Ubundled libjpeg and cbflib

Package-Manager: portage-2.2_rc62/cvs/Linux x86_64

3 files changed, 428 insertions, 1 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index a06e1842562f..77feb7b64e02 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/ccp4-libs
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.2 2010/02/11 08:01:47 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.3 2010/02/11 22:36:00 jlec Exp $
+
+*ccp4-libs-6.1.3-r1 (11 Feb 2010)
+
+  11 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/6.1.3-unbundle-libs.patch, +ccp4-libs-6.1.3-r1.ebuild:
+  Unbundle libjpeg and CBFlib
 
   11 Feb 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
   ccp4-libs-6.1.3.ebuild:
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild
new file mode 100644
index 000000000000..6840c283e254
--- /dev/null
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild
@@ -0,0 +1,218 @@
+# 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-r1.ebuild,v 1.1 2010/02/11 22:36:00 jlec Exp $
+
+EAPI="3"
+
+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/"
+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/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+	media-libs/jpeg:0
+	app-shells/tcsh
+	!<sci-chemistry/ccp4-6.1.3
+	sci-libs/cbflib
+	=sci-libs/fftw-2*
+	sci-libs/mmdb
+	sci-libs/monomer-db
+	virtual/lapack
+	virtual/blas"
+DEPEND="${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 ..."
+	# 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}"/${PV}-unbundle-libs.patch
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	gnuconfig_update
+}
+
+src_configure() {
+
+	rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
+
+	# Build system is broken if we set LDFLAGS
+	userldflags="${LDFLAGS}"
+	export SHARED_LIB_FLAGS="${LDFLAGS}"
+	unset LDFLAGS
+
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "${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${EPREFIX}/usr/bin~g" \
+		"${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=${CXXFLAGS}
+	# Default to -O2 if FFLAGS is unset
+	export FC=${FORTRANC}
+	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.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
+		${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -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}" \
+		${GENTOO_OSNAME} || die "econf failed"
+}
+
+src_compile() {
+	emake -j1 onlylib || die "emake failed"
+}
+
+src_install() {
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup
+
+	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
+
+	# Bins
+	dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
+	newbin bin/superpose superpose-ccp4 || die
+
+	# 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 "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
+	dodoc "${S}"/lib/data/*.doc
+	newdoc "${S}"/lib/data/README DATA-README
+
+	# Include files
+	insinto /usr/include
+	for i in ccp4; do
+		doins -r "${S}"/include/${i} || die
+	done
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch
new file mode 100644
index 000000000000..96978320163b
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch
@@ -0,0 +1,203 @@
+diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
+index 69b32b0..602e35f 100755
+--- a/lib/DiffractionImage/DiffractionImageCBF.cpp
++++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
+@@ -6,10 +6,10 @@
+ // images.
+ 
+ #include "DiffractionImage.h"
+-#include "cbf.h"
+-#include "cbf_simple.h" 
+-#include "cbf_string.h"
+-#include "cbf_byte_offset.h"
++#include <cbflib/cbf.h>
++#include <cbflib/cbf_simple.h>
++#include <cbflib/cbf_string.h>
++#include <cbflib/cbf_byte_offset.h>
+ 
+ 
+ using namespace std;
+diff --git a/lib/DiffractionImage/MAR/Makefile.in b/lib/DiffractionImage/MAR/Makefile.in
+index 4264696..00c4d8d 100755
+--- a/lib/DiffractionImage/MAR/Makefile.in
++++ b/lib/DiffractionImage/MAR/Makefile.in
+@@ -174,7 +174,7 @@ top_builddir = @top_builddir@
+ top_srcdir = @top_srcdir@
+ AUTOMAKE_OPTIONS = gnu
+ noinst_LTLIBRARIES = libmar.la
+-AM_CPPFLAGS = -I../CBFlib/src -I../CBFlib/include
++AM_CPPFLAGS = 
+ libmar_la_SOURCES = mar300_header.c \
+ 		    mar345_header.c \
+ 		    marcif.c \
+diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c
+index d3f4212..2c37108 100755
+--- a/lib/DiffractionImage/MAR/marcif.c
++++ b/lib/DiffractionImage/MAR/marcif.c
+@@ -31,8 +31,7 @@
+ #include "marcif_header.h"
+ #include "mar345_header.h"
+ 
+-#include <cbf.h>
+-#include <img.h>
++#include <cbflib/cbf.h>
+ 
+ #define printe(x) 	printf("%s: %s: %s\n",prg,f,x)
+ #undef cbf_failnez
+diff --git a/lib/DiffractionImage/Makefile.in b/lib/DiffractionImage/Makefile.in
+index 8197956..807cf25 100755
+--- a/lib/DiffractionImage/Makefile.in
++++ b/lib/DiffractionImage/Makefile.in
+@@ -106,23 +106,19 @@ PROGRAMS = $(bin_PROGRAMS)
+ am_automask_OBJECTS = automask.$(OBJEXT)
+ automask_OBJECTS = $(am_automask_OBJECTS)
+ automask_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
+-	./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
+-	./jpg/libjpeg.la
++	./MAR/libmar.la ./Rigaku/librigaku.la
+ am_diff2jpeg_OBJECTS = diff2jpeg.$(OBJEXT)
+ diff2jpeg_OBJECTS = $(am_diff2jpeg_OBJECTS)
+ diff2jpeg_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
+-	./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
+-	./jpg/libjpeg.la
++	./MAR/libmar.la ./Rigaku/librigaku.la
+ am_diffdump_OBJECTS = diffdump.$(OBJEXT)
+ diffdump_OBJECTS = $(am_diffdump_OBJECTS)
+ diffdump_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
+-	./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
+-	./jpg/libjpeg.la
++	./MAR/libmar.la ./Rigaku/librigaku.la
+ am_printpeaks_OBJECTS = printpeaks.$(OBJEXT)
+ printpeaks_OBJECTS = $(am_printpeaks_OBJECTS)
+ printpeaks_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
+-	./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
+-	./jpg/libjpeg.la
++	./MAR/libmar.la ./Rigaku/librigaku.la
