGURE""1184	found=""`grep \""^$feature.*\"" $CONFIGURE`""1185	if [ ! ""x$found"" = ""x"" ] ; then1186	    ret=0 # means yes, need to run libtoolize1187	    break1188	fi1189    done1190    return ${ret}1191}1192 1193 1194 1195############################################1196# prepare build via autoreconf or manually #1197############################################1198reconfigure_manually=no1199if [ ""x$HAVE_AUTORECONF"" = ""xyes"" ] ; then1200    $ECHO

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