sci-libs/ccp4-libs -- Version bump

(Portage version: 2.2_rc60/git/Linux x86_64)
 (Signed Manifest commit)

8 files changed, 654 insertions, 4 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index de1824b92..318892dc2 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -2,6 +2,16 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ccp4-libs-6.1.3 (22 Dec 2009)
+
+  22 Dec 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/6.1.3-ccif-shared.patch,
+  +files/6.1.3-dont-build-mmdb.patch,
+  +files/6.1.3-dont-make-dirs-in-configure.patch,
+  +files/6.1.3-glibc2.10.patch, +ccp4-libs-6.1.3.ebuild,
+  +files/6.1.3-link-proberly.patch:
+  Version bump
+
 *ccp4-libs-6.1.2-r1 (29 Oct 2009)
 
   29 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
index 8ab6bf01c..6149c89d9 100644
--- a/sci-libs/ccp4-libs/Manifest
+++ b/sci-libs/ccp4-libs/Manifest
@@ -11,23 +11,30 @@ AUX 6.1.2-dont-build-mmdb.patch 861 RMD160 f2cfce178bb421c36e1b1114435f8e0ee9710
 AUX 6.1.2-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
 AUX 6.1.2-glibc2.10.patch 1018 RMD160 577ee4a6174df36bb8bac82738523f5c757df4b9 SHA1 48ad6d0d024c43d64277e4decba420d51e75a510 SHA256 d2a2ddf2a66738d94723b50797e279f64c8e057a3e584e33f9eb9c8d7ea0e532
 AUX 6.1.2-link-proberly.patch 9325 RMD160 0457062deb5d71f7419d134e89d3d99989fc12b7 SHA1 c7c0453b82b85ae22ea42b562dd2d4ac95b134e7 SHA256 81c4eda497ffa3a0f2d757b7c6b3f6cc35a06ced18ebede2faa31f18667ea8b7
+AUX 6.1.3-ccif-shared.patch 1668 RMD160 803687b13dbe93aaeed8264a73dfe7303b5fcdfb SHA1 3d833aefea874c08e61140613b0a5c75a90e0382 SHA256 57c201ee81e3fd95f174fecfd810ddf12509f0c2bfb1b2f317f893561eb60e3f
+AUX 6.1.3-dont-build-mmdb.patch 861 RMD160 f2cfce178bb421c36e1b1114435f8e0ee97102d8 SHA1 d39439dfd9c23781a232551ef9690df6f9ea7681 SHA256 fb4711188e41e6be0a86464425fd9b04ae5dba58fb00202c7234182d002dc795
+AUX 6.1.3-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
+AUX 6.1.3-glibc2.10.patch 1018 RMD160 577ee4a6174df36bb8bac82738523f5c757df4b9 SHA1 48ad6d0d024c43d64277e4decba420d51e75a510 SHA256 d2a2ddf2a66738d94723b50797e279f64c8e057a3e584e33f9eb9c8d7ea0e532
+AUX 6.1.3-link-proberly.patch 9325 RMD160 0457062deb5d71f7419d134e89d3d99989fc12b7 SHA1 c7c0453b82b85ae22ea42b562dd2d4ac95b134e7 SHA256 81c4eda497ffa3a0f2d757b7c6b3f6cc35a06ced18ebede2faa31f18667ea8b7
 AUX pass-clipper-enablevals.patch 501 RMD160 23466922268a91570b0f64cf79809b988e32689b SHA1 c254d31fe88ed1716a53bd549cf7aee537ca5204 SHA256 d476c9f231fb6cdfb5e57004b393644a88016318cdeed9c33c32de25e0d91b79
 DIST 6.1.1-090511-updates.patch.bz2 8915 RMD160 58114b0ba6d225078044a8a6f9245aab66c6b572 SHA1 15c327c0b218b542b0c3955a9e63d2c6de299f7e SHA256 c0dbbde05b72f2460ada22f556d4cfe1f286a448ceb1181fd48b758468e509ac
 DIST ccp4-6.1.1-core-src.tar.gz 246661086 RMD160 6722367727e4b6b1f8456f1458c9aac124923a89 SHA1 9141801e021f8a5107ed1e3989840e4de849b39c SHA256 56f971e05fe4543173451e48600813492fd0081b25d4a659cb0fed1fd2529407
 DIST ccp4-6.1.1-src-patch-04_03_09.tar.gz 279642 RMD160 1a7c3b6cc846d315fc577e78b4aa00ab85a3d3d2 SHA1 29dbb84f3d63fc860694473ca99cf8bb71dae18a SHA256 eb806168235b55fbafdd72591ba94d35b78cc715a56a8b90979644d420ad672a
