Fix to link correctly

Package-Manager: portage-2.2.0_alpha26/cvs/Linux x86_64

4 files changed, 717 insertions, 6 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index 5a295bd2819c..176ddada9486 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/ccp4-libs
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.30 2011/02/19 15:10:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.31 2011/03/04 13:49:29 jlec Exp $
+
+*ccp4-libs-6.1.3-r9 (04 Mar 2011)
+
+  04 Mar 2011; Justin Lecher <jlec@gentoo.org>
+  +files/6.1.3-unbundle-libs-ng.patch, +ccp4-libs-6.1.3-r9.ebuild:
+  Fix to link correctly
 
 *ccp4-libs-6.1.3-r8 (19 Feb 2011)
 
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
index d2ff7f6262a3..e999dc166fb8 100644
--- a/sci-libs/ccp4-libs/Manifest
+++ b/sci-libs/ccp4-libs/Manifest
@@ -10,15 +10,17 @@ AUX 6.1.3-impl-dec.patch 3957 RMD160 dbf3f5fd553a2f409a90affafa089574631155c8 SH
 AUX 6.1.3-link-proberly.patch 8282 RMD160 c45d3d1931e6a083c0c96b819aff3f67873659b8 SHA1 b1be6f1f7162616a60f3e12fe02dbe4dd426e990 SHA256 f6623dfb0d270e5fbffe03f95b23c967ec8da34b3d0a1c5262941979a965f9ea
 AUX 6.1.3-noinstall.patch 5188 RMD160 d3b22f11d7c27b37243b003f03615af377c8e632 SHA1 d75402e7b23d3aa15e67cda6cec8c93864d509c2 SHA256 22d96aea9d3d5e6e090713e610b35bdb34eaff9157c41687b47294f0d62ccff7
 AUX 6.1.3-overflows.patch 904 RMD160 03d5f10e901734c6e21be3e68592711450df32cd SHA1 24a740658fae2f917061c2a032a43a60e75c5478 SHA256 e5c62922daf832b62e9ea1e14a2be0d54c88b035b78b5831eee07025dff9222a
+AUX 6.1.3-unbundle-libs-ng.patch 13925 RMD160 eb96be062a507906f2e1d2659db0663ef026a54b SHA1 4b909c545843e2d22c49ea35a84da2d3d047de4a SHA256 e24757ac37a173fc501f1036e283f048faf7705b28cb8345492c4a8683a37e90
 AUX 6.1.3-unbundle-libs.patch 9063 RMD160 326af0e6990134546fb2607dae707b94d4588149 SHA1 ef929532e45c12fb168e5fca4eb7fa8c857c376a SHA256 7e5fc919b5204e2d9141f7715afdd8a8b4e3e2a96e2bf95aa00fbd56046f1aa4
 DIST ccp4-6.1.3-core-src.tar.gz 242134076 RMD160 e9b7deb0766fb95d5e8946881f20e086f0896fe9 SHA1 ee5ada892694db5dc9b2d7d2330b4ac694f56580 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324
 EBUILD ccp4-libs-6.1.3-r8.ebuild 10816 RMD160 f001019f12ffbbf1e4a8448504a8eac347e759de SHA1 0f8c8618f0f66dde8c86aa2d08cf696ec91bc18c SHA256 1f3f02adb2882f9b22344529df443f94c2a803dc3756914b6a713fc41d2bb237
-MISC ChangeLog 4629 RMD160 ed5c85e5e5b9fbfe95d3cfe330a1b33cea42e768 SHA1 8afe94fdc614695804d5452969fa65f4fae28c38 SHA256 815a14467d556d0db45b55ee6ce9c733eaa775d966560539f0d0b61dc11f65e4
+EBUILD ccp4-libs-6.1.3-r9.ebuild 11121 RMD160 fe228f541f6c5f07f03a0fb606231304da5c1754 SHA1 75db2f0328eeb37fd05c3c7ce602342c46865fa7 SHA256 303daeada1c3470151692d8d6dbccee3b6e2148cd6ac1760623284877b5cafca
+MISC ChangeLog 4803 RMD160 7a71cb37e70c60669b53e297dd6f1f9723f7b314 SHA1 3bd3fda8711fad83a7017ad9e591a071fa9ae3b5 SHA256 3f7d3d21bfcf3ca0a831af5858d3d8d705f59ca2e4f19f628ceb3e9927f50e65
 MISC metadata.xml 306 RMD160 57ba72f54388a666851bda87e52d313d618084e3 SHA1 7d2f57cb3f35eb6d4567b211e01251b5945d4eb2 SHA256 af351be5ead71b377b6fa2fa118fb9aee74129afdc19f736b41596d3033106aa
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.16 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
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-=Z/ea
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diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r9.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r9.ebuild
new file mode 100644
index 000000000000..be7f6fc66f5e
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r9.ebuild
@@ -0,0 +1,336 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r9.ebuild,v 1.1 2011/03/04 13:49:29 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit autotools eutils gnuconfig multilib python toolchain-funcs
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+MY_P="${P/-libs}"
+
+PATCH_TOT="0"
+# Here's a little scriptlet to generate this list from the provided
+# index.patches file
+#
+# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
+# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
+# index.patches
+#PATCH1=( src/topp_
+#topp.f-r1.16.2.5-r1.16.2.6.diff )
+#PATCH2=( .
