Move ccp4-libs to sci-libs.

8 files changed, 410 insertions, 0 deletions

diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
new file mode 100644
index 0000000..4e71bed
--- /dev/null
+++ b/sci-libs/ccp4-libs/Manifest
@@ -0,0 +1,8 @@
+AUX 6.0.2-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 SHA1 209fa1bdf1e59b4055177e343b69e487d9183fb3 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61
+AUX 6.0.99e-clipper-mmdbold-ggc-4.3.patch 656 RMD160 6b302779b48217a14f5ac9110bc307db3a3b51eb SHA1 f5813d6769fa9dc11605425cdbda85691d3016bc SHA256 982eff0336a6dfaf4e280d51a59cf722fc063ca89d15ca0af46ce83727fb9a8a
+AUX 6.0.99e-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 36c9329c3768c08687ef062c9ab649d32833b422 SHA256 1b5997f17526a4fd60ffa9eccf4b765aadf3a78c9394657000e0454f364240ca
+AUX 6.0.99e-fix-setup-bash-incompatibility.patch 422 RMD160 e7e886ab030cf3324302c8fd0c866b48eeb34f8c SHA1 4e549abcd3ced1e6ecf9d3f2bddfed70425d61aa SHA256 109a0e806f9c0e1b8bf5e5f0c58be6f1dae06396b62ee4dae9f579ff7dcb5a01
+AUX pass-clipper-enablevals.patch 501 RMD160 23466922268a91570b0f64cf79809b988e32689b SHA1 c254d31fe88ed1716a53bd549cf7aee537ca5204 SHA256 d476c9f231fb6cdfb5e57004b393644a88016318cdeed9c33c32de25e0d91b79
+DIST ccp4-6.0.99e-core-src.tar.gz 202226972 RMD160 5f88c763c028acad02bb81e75c490184331bb01d SHA1 c3a610f0eabb452e355ba07be3387175583e4e64 SHA256 51484c9e9a60d1983f8c05edddb4bb5215e6f7cc7dd83d5546b0d16c38624a08
+EBUILD ccp4-libs-6.0.99e.ebuild 6827 RMD160 e29f257437241ada02f3623e57a51e0ff30900c0 SHA1 8cf97bb2cea3da06fd71cf9738500977ae5f8bf9 SHA256 449d05000a825573a42aa6f88d3b5eb75087fb731e22b5f319e5c7f60bb4fa56
+MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.0.99e.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.0.99e.ebuild
new file mode 100644
index 0000000..5a1bca4
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.0.99e.ebuild
@@ -0,0 +1,255 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.0.2-r1.ebuild,v 1.6 2008/06/03 02:11:18 mr_bones_ Exp $
+
+inherit fortran eutils gnuconfig toolchain-funcs
+
+FORTRAN="g77 gfortran ifc"
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+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}/source/${P/-libs}-core-src.tar.gz"
+SRC_URI="${SRC}/6.1/${P/-libs}-core-src.tar.gz"
+for i in $(seq $PATCH_TOT); do
+	NAME="PATCH${i}[1]"
+	SRC_URI="${SRC_URI}
+		${SRC}/${PV}/patches/${!NAME}"
+done
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+RDEPEND="virtual/lapack
+		virtual/blas
+		=sci-libs/fftw-2*
+		app-shells/tcsh"
+DEPEND="${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
+
+	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
+
+	# Don't use this when we aren't building clipper
+	# For some reason clipper check for $enableval even when --enable is passed
+	ccp_patch ${FILESDIR}/pass-clipper-enablevals.patch
+
+	# gerror_ gets defined twice on ppc if you're using gfortran/g95
+	ccp_patch ${FILESDIR}/6.0.2-ppc-double-define-gerror.patch
+
+	# csh syntax doesn't work in a bash script
+	ccp_patch ${FILESDIR}/${PV}-fix-setup-bash-incompatibility.patch
+
+	# gcc-4.3 fixes
+	ccp_patch ${FILESDIR}/${PV}-clipper-mmdbold-ggc-4.3.patch
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	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=${FFLAGS:- -O2}
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		--onlylibs \
+		--with-shared-libs \
+		--with-fftw=/usr \
+		--with-warnings \
+		--disable-cctbx \
+		--tmpdir="${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"
+
+	# Get rid of S instances
+	# Also the main clipper library is built as libclipper-core, not libclipper
+	sed -i \
+		-e "s:${S}:$usr:g" \
+		-e "s:lclipper :lclipper-core :g" \
+		${S}/bin/clipper-config
+
+	# 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
+
+	# Library symlinks
+	local LIBNAMES="libclipper-ccp4.so.0.0.0
+		libclipper-cif.so.0.0.0
+		libclipper-contrib.so.0.0.0
+		libclipper-core.so.0.0.0
+		libclipper-minimol.so.0.0.0
+		libclipper-mmdbold.so.0.0.0
+		libclipper-mmdb.so.0.0.0
+		libclipper-mtz.so.1.0.0
+		libclipper-phs.so.0.0.0
+		libssm.so.0.0.0"
+
+	for LIBNAME in ${LIBNAMES}; do
+		library_dosym ${LIBNAME}
+	done
+
+	# Data
+	insinto /usr/share/ccp4
+	doins -r ${S}/lib/data || die
+
+	# Include files
+	insinto /usr/include
+	for i in ccp4 mmdb; do
+		doins -r ${S}/include/${i} || die
+	done
+
+	# Fix wrongly installed HTML pages from clipper
+	dohtml "${D}"/usr/html/*
+	rm -rf "${D}"/usr/html
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}
+
+# Links libname.so, libname.so.major and libname.so.major.minor
