NEVER set LD_LIBRARY_PATH in /etc/profile.d, 352962

Package-Manager: portage-2.2.0_alpha24/cvs/Linux x86_64
RepoMan-Options: --force

4 files changed, 14 insertions, 244 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index ce680a41ee95..5a295bd2819c 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 1.29 2011/01/17 08:01:36 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.30 2011/02/19 15:10:35 jlec Exp $
+
+*ccp4-libs-6.1.3-r8 (19 Feb 2011)
+
+  19 Feb 2011; Justin Lecher <jlec@gentoo.org> -ccp4-libs-6.1.3-r5.ebuild,
+  -ccp4-libs-6.1.3-r7.ebuild, +ccp4-libs-6.1.3-r8.ebuild:
+  NEVER set LD_LIBRARY_PATH in /etc/profile.d, 352962
 
   17 Jan 2011; Justin Lecher <jlec@gentoo.org> ccp4-libs-6.1.3-r7.ebuild:
   Remove IMOSFLM_VERSION from setup
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
index b9d1741632fe..d2ff7f6262a3 100644
--- a/sci-libs/ccp4-libs/Manifest
+++ b/sci-libs/ccp4-libs/Manifest
@@ -12,14 +12,13 @@ AUX 6.1.3-noinstall.patch 5188 RMD160 d3b22f11d7c27b37243b003f03615af377c8e632 S
 AUX 6.1.3-overflows.patch 904 RMD160 03d5f10e901734c6e21be3e68592711450df32cd SHA1 24a740658fae2f917061c2a032a43a60e75c5478 SHA256 e5c62922daf832b62e9ea1e14a2be0d54c88b035b78b5831eee07025dff9222a
 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-r5.ebuild 6721 RMD160 247393a4f9da5dab470d34c1330e1d57f1c3d511 SHA1 76ec1c47f549587c6f6d3559ef14de73a10c3394 SHA256 fc6f8fc3ac848137eaa94c8bf4210abc387ebec9fb2eddbaeaf688404bb18f01
-EBUILD ccp4-libs-6.1.3-r7.ebuild 10770 RMD160 c3eed9313b8a81e88ba1a0add703a3743ca6ab99 SHA1 314529237a1f7a4e7e7c62a154d6ce5617857af8 SHA256 4e6a98287b7372f8a45d8cb9f1573396375845261a30706d6bc1fdc1795c3cc8
-MISC ChangeLog 4406 RMD160 bac8e03c762a6e1ba9a0009be2397f20dee3a9c6 SHA1 4ec9765204f6c61860a51b33057c57a29be95fa7 SHA256 0d02af3d8bb46c16a03e8d0311d0685eb87eb5dea249153b26447f39ee27ba9d
+EBUILD ccp4-libs-6.1.3-r8.ebuild 10816 RMD160 f001019f12ffbbf1e4a8448504a8eac347e759de SHA1 0f8c8618f0f66dde8c86aa2d08cf696ec91bc18c SHA256 1f3f02adb2882f9b22344529df443f94c2a803dc3756914b6a713fc41d2bb237
+MISC ChangeLog 4629 RMD160 ed5c85e5e5b9fbfe95d3cfe330a1b33cea42e768 SHA1 8afe94fdc614695804d5452969fa65f4fae28c38 SHA256 815a14467d556d0db45b55ee6ce9c733eaa775d966560539f0d0b61dc11f65e4
 MISC metadata.xml 306 RMD160 57ba72f54388a666851bda87e52d313d618084e3 SHA1 7d2f57cb3f35eb6d4567b211e01251b5945d4eb2 SHA256 af351be5ead71b377b6fa2fa118fb9aee74129afdc19f736b41596d3033106aa
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.16 (GNU/Linux)
 
-iEYEARECAAYFAk0z92YACgkQgAnW8HDreRZuDwCeLOz+kVhAbtLeBAhyUvId1pnT
-Wa8AnRRywgVQpOFJStGJEG4J09VhQ8vR
-=Ghkd
+iEYEARECAAYFAk1f3XEACgkQgAnW8HDreRZm5wCg0WfNjvQQ6gEKYJO6b4AYKIos
+7A0AoKq0dNHp4pNRcvBP3x61Hfc1aiI3
+=Z/ea
 -----END PGP SIGNATURE-----
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
deleted file mode 100644
index 8c531307d5d1..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r5.ebuild
+++ /dev/null
@@ -1,236 +0,0 @@
-# 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-r5.ebuild,v 1.3 2011/01/15 11:57:01 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 - 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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	virtual/jpeg
-	app-shells/tcsh
-	!<sci-chemistry/ccp4-6.1.3
-	!<sci-chemistry/ccp4-apps-6.1.3-r6
-	sci-libs/cbflib
-	sci-libs/fftw:2.1
-	sci-libs/mmdb
-	sci-libs/monomer-db
-	virtual/lapack
-	virtual/blas"
-DEPEND="${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}
-
-	# 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}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r7.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r8.ebuild
index 28fcdffc73cc..35d6fb466f5f 100644
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r7.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-r7.ebuild,v 1.11 2011/01/17 08:01:36 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r8.ebuild,v 1.1 2011/02/19 15:10:35 jlec Exp $
 
 EAPI="3"
 
@@ -259,6 +259,7 @@ src_install() {
 		-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