 DIST ccp4-6.1.2-core-src.tar.gz 247203188 RMD160 19019c6cd37e83cf6d2d19f91979edc978d18395 SHA1 2423178d3877dd44d3671a7eb4d6666de6852cb7 SHA256 bcae870675270be410278d9a6f2ee19f9caf32b73fd969e9381a4d510f174c75
+DIST ccp4-6.1.3-core-src.tar.gz 241654695 RMD160 922e723521a94b787f187e714704fce6d705fc5e SHA1 6fc20a2c5956f8640267733dd419a863213bbfc1 SHA256 c76ddeecacfb396416f6e067f0b21532c1376dfc34dcaaa4edc89389cd20f8eb
 EBUILD ccp4-libs-6.1.1-r4.ebuild 5776 RMD160 3a36e4a2fff69e2a17028c39f8849a4cfd73c64e SHA1 7693f8aa4a3e6106876e68fcdf25fada3b2e61e5 SHA256 f541ab2ffa172978b11c91c11754be4c75bb63174e2c3a4a1990f7e8fa5ddd57
 EBUILD ccp4-libs-6.1.1-r6.ebuild 5956 RMD160 88f4d6e5c9067225501f214002bc5924bc07c1a2 SHA1 8e61890578007833d8a923eeada3bdf064354056 SHA256 1e7bde2c6f9319d699cf95565aa74bd26372b9d1275fdeaaa8ee75fb4001b30a
 EBUILD ccp4-libs-6.1.1-r7.ebuild 6093 RMD160 99176fde51fd41e7b29610a15720859e97b22d01 SHA1 6a52cfb8e4cddd9454db90bb90bad600c3b753ec SHA256 2143d0c1a7905107b9699cce41d7f33a6fedc99cf9046de33d7b42ddafdfa937
 EBUILD ccp4-libs-6.1.1.ebuild 5211 RMD160 6f3705f7ab0c48bbda073eb7dc1a283b3dcaa39a SHA1 8b09909daae034fc393b49b5fda7e06a783bcd14 SHA256 e9b4a3183a8f753ced59968b261bb655c87d13ade8c9964c71f1f2948c42067e
 EBUILD ccp4-libs-6.1.2-r1.ebuild 5841 RMD160 83d0f6b8c6635e630a45b8adcd0f7564112f0c02 SHA1 9ba4da47a9227f1f91fb3cce0b7cd99202030975 SHA256 d526dfd1368290cd15e395338655f57e33bb3fce410a6642ceefe38bef707b7d
 EBUILD ccp4-libs-6.1.2.ebuild 5766 RMD160 aa4054b10c8122ac719c7300a3395d210e648a31 SHA1 29a5d1d07c87f78aea587ac5f2d4fc50a4e5afee SHA256 58c14a0f2def77683bd3db096fa28f30a8dd0fce4adaf7774c307c7e478d5eca
-MISC ChangeLog 2810 RMD160 aea56b0049c3e25a108018a3c2417736519c8f30 SHA1 fff879d14890be376cfb626cb80e988ae163c9d4 SHA256 7454aaf9fcec6eb37a6a518790c69fe4b9c3aaf8324fe2a347d040a071c59424
+EBUILD ccp4-libs-6.1.3.ebuild 5766 RMD160 aa4054b10c8122ac719c7300a3395d210e648a31 SHA1 29a5d1d07c87f78aea587ac5f2d4fc50a4e5afee SHA256 58c14a0f2def77683bd3db096fa28f30a8dd0fce4adaf7774c307c7e478d5eca
+MISC ChangeLog 3130 RMD160 889f9ca1793489deacb6c970b908f22431fc08f1 SHA1 8c2108d6f9cb59873b74ace42cd1d01dcda5dd78 SHA256 53c600800195cb8a04a49d0ff6a31a6e0d11eb2e12186b011f4261bbae267b19
 MISC metadata.xml 309 RMD160 b9d7f0a63f8fb51e9b4e2d6b4f4028541df5400c SHA1 26ee4b64e0e4d52b1afe00957d53b0cc2956da00 SHA256 04f156de856eae11c0cf8af213f74a9852213844cdd5133aa01dbe60371d57e7
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diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3.ebuild
new file mode 100644
index 000000000..7191ff805
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3.ebuild
@@ -0,0 +1,210 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit fortran eutils gnuconfig toolchain-funcs
+
+FORTRAN="g77 gfortran ifc"
+
+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"
+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/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+	app-shells/tcsh
+	!<sci-chemistry/ccp4-6.0.99
+	=sci-libs/fftw-2*
+	sci-libs/mmdb
+	sci-libs/monomer-db
+	virtual/lapack
+	virtual/blas"
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	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 ..."
