From: Egon W. <eg...@us...> - 2002-08-31 14:43:08
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Update of /cvsroot/cdk/cdk/packages/tar/cdk In directory usw-pr-cvs1:/tmp/cvs-serv7875 Added Files: AUTHORS COPYING INSTALL Makefile.am NEWS README VERSION bootstrap configure.in install-sh missing mkinstalldirs Log Message: Uploaded files for making the "cdk" package which replaces the other tar packages. --- NEW FILE: AUTHORS --- The CDK project. --- NEW FILE: COPYING --- Copyright 1997-2001 The CDK project The Java jars files have the LGPL license. The shell scripts are licensed GPL. --- NEW FILE: INSTALL --- INSTALL GUIDE This is a quickly made installation manual... There are a couple of things you must do before you can use this software. 1. SOFTWARE DEPENDENCIES 1.1 COMPILING CDK First thing it do, is to check wether you have all the required software to compile CDK. You need: - Java 1.3 or better - Ant (see http://www.apache.org/) - Java 3D The generation of the man pages need the xsltproc tool. 1.2 RUNNING CDK Running CDK in principle requires only: - Java 1.3 or better But some applications of CDK need additional tools. The shell scripts cdk-* for Unix systems need Perl installed. The CDK can store structures in a database but this requires MySQL or PostgreSQL. 2. INSTALLATION 2.1 AUTOMATIC COMPILATION AND INSTALLATION Do: ./configure make make install By default the software is installed in /usr/local. You can configure the location by doing: ./configure --prefix=/usr or ./configure --prefix=${HOME}/cdk-bin 2.2 MANUAL COMPILATION There is no installation system for systems without Autotools, but you can still compile and run CDK. Compiling is done with Ant: ant dist-all Running CDK is done with: java -cp $CLASSPATH cdk-apps.jar org.openscience.cdk.applications.Viewer --- NEW FILE: Makefile.am --- PREFIX="@prefix@" SUBDIRS=jar doc bin man JAVA3DDIR=@JAVA3DDIR@ JARLIBDIR=@CDKJARDIR@ JARLIBS=cdk-core.jar cdk-extra.jar \ cdk-libio.jar cdk-apps.jar alljardir = "${JARLIBDIR}" alljar_DATA = ${JARLIBS} EXTRA_DIST=VERSION ChangeLog build.xml javadoc.xml src CLEANFILES=doc dist sourcedist reports \ cdk-core.jar cdk-extra.jar \ cdk-libio.jar cdk-apps.jar cdk-core.jar: ant dist-core cp dist/jar/cdk-core.jar . cdk-extra.jar: ant -Dpathtojava3d=${JAVA3DDIR} dist-with-java3d cp dist/jar/cdk-extra-with-java3d.jar cdk-extra.jar cdk-libio.jar: ant dist-libio cp dist/jar/cdk-libio.jar . cdk-apps.jar: ant dist-apps cp dist/jar/cdk-apps.jar . --- NEW FILE: NEWS --- See ChangeLog. --- NEW FILE: README --- The Chemical Development Kit (CDK) Maintainers: Christoph Steinbeck Dan Gezelter Egon Willighagen Co-authors: <these must be added> Contributors: <these must be added> Thanks to: <these must be added> --- NEW FILE: VERSION --- 20020831 --- NEW FILE: bootstrap --- #! /bin/sh -e # bootstrap this software cp ../../../CHANGELOG ChangeLog cp ../../../build.xml . cp ../../../javadoc.xml . cp -R ../../../src . find src -name "CVS" | xargs rm -R find src -name ".cvsignore" | xargs rm aclocal && automake --verbose --gnu && autoconf --- NEW FILE: configure.in --- dnl dnl $Id: configure.in,v 1.1 2002/08/31 14:43:04 egonw Exp $ dnl AC_INIT() AM_INIT_AUTOMAKE(cdk, `cat VERSION`) dnl deal with options SGMLDIR="" AC_ARG_WITH(sgmldir, [ --with-sgmldir=DIR where to find the SGML dir ], [ if test -n "$withval" then SGMLDIR="$withval" fi ] ) AC_SUBST(SGMLDIR) AC_MSG_RESULT(Using sgml dir $SGMLDIR) dnl Checks for programs. AC_PROG_INSTALL AC_PROG_LN_S AC_PROG_MAKE_SET CDKJARDIR=$prefix/share/java AC_SUBST(CDKJARDIR) CDKLIBDIR=$prefix/lib/cdk AC_SUBST(CDKLIBDIR) if test -x "$JAVA_HOME/bin/java" then AC_MSG_CHECKING(for java) AC_MSG_RESULT($JAVA_HOME/bin/java) PATHTOJAVA=$JAVA_HOME/bin/java AC_SUBST(PATHTOJAVA) else AC_CHECK_PROG(HASJAVA, java, yes, no) if test "xyes" = "x$HASJAVA" then AC_PATH_PROG(PATHTOJAVA, java, no) fi fi AC_MSG_CHECKING(for rt.jar lib) for d in "/usr/lib/j2re1.3/lib" do if test -f "$d/rt.jar" then PATHTORTJAR="$d/rt.jar" fi done if test "x$PATHTORTJAR" = "x" then AC_MSG_RESULT(no) else AC_MSG_RESULT($PATHTORTJAR) fi AC_SUBST(PATHTORTJAR) AC_MSG_CHECKING(for Java3D lib) AC_ARG_WITH(java3ddir, [ --with-java3ddir=DIR path to the Java 3D installation directory ], [ if test -n "$withval" then JAVA3DDIR="$withval" fi ]) if test -f "$JAVA3DDIR/lib/ext/j3dcore.jar" then PATHTO3DJAR="$JAVA3DDIR/lib/ext/j3dcore.jar:$JAVA3DDIR/lib/ext/j3dutils.jar:$JAVA3DDIR/lib/ext/vecmath.jar" else if test "x$prefix" = xNONE then # order these with prefered one at the end try_dirs="$ac_default_prefix" else try_dirs="$prefix" fi # Debian GNU/Linux Blackdown path: /usr/lib/j2re1.3 try_dirs="$try_dirs /usr/lib/j2re1.3 $JAVA_HOME $JAVA_HOME/jre" for d in $try_dirs do if test -r "$d/lib/ext/j3dcore.jar" then PATHTO3DJAR="$d/lib/ext/j3dcore.jar:$d/lib/ext/j3dutils.jar:$d/lib/ext/vecmath.jar" JAVA3DDIR="$d/lib/ext" fi done fi if test "x$PATHTO3DJAR" = "x" then AC_MSG_RESULT(no) else AC_MSG_RESULT($PATHTO3DJAR) fi AC_SUBST(JAVA3DDIR) AC_SUBST(PATHTO3DJAR) dnl needed for check_xml AC_CHECK_PROG(HASXSLTPROC, xsltproc, yes, no) AC_PATH_PROG(PATHTOXSLTPROC, xsltproc) AC_CHECK_PROG(HASXMLLINT, xmllint, yes, no) AC_PATH_PROG(PATHTOXMLLINT, xmllint) dnl other AC_CHECK_PROG(HASANT, ant, yes, no) AC_PATH_PROG(PATHTOANT, ant) AC_CHECK_PROG(HASTAR, tar, yes, no) AC_PATH_PROG(PATHTOTAR, tar, no) AC_CHECK_PROG(HASGZIP, gzip, yes, no) AC_PATH_PROG(PATHTOGZIP, gzip, no) dnl detection copied from Lire 1.0 (www.logreport.org) dnl Try to find the SGML directory layout dnl Find a list of potential SGML/XML trees, we will look into subdirectories dnl of this one to find the DSSSL/DTD/XSLT stuff. sgmldirs=$SGMLDIR try_dirs="/usr/lib/sgml /usr/share/sgml /usr/local/lib/sgml /usr/local/share/sgml /usr/share/xml /usr/local/share/xml /usr/local/share/xsl" if test x"$prefix" != "xNONE" then try_dirs="$try_dirs $prefix/lib/sgml $prefix/share/sgml $prefix/share/xml" fi AC_MSG_CHECKING(for SGML/XML trees) for d in $try_dirs do if test -d $d then if echo "$sgmldirs" | grep $d > /dev/null then : else sgmldirs="$sgmldirs $d" fi fi done if test -z "$sgmldirs" then sgmldirs="none" fi AC_MSG_RESULT($sgmldirs) AC_MSG_CHECKING(for DocBook XSL stylesheets) if test -z "$DBK_XSL_STYLESHEETS" && test -z "$PATHTODBKXSLHTML" then for d in $sgmldirs do for f in stylesheet/xsl/docbook stylesheet/xsl stylesheet docbook/stylesheet/xsl docbook/xsl docbook do dir= if test -f "$d/$f/xhtml/docbook.xsl" then dir="$d/$f" elif test -f "$d/$f/modular/xhtml/docbook.xsl" then dir="$d/$f/modular" elif test -f "$d/$f/nwalsh/xhtml/docbook.xsl" then dir="$d/$f/nwalsh" fi if test -n "$dir" then AC_MSG_RESULT("$dir") PATHTODBKXSLHTML="$dir/html/chunker.xsl" PATHTODBKXSLCOMMON="$dir/common/common.xsl" fi test -n "$PATHTODBKXSLHTML" && break done test -n "$PATHTODBKXSLHTML" && break done else if test -n "$DBK_XSL_STYLESHEETS" then AC_MSG_RESULT($DBK_XSL_STYLESHEETS) if ! test -d "$DBK_XSL_STYLESHEETS" then AC_MSG_WARN($DBK_XSL_STYLESHEETS isn't present on the system) fi PATHTODBKXSLHTML="$DBK_XSL_STYLESHEETS/html/chunker.xsl" PATHTODBKXSLCOMMON="$DBK_XSL_STYLESHEETS/common/common.xsl" else AC_MSG_RESULT($PATHTODBKXSLHTML) AC_MSG_RESULT($PATHTODBKXSLCOMMON) if ! test -f "$PATHTODBKXSLHTML" then AC_MSG_WARN($PATHTODBKXSLHTML isn't present on system) fi fi fi if test "x$PATHTODBKXSLHTML" = "x" then AC_MSG_RESULT(no) fi AC_SUBST(PATHTODBKXSLHTML) AC_SUBST(PATHTODBKXSLCOMMON) AC_OUTPUT([ Makefile jar/Makefile jar/libio/Makefile doc/Makefile bin/Makefile bin/cdk-dbadmin bin/cdk-download bin/cdk-fileconvert bin/cdk-test bin/cdk-view man/Makefile man/xsl/Makefile man/xsl/db2man.xsl ]) --- NEW FILE: install-sh --- #!