+#configure-r1.372.2.18-r1.372.2.19.diff )
+
+DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
+# patch tarball from upstream
+	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
+# patches created by us
+	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
+
+for i in $(seq $PATCH_TOT); do
+	NAME="PATCH${i}[1]"
+	SRC_URI="${SRC_URI}
+		${SRC}/${PV}/patches/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	dev-lang/tcl
+	app-shells/tcsh
+	!<sci-chemistry/ccp4-6.1.3
+	!<sci-chemistry/ccp4-apps-${PVR}
+	sci-libs/cbflib
+	sci-libs/fftw:2.1
+	sci-libs/mmdb
+	sci-libs/monomer-db
+	virtual/jpeg
+	virtual/lapack
+	virtual/blas"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+	python_set_active_version 2
+}
+
+src_prepare() {
+	einfo "Applying upstream patches ..."
+	for patch in $(seq $PATCH_TOT); do
+		base="PATCH${patch}"
+		dir=$(eval echo \${${base}[0]})
+		p=$(eval echo \${${base}[1]})
+		pushd "${dir}" >& /dev/null
+		ccp_patch "${DISTDIR}/${p}"
+		popd >& /dev/null
+	done
+	einfo "Done."
+	echo
+
+	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
+
+	einfo "Applying Gentoo patches ..."
+	# fix buffer overflows wrt bug 339706
+	ccp_patch "${FILESDIR}"/${PV}-overflows.patch
+
+	# it tries to create libdir, bindir etc on live system in configure
+	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
+
+	# gerror_ gets defined twice on ppc if you're using gfortran/g95
+	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
+
+	# make creation of libccif.so smooth
+	ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
+
+	# lets try to build libmmdb seperatly
+	ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
+
+	# unbundle libjpeg and cbflib
+	ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng.patch
+
+	# Fix missing DESTIDR
+	# not installing during build
+	ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
+	sed \
+		-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
+		-i configure || die
+
+	# Fix upstreams code
+	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	# not needed, we have it extra
+	rm -rf src/rapper/{libxml2,gc7.0} || die
+
+	sed \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		-e 's:-Wl,-rpath,$CLIB::g' \
+		-e 's: -rpath $CLIB::g' \
+		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
+		-e 's:sleep 1:sleep .2:g' \
+		-i configure || die
+
+	gnuconfig_update
+
+	for i in	lib/DiffractionImage lib/ssm src/rapper src/pisa; do
+		pushd ${i} > /dev/null
+			eautoreconf
+		popd > /dev/null
+	done
+}
+
+src_configure() {
+
+	rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
+
+	# Build system is broken if we set LDFLAGS
+	userldflags="${LDFLAGS}"
+	export SHARED_LIB_FLAGS="${LDFLAGS}"
+	unset LDFLAGS
+
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "$(tc-getFC)" = "ifort" ]]; then
+		if use ia64; then
+			GENTOO_OSNAME="ia64_linux_intel"
+		else
+			# Should be valid for x86, maybe amd64
+			GENTOO_OSNAME="linux_intel_compilers"
+		fi
+	else
+		# Should be valid for x86 and amd64, at least
+		GENTOO_OSNAME="linux"
+	fi
+
+	# Sets up env
+	ln -s \
+		ccp4.setup-bash \
+		"${S}"/include/ccp4.setup
+
+	# We agree to the license by emerging this, set in LICENSE
+	sed -i \
+		-e "s~^\(^agreed=\).*~\1yes~g" \
+		"${S}"/configure
+
+	# Fix up variables -- need to reset CCP4_MASTER at install-time
+	sed -i \
+		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
+		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
+		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
+		"${S}"/include/ccp4.setup*
+
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup-sh
+
+	export CC=$(tc-getCC)
+	export CXX=$(tc-getCXX)
+	export COPTIM=${CFLAGS}
+	export CXXOPTIM=${CXXFLAGS}
+	# Default to -O2 if FFLAGS is unset
+	export FC=$(tc-getFC)
+	export FOPTIM=${FFLAGS:- -O2}
+
+	# Fix linking
+#	$(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \
+	export SHARE_LIB="\
+		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
+		$(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c -lmmdb $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		--onlylibs \
+		--with-shared-libs \
+		--with-fftw="${EPREFIX}/usr" \
+		--with-warnings \
+		--disable-cctbx \
+		--disable-clipper \
+		--tmpdir="${TMPDIR}" \
+		--bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \
+		--libdir="${EPREFIX}/usr/$(get_libdir)" \
