ccp4-lins fix for glbic-2.10 (getline problem)

bug 270615

4 files changed, 220 insertions, 3 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index c1bf51d34..cbab1593a 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ccp4-libs-6.1.1-r4 (03 Jun 2009)
+
+  03 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +ccp4-libs-6.1.1-r4.ebuild:
+  glibc-2.10 getline fix
+  bug 270615
+
 *ccp4-libs-6.1.1-r3 (13 May 2009)
 
   13 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
index f332c09a8..b441d2d76 100644
--- a/sci-libs/ccp4-libs/Manifest
+++ b/sci-libs/ccp4-libs/Manifest
@@ -6,7 +6,8 @@ DIST 6.1.1-090511-updates.patch.bz2 8915 RMD160 58114b0ba6d225078044a8a6f9245aab
 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
 EBUILD ccp4-libs-6.1.1-r2.ebuild 5399 RMD160 8a755cfda81ea80d7da43456c8111a5462df492f SHA1 b424554967c59f6f716ac6ffa8013cfabef16edd SHA256 f46a9f6ef7d47b28c97f8d3ad00b3dc618db291ca88ccfd71c5cef9383cead5a
-EBUILD ccp4-libs-6.1.1-r3.ebuild 5659 RMD160 b777c3967bea5bde4e20111fc02034a6dbe735ef SHA1 7e0a6cc10679c581c25a7ae826ab0227e0796607 SHA256 57e03f4b06324eadd0b2933336bd2bd730f934e07f7ca99de239594e041804bd
+EBUILD ccp4-libs-6.1.1-r3.ebuild 5657 RMD160 2329b1d0d887c10e8802c251502c913d285c1dc3 SHA1 83e86921656e8153f25c9ebed074dffdc888fd49 SHA256 4c80100368aca56839101591cee5259d4defbed6251a7ec9c62395211233a2dc
+EBUILD ccp4-libs-6.1.1-r4.ebuild 5776 RMD160 3a36e4a2fff69e2a17028c39f8849a4cfd73c64e SHA1 7693f8aa4a3e6106876e68fcdf25fada3b2e61e5 SHA256 f541ab2ffa172978b11c91c11754be4c75bb63174e2c3a4a1990f7e8fa5ddd57
 EBUILD ccp4-libs-6.1.1.ebuild 5211 RMD160 6f3705f7ab0c48bbda073eb7dc1a283b3dcaa39a SHA1 8b09909daae034fc393b49b5fda7e06a783bcd14 SHA256 e9b4a3183a8f753ced59968b261bb655c87d13ade8c9964c71f1f2948c42067e
-MISC ChangeLog 1265 RMD160 4337d789a73960f5f20d5e1de282aa9a6ab6b9d8 SHA1 ef0b921a384ac91b55cab5784fe890ed9d8d788c SHA256 28af8f190d9fadaccf5ffd44b1a2c0e720514d5b58207353dd747194cd78ce95
+MISC ChangeLog 1426 RMD160 d0bcf8ff9dd22ee4e575c3fbbeb5660bad75eb0a SHA1 0b24bed44194ce88a590ad67ff25d2cec2447525 SHA256 f17caa9906b6b7884e5ffde403f75b80498bfb6071a46b2ff2f46969c2a87404
 MISC metadata.xml 309 RMD160 b9d7f0a63f8fb51e9b4e2d6b4f4028541df5400c SHA1 26ee4b64e0e4d52b1afe00957d53b0cc2956da00 SHA256 04f156de856eae11c0cf8af213f74a9852213844cdd5133aa01dbe60371d57e7
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r3.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r3.ebuild
index 8cf1fa79d..0a7461721 100644
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r3.ebuild
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r3.ebuild
@@ -30,7 +30,7 @@ HOMEPAGE="http://www.ccp4.ac.uk/"
 RESTRICT="mirror"
 SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz
 	${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz
-   http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
+	http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
 
 for i in $(seq $PATCH_TOT); do
 	NAME="PATCH${i}[1]"
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r4.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r4.ebuild
new file mode 100644
index 000000000..201228553
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r4.ebuild
@@ -0,0 +1,209 @@
+# 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/"
+RESTRICT="mirror"
+SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz
+	${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz
+	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/${!NAME}"
+done
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+RDEPEND="virtual/lapack
+	virtual/blas
+	=sci-libs/fftw-2*
+	app-shells/tcsh
+	!<sci-chemistry/ccp4-6.0.99
+	sci-libs/monomer-db"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${P/-libs}"
+
+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}/${p}"
+		popd >& /dev/null
+	done
+	einfo "Done."
+	echo
+
+	epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
+
+	einfo "Applying Gentoo patches ..."
+	# These two only needed when attempting to install outside build dir via
+	# --bindir and --libdir instead of straight copying after build
+
+	# it attempts to install some libraries during the build
+	#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
+	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
+	# without this patch when --libdir is set
+	# Rotgen still needs more patching to find it
+	#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
+
+	# it tries to create libdir, bindir etc on live system in configure
+	ccp_patch "${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
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	# glibc-2.10 getline fix
+	ls -l lib/src/fsplit.c
+	sed -e "s:getline:${PN/-libs}getline:g" -i lib/src/fsplit.c || die
+
+	gnuconfig_update
+}
+
+src_compile() {
+	# Build system is broken if we set LDFLAGS
+	unset LDFLAGS
+
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "${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}
+
+	# Fix linking
+	export SHARE_LIB="ld -shared -soname libmmdb.so --whole-archive -o libmmdb.so libmmdb.a ../libccif.a; \
+			  ld -shared -soname libccp4c.so --whole-archive -o libccp4c.so libccp4c.a ../libccif.a; \
+			  ld -shared -soname libccp4f.so --whole-archive -o libccp4f.so libccp4f.a libmmdb.a libccp4c.a ../libccif.a -lstdc++ $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		--onlylibs \
+		--with-shared-libs \
+		--with-fftw=/usr \
+		--with-warnings \
+		--disable-cctbx \
+		--disable-clipper \
+		--tmpdir="${TMPDIR}" \
+		${GENTOO_OSNAME} || die "econf failed"
+	emake -j1 onlylib || die "emake failed"
+}
+
+src_install() {
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup
+
+# Only needed when using --bindir and --libdir
+	# Needed to avoid errors. Originally tried to make lib and bin
+	# in configure script, now patched out by dont-make-dirs-in-configure.patch
+#	dodir /usr/include /usr/$(get_libdir) /usr/bin
+
+#	make install || die "install failed"
+	einstall || die "install failed"
+
+	# Libs
+	for file in "${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
+
+	# 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 mmdb; do
+		doins -r "${S}"/include/${i} || die
+	done
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}