+	# 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}"/${PV}-dont-build-mmdb.patch
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	gnuconfig_update
+}
+
+src_compile() {
+	# Build system is broken if we set LDFLAGS
+	userldflags="${LDFLAGS}"
+	export SHARED_LIB_FLAGS="${LDFLAGS}"
+	unset LDFLAGS
+
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "${FORTRANC}" = "ifc" ]]; 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~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
+		"${S}"/include/ccp4.setup*
+
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup
+
+	export CC=$(tc-getCC)
+	export CXX=$(tc-getCXX)
+	export COPTIM=${CFLAGS}
+	export CXXOPTIM=${CXXFLAGS}
+	# Default to -O2 if FFLAGS is unset
+	export FC=${FORTRANC}
+	export FOPTIM=${FFLAGS:- -O2}
+#	export CCP4_SCR="${T}"
+
+	# 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.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
+		${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		--onlylibs \
+		--with-shared-libs \
+		--with-fftw=/usr \
+		--with-warnings \
+		--disable-cctbx \
+		--disable-clipper \
+		--tmpdir="${TMPDIR}" \
+		${GENTOO_OSNAME} || die "econf failed"
+	emake -j1 onlylib || die "emake failed"
+}
+
+src_install() {
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup
+
+	einstall || die "install failed"
+
+	# 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
+
+	# Bins
+	dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
+	newbin bin/superpose superpose-ccp4 || die
+
+	# Fix libdir in all *.la files
+	sed -i \
+		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
+		"${D}"/usr/$(get_libdir)/*.la
+
+	# Data
+	insinto /usr/share/ccp4/data/
+	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
+	dodoc "${S}"/lib/data/*.doc
+	newdoc "${S}"/lib/data/README DATA-README
+
+	# Include files
+	insinto /usr/include
+	for i in ccp4; do
+		doins -r "${S}"/include/${i} || die
+	done
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}
diff --git a/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch b/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch
new file mode 100644
index 000000000..ca18d75bc
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch
@@ -0,0 +1,33 @@
+--- configure	2009-08-04 22:35:34.000000000 +0200
++++ configure.new	2009-08-04 22:54:32.000000000 +0200
+@@ -3136,8 +3136,8 @@
+   fi
+   ( touch /tmp/$$.cache_file 2>/dev/null && \
+     cat /dev/null > /tmp/$$.cache_file && \
+-    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \
+-    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif
++    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file --enable-shared-lib ) || \
++    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --enable-shared-lib
+   rm -f /tmp/$$.cache_file
+   if [ "X$LIBFOPTIM" != "X" ]; then
+     FOPTIM=$FOPTIM_save
+--- lib/ccif/configure	2009-08-04 22:35:37.000000000 +0200
++++ lib/ccif/configure.new	2009-08-04 23:05:44.000000000 +0200
+@@ -5568,7 +5568,7 @@
+       enable_shared_lib=no
+    ;;
+ 
+-   i?86-unknown-linux | i?86-pc-linux-gnu )
++   i?86-unknown-linux | i?86-pc-linux-gnu | x86_64-unknown-linux-gnu)
+       if test $enable_shared_lib = yes ; then
+ 
+          SO_LOC_VAR='LD_LIBRARY_PATH'
+@@ -5585,7 +5585,7 @@
+          else
+            SHARED_LIB_PATH='LD_LIBRARY_PATH=`pwd`'
+          fi
+-         SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
++         SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
+          # SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
+          SHARED_LIB_EXPORTS_CMD=''
+       fi
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
new file mode 100644
index 000000000..b3fefacda
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
@@ -0,0 +1,26 @@
+--- lib/src/Makefile.in	2009-06-18 15:44:08.000000000 +0200
++++ lib/src/Makefile.in.new	2009-08-11 11:58:25.000000000 +0200
+@@ -176,7 +176,7 @@
+ 
+ ##### Makefile targets ######
+ 
+-all:  fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
++all:  fsplit $(LC) $(LF) $(SCRIPT_MODULES)
+ # maybe create shared library
+ 	$(SHARE_LIB)
+ 
+--- lib/src/Makefile.in	2009-06-18 15:44:08.000000000 +0200
++++ lib/src/Makefile.in.new	2009-08-11 12:17:53.000000000 +0200
+@@ -716,11 +716,9 @@
+ 	  rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \
+ 	done
+ 
+-install : all install-ccp4HEADERS install-mmdbHEADERS
+-	$(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB)
++install : all install-ccp4HEADERS
+ 	$(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC)
+ 	$(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF)
+-	$(RANLIB) $(libdir)/$(LMMDB)
+ 	$(RANLIB) $(libdir)/$(LC)
+ 	$(RANLIB) $(libdir)/$(LF)
+ 	$(SHARE_INST)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch
new file mode 100644
index 000000000..583697cea
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch
@@ -0,0 +1,87 @@
+--- ccp4-6.0.99e.orig/configure	2008-07-31 10:37:22.000000000 -0700
++++ ccp4-6.0.99e/configure	2008-07-31 10:39:18.000000000 -0700
+@@ -643,45 +643,45 @@
+ #     echo "! Beware -- the $system installation isn't properly tested." ; }
+ syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
+ 
+-if test -z "$onlylibs" ; then 
+-   for i in CCP4_SCR BINSORT_SCR; do
+-     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
+-     else
+-       eval echo "! No directory \$$i and can\'t create it."
+-       echo "  Check the value of $i."
+-       badvar=1
+-     fi
+-   done
+-
+-   for i in libdir bindir includedir; do
+-     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
+-     else
+-       eval echo "! No directory \$$i and can\'t create it."
+-       echo "  Check the argument of --$i."
+-       badvar=1
+-     fi
+-   done
+-
+-   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
+-     if test -d $i || mkdir $i; then :
+-     else
+-       eval echo "! No directory $i and can\'t create it."
+-       badvar=1
+-     fi
+-   done
+-else
+-   # Kludge to fool the "Makefile" target in the top-level CCP4
+-   # Makefile into not trying to remake src/Makefile.in
+-   for i in $srcdir/src $srcdir/lib/src ; do
+-     if test -d $i || mkdir $i; then
+-       if ! test -f $i/Makefile.in ; then
+-         echo
+-         echo "onlylibs: making dummy file $i/Makefile.in"
+-	 touch $i/Makefile.in
+-       fi
+-     fi
+-   done
+-fi
++#if test -z "$onlylibs" ; then 
++#   for i in CCP4_SCR BINSORT_SCR; do
++#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
++#     else
++#       eval echo "! No directory \$$i and can\'t create it."
++#       echo "  Check the value of $i."
++#       badvar=1
++#     fi
++#   done
++#
++#   for i in libdir bindir includedir; do
++#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
++#     else
++#       eval echo "! No directory \$$i and can\'t create it."
++#       echo "  Check the argument of --$i."
++#       badvar=1
++#     fi
++#   done
++#
++#   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
++#     if test -d $i || mkdir $i; then :
++#     else
++#       eval echo "! No directory $i and can\'t create it."
++#       badvar=1
++#     fi
++#   done
++#else
++#   # Kludge to fool the "Makefile" target in the top-level CCP4
++#   # Makefile into not trying to remake src/Makefile.in
++#   for i in $srcdir/src $srcdir/lib/src ; do
++#     if test -d $i || mkdir $i; then
++#       if ! test -f $i/Makefile.in ; then
++#         echo
++#         echo "onlylibs: making dummy file $i/Makefile.in"
++#	 touch $i/Makefile.in
++#       fi
++#     fi
++#   done
++#fi
+ 
+ ### sanity checks
+ 
diff --git a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch
new file mode 100644
index 000000000..6e3997647
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch
@@ -0,0 +1,22 @@
+--- lib/ccif/configure.in	2009-06-10 13:52:59.000000000 +0200
++++ lib/ccif/configure.in.new	2009-06-10 14:04:31.000000000 +0200
+@@ -363,7 +363,7 @@
+          fi
+          SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\
+                         --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\
+-                        $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
++                        $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
+          SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
+       fi
+    ;;
+--- lib/ccif/configure	2009-06-10 14:26:58.000000000 +0200
++++ lib/ccif/configure.new	2009-06-10 14:43:31.000000000 +0200
+@@ -1807,7 +1807,7 @@
+          SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\
+ 				$(SHARED_LIB_NAME) \\\
+                                --whole-archive $L \\\
+-                               -o $(SHARED_LIB_NAME)'
++                               -o $(SHARED_LIB_NAME) -lm'
+          SHARED_LIB_EXPORTS_CMD=''
+       fi
+    ;;
diff --git a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch b/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch
new file mode 100644
index 000000000..0780314f0
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch
@@ -0,0 +1,255 @@
+--- lib/src/Makefile.in	2009-03-02 17:53:15.000000000 +0100
++++ lib/src/Makefile.in.new	2009-03-02 17:52:09.000000000 +0100
+@@ -172,9 +172,8 @@
+ 
+ ##### Makefile targets ######
+ 
+-all:  fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
++all:  fsplit $(LMMDB) LMMDB_SO $(LC) LC_SO $(LF) LF_SO $(SCRIPT_MODULES)
+ # maybe create shared library
+-	$(SHARE_LIB)
+ 
+ $(LC) : $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS)
+ 	$(AR) $(LC) $?