+		${GENTOO_OSNAME} || die "econf failed"
+}
+
+src_compile() {
+	emake -j1 \
+		DESTDIR="${D}" onlylib || die "emake failed"
+}
+
+src_install() {
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup-sh
+
+	emake -j1 \
+		DESTDIR="${D}" \
+		includedir="${EPREFIX}/usr/include" \
+		library_includedir="${EPREFIX}/usr/include" \
+		install || die
+
+	sed \
+		-e "330,1000d" \
+		-i "${S}"/include/ccp4.setup-sh || die
+
+	sed \
+		-e "378,1000d" \
+		-i "${S}"/include/ccp4.setup-csh || die
+
+	sed \
+		-e "s:-${PV/-r*/}::g" \
+		-e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \
+		-e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \
+		-e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \
+		-e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \
+		-e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \
+		-e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \
+		-e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \
+		-e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \
+		-e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
+		-e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
+		-e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \
+		-e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \
+		-e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
+		-e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
+		-e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+		-e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+		-e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+		-e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
+		-e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+		-e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+		-e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
+		-e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
+		-e "s:^\(.*export CLIBS=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*setenv CLIBS \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*export CLIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*setenv CLIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \
+		-e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \
+		-e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \
+		-e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \
+		-e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
+		-e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
+		-e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+		-e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
+		-e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \
+		-e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \
+		-e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \
+		-e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \
+		-e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
+		-e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
+		-e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \
+		-e "/CCP4_HELPDIR/d" \
+		-e "/IMOSFLM_VERSION/d" \
+		-i "${S}"/include/ccp4.setup* || die
+
+	# Don't check for updates on every sourcing of /etc/profile
+	sed -i \
+		-e "s:\(eval python.*\):#\1:g" \
+		"${S}"/include/ccp4.setup* || die
+
+	# Libs
+	for file in "${S}"/lib/*; do
+		if [[ -d ${file} ]]; then
+			continue
+		elif [[ -x ${file} ]]; then
+			dolib.so ${file} || die
+		else
+			insinto /usr/$(get_libdir)
+			doins ${file} || die
+		fi
+	done
+
+	sed \
+		-e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
+		-i "${S}"/include/ccp4.setup-sh || die
+
+	# Setup scripts
+	insinto /etc/profile.d
+	newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh || die
+	newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh || die
+	rm -f "${S}"/include/ccp4.setup*
+
+	# Fix libdir in all *.la files
+	sed -i \
+		-e "s:^\(libdir=\).*:\1\'${EPREFIX}/usr/$(get_libdir)\':g" \
+		"${ED}"/usr/$(get_libdir)/*.la || die
+
+	# Data
+	insinto /usr/share/ccp4/data/
+	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
+
+	# Environment files, setup scripts, etc.
+	rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die
+	insinto /usr/share/ccp4/
+	doins -r "${S}"/include || die
+
+	dodoc "${S}"/lib/data/*.doc || die
+	newdoc "${S}"/lib/data/README DATA-README || die
+}
+
+pkg_postinst() {
+	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
+	einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this."
