Fix for changes in cbflib-0.9.2.2

(Portage version: 2.2.0_alpha80/cvs/Linux x86_64)

5 files changed, 366 insertions, 5 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index 4de4079bba34..cc06b8332777 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.43 2011/08/26 14:26:09 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.44 2011/12/14 12:20:17 jlec Exp $
+
+*ccp4-libs-6.1.3-r11 (14 Dec 2011)
+
+  14 Dec 2011; Justin Lecher <jlec@gentoo.org> +files/6.1.3-cbf.patch,
+  ccp4-libs-6.1.3-r8.ebuild, ccp4-libs-6.1.3-r10.ebuild,
+  +ccp4-libs-6.1.3-r11.ebuild:
+  Fix for changes in cbflib-0.9.2.2
 
   26 Aug 2011; Markos Chandras <hwoarang@gentoo.org>
   ccp4-libs-6.1.3-r10.ebuild:
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r10.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r10.ebuild
index 47ca1d014b6c..bd4b1a370bdf 100644
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r10.ebuild
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r10.ebuild
@@ -1,6 +1,6 @@
 # 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-r10.ebuild,v 1.7 2011/08/26 14:26:09 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r10.ebuild,v 1.8 2011/12/14 12:20:17 jlec Exp $
 
 EAPI=3
 
@@ -41,7 +41,7 @@ RDEPEND="
 	!<sci-chemistry/ccp4-apps-${PVR}
 	app-shells/tcsh
 	dev-lang/tcl
-	sci-libs/cbflib
+	<sci-libs/cbflib-0.9.2.2
 	sci-libs/fftw:2.1
 	sci-libs/mmdb
 	sci-libs/monomer-db
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild
new file mode 100644
index 000000000000..63528e377cf1
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild
@@ -0,0 +1,338 @@
+# 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-r11.ebuild,v 1.1 2011/12/14 12:20:17 jlec Exp $
+
+EAPI=3
+
+PYTHON_DEPEND="2"
+
+inherit autotools eutils fortran-2 gnuconfig multilib python toolchain-funcs
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+MY_P="${P/-libs}"
+
+PATCH_TOT="0"
+
+DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+SRC_URI="${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/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	!<sci-chemistry/ccp4-6.1.3
+	!<sci-chemistry/ccp4-apps-${PVR}
+	app-shells/tcsh
+	dev-lang/tcl
+	>=sci-libs/cbflib-0.9.2.2
+	sci-libs/fftw:2.1
+	sci-libs/mmdb
+	sci-libs/monomer-db
+	sci-libs/ssm
+	virtual/fortran
+	virtual/jpeg
+	virtual/lapack
+	virtual/blas"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+	fortran-2_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}"/${PV}-unbundle-libs-ng2.patch
+
+	# Fix missing DESTIDR
+	# not installing during build
+	ccp_patch "${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
+
+	# use pkg-config to detect BLAS/LAPACK
+	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
+
+	# proto type changing in version 0.9.2.2
+	ccp_patch "${FILESDIR}"/${PV}-cbf.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 src/rapper src/pisa; do
+		pushd ${i} > /dev/null
+			sed 's:-g::g' -i configure* || die
+			eautoreconf
+		popd > /dev/null
+	done
+
+	## unbundle libssm
+	sed '/libdir/s:ssm::g' -i Makefile.in
+	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete
+}
+
+src_configure() {
+	rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
+
+	# Build system is broken if we set LDFLAGS
+	userldflags="${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}
+
+	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 $(pkg-config --libs mmdb) $(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 \
+		--disable-ssm \
+		--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/ccp4-libs-6.1.3-r8.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r8.ebuild
index 7eaa55c4c5b9..f3bfaffa089c 100644
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r8.ebuild
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r8.ebuild
@@ -1,6 +1,6 @@
 # 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-r8.ebuild,v 1.5 2011/07/16 12:21:05 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r8.ebuild,v 1.6 2011/12/14 12:20:17 jlec Exp $
 
 EAPI=3
 
@@ -40,7 +40,7 @@ RDEPEND="
 	!sci-libs/ssm
 	app-shells/tcsh
 	dev-lang/tcl
-	sci-libs/cbflib
+	<sci-libs/cbflib-0.9.2.2
 	sci-libs/fftw:2.1
 	sci-libs/mmdb
 	sci-libs/monomer-db
diff --git a/sci-libs/ccp4-libs/files/6.1.3-cbf.patch b/sci-libs/ccp4-libs/files/6.1.3-cbf.patch
new file mode 100644
index 000000000000..6930fcad766a
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-cbf.patch
@@ -0,0 +1,16 @@
+ lib/DiffractionImage/DiffractionImageCBF.cpp |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
+index 69b32b0..3ffee26 100755
+--- a/lib/DiffractionImage/DiffractionImageCBF.cpp
++++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
+@@ -62,7 +62,7 @@ namespace DI
+ 			int* tmpimg;
+ 			tmpimg=new int[height*width];
+ 			test= cbf_decompress_byte_offset ((void *)tmpimg,sizeof(int),sign,
+-                               			nelements,&nread,0,32,sign,ccbbff,0,
++                               			nelements,&nread,0,0,32,sign,ccbbff,0,
+ 										byte_ord.c_str(),2,(size_t) width,
+ 										(size_t) height,1,(size_t) padding);
+ 			for(int i=0;i<height*width;i++)