/bin/sh # # install - install a program, script, or datafile # This comes from X11R5 (mit/util/scripts/install.sh). # # Copyright 1991 by the Massachusetts Institute of Technology # # Permission to use, copy, modify, distribute, and sell this software and its # documentation for any purpose is hereby granted without fee, provided that # the above copyright notice appear in all copies and that both that # copyright notice and this permission notice appear in supporting # documentation, and that the name of M.I.T. not be used in advertising or # publicity pertaining to distribution of the software without specific, # written prior permission. M.I.T. makes no representations about the # suitability of this software for any purpose. It is provided "as is" # without express or implied warranty. # # Calling this script install-sh is preferred over install.sh, to prevent # `make' implicit rules from creating a file called install from it # when there is no Makefile. # # This script is compatible with the BSD install script, but was written # from scratch. It can only install one file at a time, a restriction # shared with many OS's install programs. # set DOITPROG to echo to test this script # Don't use :- since 4.3BSD and earlier shells don't like it. doit="${DOITPROG-}" # put in absolute paths if you don't have them in your path; or use env. vars. mvprog="${MVPROG-mv}" cpprog="${CPPROG-cp}" chmodprog="${CHMODPROG-chmod}" chownprog="${CHOWNPROG-chown}" chgrpprog="${CHGRPPROG-chgrp}" stripprog="${STRIPPROG-strip}" rmprog="${RMPROG-rm}" mkdirprog="${MKDIRPROG-mkdir}" transformbasename="" transform_arg="" instcmd="$mvprog" chmodcmd="$chmodprog 0755" chowncmd="" chgrpcmd="" stripcmd="" rmcmd="$rmprog -f" mvcmd="$mvprog" src="" dst="" dir_arg="" while [ x"$1" != x ]; do case $1 in -c) instcmd="$cpprog" shift continue;; -d) dir_arg=true shift continue;; -m) chmodcmd="$chmodprog $2" shift shift continue;; -o) chowncmd="$chownprog $2" shift shift continue;; -g) chgrpcmd="$chgrpprog $2" shift shift continue;; -s) stripcmd="$stripprog" shift continue;; -t=*) transformarg=`echo $1 | sed 's/-t=//'` shift continue;; -b=*) transformbasename=`echo $1 | sed 's/-b=//'` shift continue;; *) if [ x"$src" = x ] then src=$1 else # this colon is to work around a 386BSD /bin/sh bug : dst=$1 fi shift continue;; esac done if [ x"$src" = x ] then echo "install: no input file specified" exit 1 else true fi if [ x"$dir_arg" != x ]; then dst=$src src="" if [ -d $dst ]; then instcmd=: chmodcmd="" else instcmd=mkdir fi else # Waiting for this to be detected by the "$instcmd $src $dsttmp" command # might cause directories to be created, which would be especially bad # if $src (and thus $dsttmp) contains '*'. if [ -f $src -o -d $src ] then true else echo "install: $src does not exist" exit 1 fi if [ x"$dst" = x ] then echo "install: no destination specified" exit 1 else true fi # If destination is a directory, append the input filename; if your system # does not like double slashes in filenames, you may need to add some logic if [ -d $dst ] then dst="$dst"/`basename $src` else true fi fi ## this sed command emulates the dirname command dstdir=`echo $dst | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'` # Make sure that the destination directory exists. # this part is taken from Noah Friedman's mkinstalldirs script # Skip lots of stat calls in the usual case. if [ ! -d "$dstdir" ]; then defaultIFS=' ' IFS="${IFS-${defaultIFS}}" oIFS="${IFS}" # Some sh's can't handle IFS=/ for some reason. IFS='%' set - `echo ${dstdir} | sed -e 's@/@%@g' -e 's@^%@/@'` IFS="${oIFS}" pathcomp='' while [ $# -ne 0 ] ; do pathcomp="${pathcomp}${1}" shift if [ ! -d "${pathcomp}" ] ; then $mkdirprog "${pathcomp}" else true fi pathcomp="${pathcomp}/" done fi if [ x"$dir_arg" != x ] then $doit $instcmd $dst && if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else true ; fi && if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else true ; fi && if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else true ; fi && if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else true ; fi else # If we're going to rename the final executable, determine the name now. if [ x"$transformarg" = x ] then dstfile=`basename $dst` else dstfile=`basename $dst $transformbasename | sed $transformarg`$transformbasename fi # don't allow the sed command to completely eliminate the filename if [ x"$dstfile" = x ] then dstfile=`basename $dst` else true fi # Make a temp file name in the proper directory. dsttmp=$dstdir/#inst.$$# # Move or copy the file name to the temp name $doit $instcmd $src $dsttmp && trap "rm -f ${dsttmp}" 0 && # and set any options; do chmod last to preserve setuid bits # If any of these fail, we abort the whole thing. If we want to # ignore errors from any of these, just make sure not to ignore # errors from the above "$doit $instcmd $src $dsttmp" command. if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else true;fi && if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else true;fi && if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else true;fi && if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else true;fi && # Now rename the file to the real destination. $doit $rmcmd -f $dstdir/$dstfile && $doit $mvcmd $dsttmp $dstdir/$dstfile fi && exit 0 --- NEW FILE: missing --- #! /bin/sh # Common stub for a few missing GNU programs while installing. # Copyright (C) 1996, 1997, 1999 Free Software Foundation, Inc. # Originally by Fran,cois Pinard <pi...@ir...>, 1996. # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2, or (at your option) # any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA # 02111-1307, USA. if test $# -eq 0; then echo 1>&2 "Try \`$0 --help' for more information" exit 1 fi run=: case "$1" in --run) # Try to run requested program, and just exit if it succeeds. run= shift "$@" && exit 0 ;; esac # If it does not exist, or fails to run (possibly an outdated version), # try to emulate it. case "$1" in -h|--h|--he|--hel|--help) echo "\ $0 [OPTION]... PROGRAM [ARGUMENT]... Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an error status if there is no known handling for PROGRAM. Options: -h, --help display this help and exit -v, --version output version information and exit --run try to run the given command, and emulate it if it fails Supported PROGRAM values: aclocal touch file \`aclocal.m4' autoconf touch file \`configure' autoheader touch file \`config.h.in' automake touch all \`Makefile.in' files bison create \`y.tab.[ch]', if possible, from existing .[ch] flex create \`lex.yy.c', if possible, from existing .c lex create \`lex.yy.c', if possible, from existing .c makeinfo touch the output file tar try tar, gnutar, gtar, then tar without non-portable flags yacc create \`y.tab.[ch]', if possible, from existing .