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch
new file mode 100644
index 000000000000..4271d5b76aec
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch
@@ -0,0 +1,367 @@
+diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
+index 69b32b0..602e35f 100755
+--- a/lib/DiffractionImage/DiffractionImageCBF.cpp
++++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
+@@ -6,10 +6,10 @@
+ // images.
+ 
+ #include "DiffractionImage.h"
+-#include "cbf.h"
+-#include "cbf_simple.h" 
+-#include "cbf_string.h"
+-#include "cbf_byte_offset.h"
++#include <cbflib/cbf.h>
++#include <cbflib/cbf_simple.h>
++#include <cbflib/cbf_string.h>
++#include <cbflib/cbf_byte_offset.h>
+ 
+ 
+ using namespace std;
+diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am
+index fedb7ac..89a048e 100755
+--- a/lib/DiffractionImage/MAR/Makefile.am
++++ b/lib/DiffractionImage/MAR/Makefile.am
+@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu
+ 
+ noinst_LTLIBRARIES = libmar.la
+ 
+-AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include
++AM_CPPFLAGS =
+ 
+ libmar_la_SOURCES = mar300_header.c \
+ 		    mar345_header.c \
+@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \
+ 		    utils.c \
+ 		    pck.c
+ 
+-libmar_la_LDFLAGS = -static
+diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c
+index d3f4212..2c37108 100755
+--- a/lib/DiffractionImage/MAR/marcif.c
++++ b/lib/DiffractionImage/MAR/marcif.c
+@@ -31,8 +31,7 @@
+ #include "marcif_header.h"
+ #include "mar345_header.h"
+ 
+-#include <cbf.h>
+-#include <img.h>
++#include <cbflib/cbf.h>
+ 
+ #define printe(x) 	printf("%s: %s: %s\n",prg,f,x)
+ #undef cbf_failnez
+diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am
+index 189a1d7..6652576 100755
+--- a/lib/DiffractionImage/Makefile.am
++++ b/lib/DiffractionImage/Makefile.am
+@@ -1,7 +1,9 @@
+ AUTOMAKE_OPTIONS = gnu
+-SUBDIRS = CBFlib Bruker MAR Rigaku jpg
++SUBDIRS = Bruker MAR Rigaku
+ 
+-AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg
++SYSLIBS = -ljpeg -lcbf
++
++AM_CPPFLAGS =-I./MAR
+ lib_LTLIBRARIES = libDiffImage.la 
+ 
+ if WANT_PYTHONMOD
+@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES =	DiffractionImageJpeg.cpp \
+ 							Profile.cpp \
+ 							Peak.cpp \
+ 							dps_peaksearch_cn.c 
+-libDiffImage_la_LDFLAGS = -static
++libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
++libDiffImage_la_LIBADD = $(SYSLIBS) \
++                         ./MAR/libmar.la ./Bruker/libbruker.la \
++                         ./Rigaku/librigaku.la
+ 
+-libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \
++libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \
+                                      ./Bruker/libbruker.la ./MAR/libmar.la \
+-                                     ./Rigaku/librigaku.la ./jpg/libjpeg.la
++                                     ./Rigaku/librigaku.la
+ libDiffractionImage_la_SOURCES =  DiffractionImageTclInterface.cpp
+-libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
+-                                 ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
+-				 				 ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
+-								 --no-whole-archive -rpath '$(libdir)'
++libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
++libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \
++                                libDiffImage.la \
++                                 ./Bruker/libbruker.la \
++				 				 ./MAR/libmar.la ./Rigaku/librigaku.la
+ 
+-lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
++lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \
+                                        ./Bruker/libbruker.la ./MAR/libmar.la \
+-                                       ./Rigaku/librigaku.la ./jpg/libjpeg.la
++                                       ./Rigaku/librigaku.la
+ lib_DiffractionImage_la_SOURCES =  DiffractionImagePythonInterface.cpp
+-lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
+-                                   ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
+-				   			       ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
+-								   --no-whole-archive -rpath '$(libdir)'
++lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
++lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \
++                                   ./Bruker/libbruker.la \
++				   			       ./MAR/libmar.la ./Rigaku/librigaku.la
+ 
+-libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
++libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la  \
+                                        ./Bruker/libbruker.la ./MAR/libmar.la \
+-                                       ./Rigaku/librigaku.la ./jpg/libjpeg.la
++                                       ./Rigaku/librigaku.la
+ libDiffractionImaJ_la_SOURCES =  DiffractionImageJavaInterface.cpp
+-libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
