Install missing file like enviro.def

Package-Manager: portage-2.2.0_alpha10/cvs/Linux x86_64

3 files changed, 248 insertions, 5 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index 77a67c671c57..82be6b077eae 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-libs/ccp4-libs
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.17 2010/12/20 12:28:01 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.18 2010/12/31 12:24:48 jlec Exp $
+
+*ccp4-libs-6.1.3-r5 (31 Dec 2010)
+
+  31 Dec 2010; <justin@gentoo.org> +ccp4-libs-6.1.3-r5.ebuild:
+  Install missing file like enviro.def
 
   20 Dec 2010; Markos Chandras <hwoarang@gentoo.org> ccp4-libs-6.1.3-r4.ebuild:
   Stable on amd64 wrt bug #348872
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
index af8dca85824e..ead55206a40b 100644
--- a/sci-libs/ccp4-libs/Manifest
+++ b/sci-libs/ccp4-libs/Manifest
@@ -13,12 +13,13 @@ AUX 6.1.3-unbundle-libs.patch 9063 RMD160 326af0e6990134546fb2607dae707b94d45881
 DIST ccp4-6.1.3-core-src.tar.gz 242134076 RMD160 e9b7deb0766fb95d5e8946881f20e086f0896fe9 SHA1 ee5ada892694db5dc9b2d7d2330b4ac694f56580 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324
 EBUILD ccp4-libs-6.1.3-r3.ebuild 6445 RMD160 adc496b6388295d8dd876c8903f4b16590f89825 SHA1 4a1ed802b0605711bdc7f0d6992481e15c6e4e05 SHA256 954982b8d851e6de8fb2b6134b78ab3cac39dcfb941bce1bdfdb4a98c3dca0f2
 EBUILD ccp4-libs-6.1.3-r4.ebuild 6534 RMD160 fa285ee4a423854b6386c53bd1c46ec9516b2822 SHA1 5e02e7766d2ddcc9fa778fb63c1be28835f4815f SHA256 e025888a7f3ca3c0ebe972bc33aed85fa06f5c21b13a7d74f4bd3cba77f86981
-MISC ChangeLog 2844 RMD160 84a91480f651bd4035fb7108babb075ba31a5da6 SHA1 308ce3fdf6b8060ebb67c34c68bd3711bd0e6885 SHA256 3b984d81e20c7d5d7f726d792b610f0c9ef6cbf430ce56b9c35829f95322c6f1
+EBUILD ccp4-libs-6.1.3-r5.ebuild 6735 RMD160 12e822a411ced2144be98a3afe92b7ef0a8f7624 SHA1 8632a8646c91ac2c4d22e58aabf7d0661b183b88 SHA256 38fc85cfdcd45e0e7cf41b3c49d8a252db4014171d8b27608809c9e2a532ee87
+MISC ChangeLog 2978 RMD160 0bc88bed0046cbcbdcb5457678458011046d4b0a SHA1 79379f20af27d98995e6833dc29c6df4e2551019 SHA256 d5b9043a2a292d4c98718d4d923bc83bdb54fd329f35d35ae5e9c413b3ac8a18
 MISC metadata.xml 306 RMD160 57ba72f54388a666851bda87e52d313d618084e3 SHA1 7d2f57cb3f35eb6d4567b211e01251b5945d4eb2 SHA256 af351be5ead71b377b6fa2fa118fb9aee74129afdc19f736b41596d3033106aa
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-OV8An0p4zqKgVIC0HMl2x0tslDiWX8pm
-=T6Hg
+iEYEARECAAYFAk0dy5wACgkQgAnW8HDreRZM2ACfZHKx560TVtOqCilWi8MpUK0S
+ykkAoJT95ljZYdfMBEMbGpZf2IlS3y9Z
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diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r5.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r5.ebuild
new file mode 100644
index 000000000000..a48d4a6c5875
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r5.ebuild
@@ -0,0 +1,237 @@
+# Copyright 1999-2010 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-r5.ebuild,v 1.1 2010/12/31 12:24:48 jlec Exp $
+
+EAPI="3"
+
+inherit eutils gnuconfig multilib 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"
+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/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	virtual/jpeg
+	app-shells/tcsh
+	!<sci-chemistry/ccp4-6.1.3
+	!<sci-chemistry/ccp4-apps-6.1.3-r6
+	sci-libs/cbflib
+	=sci-libs/fftw-2*
+	sci-libs/mmdb
+	sci-libs/monomer-db
+	virtual/lapack
+	virtual/blas"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+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}"/${PV}-unbundle-libs.patch
+
+	# Fix missing DESTIDR
+	# not installing during build
+	ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
+	sed \
+		-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
+		-i configure || die
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	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' \
+		-i configure || die
+
+	gnuconfig_update
+}
+
+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~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
+		"${S}"/include/ccp4.setup*
+
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup
+
+	export CC=$(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=${FFLAGS:- -O2}
+#	export CCP4_SCR="${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../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 "${S}"/include/ccp4.setup
+
+	emake -j1 \
+		DESTDIR="${D}" \
+		includedir="${EPREFIX}"/usr/include \
+		library_includedir="${EPREFIX}"/usr/include \
+		install || 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
+
+	# 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
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}