+ DEFAULT_INCLUDES = -I.@am__isrc@
+ depcomp = $(SHELL) $(top_srcdir)/depcomp
+ am__depfiles_maybe = depfiles
+@@ -284,8 +280,8 @@ target_alias = @target_alias@
+ top_builddir = @top_builddir@
+ top_srcdir = @top_srcdir@
+ AUTOMAKE_OPTIONS = gnu
+-SUBDIRS = CBFlib Bruker MAR Rigaku jpg
+-AM_CPPFLAGS = -I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg
++SUBDIRS = Bruker MAR Rigaku
++AM_CPPFLAGS = -I./MAR
+ lib_LTLIBRARIES = libDiffImage.la $(am__append_1) $(am__append_2) \
+ 	$(am__append_3)
+ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \
+@@ -311,50 +307,50 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \
+ 							dps_peaksearch_cn.c 
+ 
+ libDiffImage_la_LDFLAGS = -static
+-libDiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
++libDiffractionImage_la_DEPENDENCIES = libDiffImage.la \
+                                      ./Bruker/libbruker.la ./MAR/libmar.la \
+-                                     ./Rigaku/librigaku.la ./jpg/libjpeg.la
++                                     ./Rigaku/librigaku.la
+ 
+ libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp
+ libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
+-                                 ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
+-				 				 ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
++                                 -lcbf ./Bruker/libbruker.la \
++				 				 ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \
+ 								 --no-whole-archive -rpath '$(libdir)'
+ 
+-lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
++lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \
+                                        ./Bruker/libbruker.la ./MAR/libmar.la \
+-                                       ./Rigaku/librigaku.la ./jpg/libjpeg.la
++                                       ./Rigaku/librigaku.la
+ 
+ lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp
+ lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
+-                                   ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
+-				   			       ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
++                                   -lcbf ./Bruker/libbruker.la \
++				   			       ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \
+ 								   --no-whole-archive -rpath '$(libdir)'
+ 
+-libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
++libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \
+                                        ./Bruker/libbruker.la ./MAR/libmar.la \
+-                                       ./Rigaku/librigaku.la ./jpg/libjpeg.la
++                                       ./Rigaku/librigaku.la
+ 
+ libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp
+ libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
+-                                   ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
+-				                   ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
++                                   -lcbf ./Bruker/libbruker.la \
++				                   ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \
+ 								   --no-whole-archive -rpath '$(libdir)'
+ 
+-automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
+-                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
++automask_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
++                  ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
+ 
+ automask_SOURCES = automask.cpp
+-diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
+-                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
++diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
++                  ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
+ 
+ diffdump_SOURCES = diffdump.cpp
+-printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
+-                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
++printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
++                  ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
+ 
+ printpeaks_SOURCES = printpeaks.cpp
+-diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
+-                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
++diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
++                  ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
+ 
+ diff2jpeg_SOURCES = diff2jpeg.cpp
+ all: all-recursive
+diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure
+index 3fb5784..fdf9683 100755
+--- a/lib/DiffractionImage/configure
++++ b/lib/DiffractionImage/configure
+@@ -21768,7 +21768,7 @@ _ACEOF
+ fi
+ 
+ 
+-ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile"
++ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile "
+ 
+ 
+ cat >confcache <<\_ACEOF
+@@ -22407,12 +22407,9 @@ do
+   case $ac_config_target in
+     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+-    "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;;
+-    "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;;
+     "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;;
+     "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;;
+     "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;;
+-    "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;;
+ 
+   *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
+ echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
+diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in
+index 7f54b4b..69b10e1 100755
+--- a/lib/DiffractionImage/configure.in
++++ b/lib/DiffractionImage/configure.in
+@@ -65,11 +65,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z)
+ AC_CHECK_LIB([m], [sqrt])
+ 
+ AC_CONFIG_FILES([Makefile
+-                 CBFlib/Makefile
+-                 CBFlib/src/Makefile
+                  MAR/Makefile
+ 		 Rigaku/Makefile
+-		 Bruker/Makefile
+-		 jpg/Makefile])
++		 Bruker/Makefile])
+                  
+ AC_OUTPUT