+-                                   ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
+-				                   ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
+-								   --no-whole-archive -rpath '$(libdir)'
++libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
++libDiffractionImaJ_la_LIBADD = libDiffImage.la \
++                                   ./Bruker/libbruker.la $(SYSLIBS) \
++				                   ./MAR/libmar.la ./Rigaku/librigaku.la
+ 
+ bin_PROGRAMS = automask diffdump printpeaks diff2jpeg
+-automask_LDADD =  libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
+-                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
++automask_LDADD =  libDiffImage.la ./Bruker/libbruker.la \
++                  ./MAR/libmar.la ./Rigaku/librigaku.la  $(SYSLIBS)
+ automask_SOURCES = automask.cpp
+-diffdump_LDADD =  libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
+-                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
++automask_LDFLAGS = $(SHARED_LIB_FLAGS)
++diffdump_LDADD =  libDiffImage.la ./Bruker/libbruker.la  $(SYSLIBS) \
++                  ./MAR/libmar.la ./Rigaku/librigaku.la
+ diffdump_SOURCES = diffdump.cpp
+-printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
+-                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
++diffdump_LDFLAGS = $(SHARED_LIB_FLAGS)
++printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \
++                  ./MAR/libmar.la ./Rigaku/librigaku.la  $(SYSLIBS)
+ printpeaks_SOURCES = printpeaks.cpp
+-diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
+-                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
++printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS)
++diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \
++                  ./MAR/libmar.la ./Rigaku/librigaku.la  $(SYSLIBS)
+ diff2jpeg_SOURCES = diff2jpeg.cpp
++diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS)
+ 
+ install-data-local: 
+ 			@INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC}
+diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure
+index 3fb5784..fdf9683 100755
+--- a/lib/DiffractionImage/configure
++++ b/lib/DiffractionImage/configure
+@@ -21768,7 +21768,7 @@ _ACEOF
+ fi
+ 
+ 
+-ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile"
++ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile "
+ 
+ 
+ cat >confcache <<\_ACEOF
+@@ -22407,12 +22407,9 @@ do
+   case $ac_config_target in
+     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+-    "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;;
+-    "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;;
+     "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;;
+     "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;;
+     "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;;
+-    "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;;
+ 
+   *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
+ echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
+diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in
+index 7f54b4b..16efc64 100755
+--- a/lib/DiffractionImage/configure.in
++++ b/lib/DiffractionImage/configure.in
+@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then
+       HAVE_PYTHON=1
+       CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}"
+     ])
++  PYLIB="-lpython${PYTHON_VER}"
++  AC_SUBST(PYLIB)
+ fi
+ AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1])
+ 
+@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z)
+ AC_CHECK_LIB([m], [sqrt])
+ 
+ AC_CONFIG_FILES([Makefile
+-                 CBFlib/Makefile
+-                 CBFlib/src/Makefile
+                  MAR/Makefile
+ 		 Rigaku/Makefile
+-		 Bruker/Makefile
+-		 jpg/Makefile])
++		 Bruker/Makefile])
+                  
+ AC_OUTPUT
+diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am
+index e9554e1..a3ba33d 100755
+--- a/lib/ssm/Makefile.am
++++ b/lib/ssm/Makefile.am
+@@ -1,7 +1,11 @@
++ACLOCAL_AMFLAGS = -I macros
+ #libtool
+ lib_LTLIBRARIES = libssm.la
++libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
++libssm_la_CFLAGS = @MMDB_CFLAGS@
+ libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \
+ ssm_align.cpp ss_graph.cpp
++libssm_la_LIBADD = @MMDB_LIBS@
+ 
+ #non libtool
+ #lib_LIBRARIES = libssm.a
+@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp
+ 
+ bin_PROGRAMS = superpose
+ 
+-INCLUDES = $(MMDB_CXXFLAGS)
+-
+-AM_LDFLAGS = $(MMDB_LIBS)
++INCLUDES = @MMDB_CFLAGS@
+ 
+ EXTRA_DIST = macros/mmdb.m4
+ 
+-superpose_LDADD = libssm.la
++superpose_LDADD = libssm.la @MMDB_LIBS@
+ 
+ libssm_a_AR = $(AR) $(AR_FLAGS)
+diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac
+index 783cb46..d637d11 100755
+--- a/lib/ssm/configure.ac
++++ b/lib/ssm/configure.ac
+@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug,
+   [ac_cv_enable_debug=no ] )
+ 
+ dnl Optional: Check for MMDB.