+@@ -186,6 +185,27 @@
+ 	$(AR) $(LF) $(FINTERFACEOBJS)
+ 	$(RANLIB) $@
+ 
++LMMDB_SO : 
++	$(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o libmmdb.so.0.0.0 \
++	$(MMDBOBJS) && \
++	ln -sf libmmdb.so.0.0.0 libmmdb.so.0 && \
++	ln -sf libmmdb.so.0.0.0 libmmdb.so
++
++LC_SO : 
++	$(CC) $(COPTIM) -shared -Wl,-soname,libccp4c.so.0 -o libccp4c.so.0.0.0 \
++	$(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
++	ln -sf libccp4c.so.0.0.0 libccp4c.so.0 && \
++	ln -sf libccp4c.so.0.0.0 libccp4c.so
++
++LF_SO : 
++	$(FC) $(FOPTIM) -shared -Wl,-soname,libccp4f.so.0 -o libccp4f.so.0.0.0 \
++	parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
++	libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
++	harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
++	modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
++	ln -sf libccp4f.so.0.0.0 libccp4f.so.0 && \
++	ln -sf libccp4f.so.0.0.0 libccp4f.so
++
+#@@ -186,6 +185,27 @@
+# 	$(AR) $(LF) $(FINTERFACEOBJS)
+# 	$(RANLIB) $@
+# 
+#+LMMDB_SO : 
+#+	$(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o ../libmmdb.so.0.0.0 \
+#+	$(MMDBOBJS) && \
+#+	ln -sf libmmdb.so.0.0.0 ../libmmdb.so.0 && \
+#+	ln -sf libmmdb.so.0.0.0 ../libmmdb.so
+#+
+#+LC_SO : 
+#+	$(CC) $(COPTIM) -shared -Wl,-soname,libccp4_c.so.0 -o ../libccp4_c.so.0.0.0 \
+#+	$(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
+#+	ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so.0 && \
+#+	ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so
+#+
+#+LF_SO : 
+#+	$(FC) $(FOPTIM) -shared -Wl,-soname,libccp4_f.so.0 -o ../libccp4_f.so.0.0.0 \
+#+	parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
+#+	libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
+#+	harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
+#+	modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
+#+	ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so.0 && \
+#+	ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so
+#+
+ # cmtz library only
+ 
+ cmtz: $(LCMTZ)
+@@ -339,9 +356,7 @@
+ 	fi
+ 	cd parser.dir && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f parser.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ parser : parser.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -351,9 +366,7 @@
+ 	echo '      END' >> ccplib.dir/ccplib.$F
+ 	cd ccplib.dir && $(fsplit_dir)/fsplit $(srcdir)/ccplib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f ccplib.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ ccplib : ccplib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -364,9 +377,7 @@
+ 	@$(SETFLAGS) ; \
+ 	cd lgglib.dir && $(fsplit_dir)/fsplit $(srcdir)/lgglib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    eval $(FC) -c  $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f lgglib.dir/*.o
++	    eval $(FC) -c  $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done
+ lgglib : lgglib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -376,9 +387,7 @@
+ 	echo '      END' >> plot84lib.dir/plot84lib.$F
+ 	cd plot84lib.dir && $(fsplit_dir)/fsplit $(srcdir)/plot84lib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f plot84lib.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ plot84lib : plot84lib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -388,9 +397,7 @@
+ 	echo '      END' >> libhtml.dir/libhtml.$F
+ 	cd libhtml.dir && $(fsplit_dir)/fsplit $(srcdir)/libhtml.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f libhtml.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ libhtml : libhtml.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -400,9 +407,7 @@
+ 	echo '      END' >> pxxml.dir/pxxml.$F
+ 	cd pxxml.dir && $(fsplit_dir)/fsplit $(srcdir)/pxxml.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f pxxml.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ pxxml : pxxml.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -412,9 +417,7 @@