[ch]" ;; -v|--v|--ve|--ver|--vers|--versi|--versio|--version) echo "missing 0.2 - GNU automake" ;; -*) echo 1>&2 "$0: Unknown \`$1' option" echo 1>&2 "Try \`$0 --help' for more information" exit 1 ;; aclocal) echo 1>&2 "\ WARNING: \`$1' is missing on your system. You should only need it if you modified \`acinclude.m4' or \`configure.in'. 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You should only need it if you modified \`Makefile.am', \`acinclude.m4' or \`configure.in'. You might want to install the \`Automake' and \`Perl' packages. Grab them from any GNU archive site." find . -type f -name Makefile.am -print | sed 's/\.am$/.in/' | while read f; do touch "$f"; done ;; bison|yacc) echo 1>&2 "\ WARNING: \`$1' is missing on your system. You should only need it if you modified a \`.y' file. You may need the \`Bison' package in order for those modifications to take effect. 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You can get \`Flex' from any GNU archive site." rm -f lex.yy.c if [ $# -ne 1 ]; then eval LASTARG="\${$#}" case "$LASTARG" in *.l) SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'` if [ -f "$SRCFILE" ]; then cp "$SRCFILE" lex.yy.c fi ;; esac fi if [ ! -f lex.yy.c ]; then echo 'main() { return 0; }' >lex.yy.c fi ;; makeinfo) echo 1>&2 "\ WARNING: \`$1' is missing on your system. You should only need it if you modified a \`.texi' or \`.texinfo' file, or any other file indirectly affecting the aspect of the manual. The spurious call might also be the consequence of using a buggy \`make' (AIX, DU, IRIX). You might want to install the \`Texinfo' package or the \`GNU make' package. Grab either from any GNU archive site." file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'` if test -z "$file"; then file=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'` file=`sed -n '/^@setfilename/ { s/.* \([^ ]*\) *$/\1/; p; q; }' $file` fi touch $file ;; tar) shift if test -n "$run"; then echo 1>&2 "ERROR: \`tar' requires --run" exit 1 fi # we have already tried tar in the generic part gnutar ${1+"$@"} && exit 0 gtar ${1+"$@"} && exit 0 firstarg="$1" if shift; then case "$firstarg" in *o*) firstarg=`echo "$firstarg" | sed s/o//` tar "$firstarg" ${1+"$@"} && exit 0 ;; esac case "$firstarg" in *h*) firstarg=`echo "$firstarg" | sed s/h//` tar "$firstarg" ${1+"$@"} && exit 0 ;; esac fi echo 1>&2 "\ WARNING: I can't seem to be able to run \`tar' with the given arguments. You may want to install GNU tar or Free paxutils, or check the command line arguments." exit 1 ;; *) echo 1>&2 "\ WARNING: \`$1' is needed, and you do not seem to have it handy on your system. You might have modified some files without having the proper tools for further handling them. Check the \`README' file, it often tells you about the needed prerequirements for installing this package. You may also peek at any GNU archive site, in case some other package would contain this missing \`$1' program." exit 1 ;; esac exit 0 --- NEW FILE: mkinstalldirs --- #! /bin/sh # mkinstalldirs --- make directory hierarchy # Author: Noah Friedman <fri...@pr...> # Created: 1993-05-16 # Public domain # $Id: mkinstalldirs,v 1.1 2002/08/31 14:43:04 egonw Exp $ errstatus=0 for file do set fnord `echo ":$file" | sed -ne 's/^:\//#/;s/^://;s/\// /g;s/^#/\//;p'` shift pathcomp= for d do pathcomp="$pathcomp$d" case "$pathcomp" in -* ) pathcomp=./$pathcomp ;; esac if test ! -d "$pathcomp"; then echo "mkdir $pathcomp" mkdir "$pathcomp" || lasterr=$? if test ! -d "$pathcomp"; then errstatus=$lasterr fi fi pathcomp="$pathcomp/" done done exit $errstatus # mkinstalldirs ends here |