+-AM_PATH_MMDB(,
+-  [ if test "x$mmdb_prefix" != x ; then
+-      if test "x$ac_MMDB_CXXFLAGS" != x ; then 
+-        case "$ac_MMDB_CXXFLAGS" in
+-        *src/mmdb )
+-        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g`
+-        ;;
+-        *include/mmdb )
+-        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g`
+-        ;;
+-        *)
+-        esac
+-	MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS"
+-        MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#`
+-        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
+-      else
+-        MMDB_CXXFLAGS="-I$mmdb_prefix/lib/src/mmdb -I$mmdb_prefix/include/mmdb"
+-        MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb"
+-        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
+-      fi
+-    else
+-     AC_MSG_WARN([mmdb not found])
+-    fi
+-  ]
+-)
++
++PKG_CHECK_MODULES([MMDB],[mmdb])
++AC_SUBST([MMDB_CFLAGS])
++AC_SUBST([MMDB_LIBS])
+ 
+ # Checks for typedefs, structures, and compiler characteristics.
+ #
+@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
+ # test for function in m
+ AC_CHECK_LIB([m], [sqrt]) 
+ 
++
+ AC_SUBST(AR_FLAGS)
+ AC_SUBST(superpose_LDFLAGS)
+ AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes)
+diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am
+index 094fd6b..922a131 100755
+--- a/src/pisa/Makefile.am
++++ b/src/pisa/Makefile.am
+@@ -1,3 +1,4 @@
++ACLOCAL_AMFLAGS = -I macros
+ SUBDIRS = molref pisastore sbase
+ 
+ pkgdatadir = $(datadir)/pisa
+@@ -20,8 +21,8 @@ pisa.cpp                pisa_lists.cpp          seq_superpose.cpp
+ 
+ bin_PROGRAMS = pisa
+ 
+-INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS)
++INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS)
+ 
+-pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS)
++pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@
+ 
+ EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in
+diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac
+index 81afdda..4f99df6 100755
+--- a/src/pisa/configure.ac
++++ b/src/pisa/configure.ac
+@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
+ AC_CHECK_LIB([m], [sqrt])
+ 
+ dnl Optional: Check for MMDB.
+-AM_PATH_MMDB(,
+-  [ if test "x$mmdb_prefix" != x ; then
+-      if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then 
+-        case "$ac_MMDB_CXXFLAGS" in
+-        *src/mmdb )
+-        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g`
+-        ;;
+-        *include/mmdb )
+-        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g`
+-        ;;
+-        *)
+-        esac
+-	MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS"
+-        MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#`
+-        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
+-      else
+-        MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb"
+-        MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb"
+-        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
+-      fi
+-    else
+-     AC_MSG_ERROR([mmdb not found])
+-    fi
+-  ]
+-)
++PKG_CHECK_MODULES([MMDB],[mmdb])
++AC_SUBST([MMDB_CFLAGS])
++AC_SUBST([MMDB_LIBS])
+ 
+ ac_saved_CXXFLAGS=$CXXFLAGS
+ ac_saved_LIBS=$LIBS
+-CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS"
++CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS"
+ LIBS="$MMDB_LIBS $LIBS"
+ AM_PATH_SSM(,
+   [ if test "x$ssm_prefix" != x ; then
+diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am
+index e78b10d..486b931 100755
+--- a/src/rapper/Makefile.am
++++ b/src/rapper/Makefile.am
+@@ -1,3 +1,3 @@
+-SUBDIRS = libxml2 gc7.0 LOOP data
++SUBDIRS = LOOP data
+ 
+ EXTRA_DIST =
+diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac
+index 5e4ef69..11b63ec 100755
+--- a/src/rapper/configure.ac
++++ b/src/rapper/configure.ac
+@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno)
+ 
+ AC_SUBST(rapper_LDFLAGS)
+ 
+-AC_CONFIG_SUBDIRS([gc7.0 libxml2])
++#AC_CONFIG_SUBDIRS([gc7.0 libxml2])
+ #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile)
+ AC_OUTPUT(Makefile LOOP/Makefile data/Makefile)