+ 	echo '      END' >> rwbrook.dir/rwbrook.$F
+ 	cd rwbrook.dir && $(fsplit_dir)/fsplit $(srcdir)/rwbrook.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f rwbrook.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ rwbrook : rwbrook.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -424,9 +427,7 @@
+ 	echo '      END' >> cciflib.dir/cciflib.$F
+ 	cd cciflib.dir && $(fsplit_dir)/fsplit $(srcdir)/cciflib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f cciflib.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done
+ cciflib : cciflib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -440,9 +441,7 @@
+ 	  && $(AR) ../$(LF) *.o ; else \
+ 	cd harvlib.dir && $(fsplit_dir)/fsplit $(srcdir)/harv_dummy.f >/dev/null && $(RMEMPTY) && \
+ 	for i in `pwd`/*.$F; do \
+-	  $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
+-	  && $(AR) ../$(LF) *.o ; fi
+-	rm -f harvlib.dir/*.o
++	  $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done; fi
+ harvlib : harvlib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -452,9 +451,7 @@
+ 	echo '      END' >> keyparse.dir/keyparse.$F
+ 	cd keyparse.dir && $(fsplit_dir)/fsplit $(srcdir)/keyparse.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f keyparse.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ keyparse : keyparse.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -464,9 +461,7 @@
+ 	echo '      END' >> dna_output.dir/dna_output.$F
+ 	cd dna_output.dir && $(fsplit_dir)/fsplit $(srcdir)/dna_output.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f dna_output.dir/*.o
++	    $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ dna_output : dna_output.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -474,10 +469,9 @@
+ #  for ipdisp. May be useful but could be moved. 
+ $(LF)(pack_c.o):   $(srcdir)/pack_c.c $(srcdir)/pack_c.h
+ 	$(CC) $(CFLAGS) $(SHARED_LIB_CFLAGS) -I$(srcdir) -c $(srcdir)/pack_c.c
+-	$(AR) $(LF) pack_c.o && rm pack_c.o
++	$(AR) $(LF) pack_c.o
+ $(LF)(pack_f.o):   $(srcdir)/pack_f.f
+-	$(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o \
+-          && rm pack_f.o
++	$(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o
+ pack:   $(LF)(pack_c.o) $(LF)(pack_f.o)
+ 	$(RANLIB) $(LF) 
+ 
+@@ -488,9 +482,7 @@
+ 	echo '      END' >> sorting_main.dir/sorting_main.$F
+ 	cd sorting_main.dir && $(fsplit_dir)/fsplit $(srcdir)/sorting_main.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f sorting_main.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ sorting_main : sorting_main.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -500,9 +492,7 @@
+ 	echo '      END' >> plotsubs.dir/plotsubs.$F
+ 	cd plotsubs.dir && $(fsplit_dir)/fsplit $(srcdir)/plotsubs.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f plotsubs.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ plotsubs : plotsubs.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -512,9 +502,7 @@
+ 	echo '      END' >> modlib.dir/modlib.$F
+ 	cd modlib.dir && $(fsplit_dir)/fsplit $(srcdir)/modlib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f modlib.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ modlib : modlib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -524,9 +512,7 @@
+ 	echo '      END' >> fftlib.dir/fftlib.$F
+ 	cd fftlib.dir && $(fsplit_dir)/fsplit $(srcdir)/fftlib.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done \
+-	  && $(AR) ../$(LF) *.o
+-	rm -f fftlib.dir/*.o
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done 
+ fftlib : fftlib.o
+ 	$(RANLIB) $(LF)
+ 
+@@ -541,9 +527,7 @@
+ 	echo '      END' >> unix.dir/unix.f
+ 	cd unix.dir && $(fsplit_dir)/fsplit ../unix.f >/dev/null && $(RMEMPTY) && \
+ 	  for i in `pwd`/*.$F; do \
+-	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
+-	  && $(AR) ../$(LF) *.o
+-	rm -f unix.dir/*.o 
++	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
+ unix : unix.o
+ 	$(RANLIB) $(LF)
+