+# to libname.so.major.minor.micro
+library_dosym() {
+	local LIBNAME LIBDIR SUFFIX CORE_LIBNAME LIB_MAJOR LIB_MINOR LIB_VERSIONS
+
+	LIBNAME=${1}
+	LIBDIR=${2:-/usr/$(get_libdir)}
+
+	# Tag / on the end of libdir if needed
+	if [[ ${LIBDIR:$((${#LIBDIR}-1)):1} != "/" ]]; then
+		LIBDIR="${LIBDIR}/"
+	fi
+
+	if [[ "${LIBNAME}" != *.so.* ]]; then
+		msg="library_dosym() requires a shared, versioned library as an argument"
+		eerror "$msg"
+		die "$msg"
+	fi
+
+	SUFFIX=${LIBNAME##*so.}
+	CORE_LIBNAME=${LIBNAME%.so.*}
+	CORE_LIBNAME="${CORE_LIBNAME}.so"
+	LIB_MAJOR=${SUFFIX%%.*}
+	LIB_MINOR=${SUFFIX#*.}
+	LIB_MINOR=${SUFFIX%%.*}
+	LIB_VERSIONS="${LIB_MAJOR} ${LIB_MAJOR}.${LIB_MINOR}"
+	for LIB_SUFFIX in .${LIB_MAJOR} ""; do
+		einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}"
+		dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX}
+	done
+}
diff --git a/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch b/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch
new file mode 100644
index 0000000..a77d949
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch
@@ -0,0 +1,11 @@
+--- ccp4-6.0.1.orig/lib/src/library_f.c	2006-06-12 07:06:22.000000000 -0700
++++ ccp4-6.0.1/lib/src/library_f.c	2006-06-12 07:21:56.000000000 -0700
+@@ -716,7 +716,7 @@
+ 
+ #endif /* end of apple xlf support */
+ 
+-#if ( defined (__linux__) && defined (_CALL_SYSV) )
++#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) )
+ /* linuxppc xlf support */
+ void gerror_ (str, Lstr)
+ char *str;
diff --git a/sci-libs/ccp4-libs/files/6.0.99e-clipper-mmdbold-ggc-4.3.patch b/sci-libs/ccp4-libs/files/6.0.99e-clipper-mmdbold-ggc-4.3.patch
new file mode 100644
index 0000000..6618660
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.0.99e-clipper-mmdbold-ggc-4.3.patch
@@ -0,0 +1,22 @@
+--- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp	2008-07-31 13:23:13.000000000 -0700
++++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp	2008-07-31 13:47:35.000000000 -0700
+@@ -43,7 +43,7 @@
+ 
+ #include <set>
+ #include <algorithm>
+-
++#include <string.h>
+ 
+ namespace clipper {
+ 
+--- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp.orig	2008-07-31 13:49:53.000000000 -0700
++++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp	2008-07-31 13:50:25.000000000 -0700
+@@ -40,7 +40,7 @@
+ //L  MA 02111-1307 USA
+ 
+ #include "clipper_mmdb_wrapper.h"
+-
++#include <string.h>
+ 
+ namespace clipper {
+ 
diff --git a/sci-libs/ccp4-libs/files/6.0.99e-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.0.99e-dont-make-dirs-in-configure.patch
new file mode 100644
index 0000000..583697c
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.0.99e-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 $i/Makefile.in
++#       fi
++#     fi
++#   done
++#fi
+ 
+ ### sanity checks
+ 
diff --git a/sci-libs/ccp4-libs/files/6.0.99e-fix-setup-bash-incompatibility.patch b/sci-libs/ccp4-libs/files/6.0.99e-fix-setup-bash-incompatibility.patch
new file mode 100644
index 0000000..d98f54c
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.0.99e-fix-setup-bash-incompatibility.patch
@@ -0,0 +1,11 @@
+--- ccp4-6.0.99e.orig/include/ccp4.setup-bash	2008-07-31 10:37:22.000000000 -0700
++++ ccp4-6.0.99e/include/ccp4.setup-bash	2008-07-31 12:47:14.000000000 -0700
+@@ -181,7 +181,7 @@
+ 
+ #Python path for the subprocess fixed module
+ 
+-if ($ccp4_first_in_path) then
++if [ $ccp4_first_in_path -eq 1 ]; then
+     setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
+ else
+     setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
diff --git a/sci-libs/ccp4-libs/files/pass-clipper-enablevals.patch b/sci-libs/ccp4-libs/files/pass-clipper-enablevals.patch
new file mode 100644
index 0000000..3e1a8b0
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/pass-clipper-enablevals.patch
@@ -0,0 +1,11 @@
+--- ccp4-5.99.5.orig/configure	2006-01-06 11:45:43.000000000 -0800
++++ ccp4-5.99.5/configure	2006-01-06 11:46:53.000000000 -0800
+@@ -3210,7 +3210,7 @@
+ #ccp4 setup
+   xopts="${xopts} --with-ccp4=${srcdir}"
+ #interface setup
+-  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol"
++  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr"
+   echo   
+   echo "********* CLIPPER CONFIGURATION ***********"
+   echo
diff --git a/sci-libs/ccp4-libs/metadata.xml b/sci-libs/ccp4-libs/metadata.xml
new file mode 100644
index 0000000..9ac9ffd
--- /dev/null
+++ b/sci-libs/ccp4-libs/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-chemistry</herd>
+</pkgmetadata>