Bump.

Package-Manager: portage-2.1.2_rc2

diff --git a/sci-chemistry/ccp4/ChangeLog b/sci-chemistry/ccp4/ChangeLog
index 00d667734a44736567929f8cc7faecde70ad252f..114f3215df60ad0ecc4b26d81d6d9d3ac83e2637 100644 (file)
--- a/sci-chemistry/ccp4/ChangeLog
+++ b/sci-chemistry/ccp4/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/ccp4
 # Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ChangeLog,v 1.6 2006/09/26 08:01:27 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ChangeLog,v 1.7 2006/11/24 10:45:41 dberkholz Exp $
+
+*ccp4-6.0.2 (24 Nov 2006)
+
+  24 Nov 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/6.0.2-dont-make-dirs-in-configure.patch,
+  +files/6.0.2-ppc-double-define-gerror.patch, +ccp4-6.0.2.ebuild:
+  Bump.
 
   26 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; ccp4-6.0.1-r1.ebuild:
   Stable on x86/ppc.

diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest
index fc81d7a946874736844f89a0d0cb6a774bb658d6..e8832515b1641f67a56afde282dd3d88408022f2 100644 (file)
--- a/sci-chemistry/ccp4/Manifest
+++ b/sci-chemistry/ccp4/Manifest
@@ -6,6 +6,14 @@ AUX 6.0.1-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0
 MD5 5a2ad632f539bc7981b55b6f52b6a227 files/6.0.1-ppc-double-define-gerror.patch 424
 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 files/6.0.1-ppc-double-define-gerror.patch 424
 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61 files/6.0.1-ppc-double-define-gerror.patch 424
+AUX 6.0.2-dont-make-dirs-in-configure.patch 2790 RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 SHA1 f8989cb867c92def86ccd88b4d67f38578d5d80b SHA256 2dbf78513ef94d88e446042e969644ad8a8462a22e80105e7481af93003a18bf
+MD5 3dc230e3cc15f5cd2a19968e8f07a9f2 files/6.0.2-dont-make-dirs-in-configure.patch 2790
+RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 files/6.0.2-dont-make-dirs-in-configure.patch 2790
+SHA256 2dbf78513ef94d88e446042e969644ad8a8462a22e80105e7481af93003a18bf files/6.0.2-dont-make-dirs-in-configure.patch 2790
+AUX 6.0.2-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 SHA1 209fa1bdf1e59b4055177e343b69e487d9183fb3 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61
+MD5 5a2ad632f539bc7981b55b6f52b6a227 files/6.0.2-ppc-double-define-gerror.patch 424
+RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 files/6.0.2-ppc-double-define-gerror.patch 424
+SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61 files/6.0.2-ppc-double-define-gerror.patch 424
 AUX ccp4i-default-to-firefox.patch 717 RMD160 626050c2ca8386e369900225f74f97fb22c3a91e SHA1 dc255e30033d1dbc422dbacd2c1814c13a003bc3 SHA256 40bc277d9353f13b490291fe0ba10c1180adc80a660afa5cf8f7c9449af909ae
 MD5 b7c4c90e38ef49651876128a209b4546 files/ccp4i-default-to-firefox.patch 717
 RMD160 626050c2ca8386e369900225f74f97fb22c3a91e files/ccp4i-default-to-firefox.patch 717
@@ -50,6 +58,7 @@ DIST act.f-6July2006.diff 16544 RMD160 24f48e95ec3363a2409da122bd0eb7ef5a91da36
 DIST anisoanl.f-r1.22-r1.24.diff 9452 RMD160 02f9561362892cbbeed24592b5ed4e3eb51ace2c SHA1 76691ac9097a4132f3618e13d41d913d92e45b9a SHA256 1308ef91c63efd1c11287f68f386a62678d1ab48ddfe6e94cefdef1c92173940
 DIST cad.f-r1.70-r1.72.diff 12196 RMD160 a18c339223c8a6a66fda4cb210f2e533fea0d240 SHA1 30da509c9b51506541b0b49adbf7836c8fc5f7d4 SHA256 ba10591643f93fb310d451aacce286d8ec9386f2e781d631f794076d1021539f
 DIST ccp4-6.0.1-core-src.tar.gz 59311291 RMD160 0f514fe30f22a4f6eb2e05c8bab567d2132e8fae SHA1 e8f5fb325a13375793f7610160337090af8fb9b5 SHA256 26a5704d707c3bc2fbe4c1d0804abccc1c50255005d26a8ec3a03fcba63335f2
+DIST ccp4-6.0.2-core-src.tar.gz 62286123 RMD160 159c71c5079422d6e540e4678fb8e4f9f83fc99d SHA1 279da65beb9c2e64a80abdeb693a78879a062cf0 SHA256 b8716198b4d5c1ad3aea190180a5c56e0e80eda0386e5c99542d169da6960875
 DIST chainsaw.cpp-11May2006.diff 4720 RMD160 62c3b3a3da0d36aa8f0c67a55c068508858eeb17 SHA1 f6a4e0cd22438a8855796e82b5492bd8870aa49c SHA256 de2d2ccd365f2992e1ba9a385f1a2fcd9e52da5ff96bcbc4fa7b4404cf0bac6e
 DIST contact.f-12June2006.diff 43051 RMD160 577b454ed229be8c9b79e8c4622c870d589e2cca SHA1 aff0071b1130a3cc62b419fed5909f94a87ff9e1 SHA256 1336ea01da83aad21669b82cd3895f724db6db8d17d78acfec53154ea7ce690e
 DIST molrep.f-r1.28-r1.28.2.1.diff 755 RMD160 96a37ea54606583647ff9cdc9da728ce05d30849 SHA1 7fa0302e9e4309a86aad3bebde5359af740cecd8 SHA256 0bb22cb2f8e1486ec5cc6037427e9ec66189684d74b5939757b4ebe771a61084
@@ -67,10 +76,14 @@ EBUILD ccp4-6.0.1.ebuild 13729 RMD160 5fe2a8f1d42a810e8fda14c61e970f9146ab0b96 S
 MD5 48bda08719da61345f9297bdecd1b975 ccp4-6.0.1.ebuild 13729
 RMD160 5fe2a8f1d42a810e8fda14c61e970f9146ab0b96 ccp4-6.0.1.ebuild 13729
 SHA256 d3d7ea08c1260eff42b49ead37d935bf3c9e38eac6e8eeb4fa86b3962ed25c7c ccp4-6.0.1.ebuild 13729
-MISC ChangeLog 2008 RMD160 e54d0d0031c60c95f7d881aee9a993a5ba1ed2fd SHA1 00e48e0273b9cead7dfdad20be1682d93397cc71 SHA256 fc2cc2839aa5e770a96f7fa857a8f215685e8644c024cc5b94e09c33e50737e8
-MD5 5ee9b4c15a1a288d5f21d8a9bb8a50a7 ChangeLog 2008
-RMD160 e54d0d0031c60c95f7d881aee9a993a5ba1ed2fd ChangeLog 2008
-SHA256 fc2cc2839aa5e770a96f7fa857a8f215685e8644c024cc5b94e09c33e50737e8 ChangeLog 2008
+EBUILD ccp4-6.0.2.ebuild 13483 RMD160 20043e32b6a1aae3e9431c2c5f793816ee754b7e SHA1 bdfadd46b8b9e75e3758a17d98a077b69035e167 SHA256 0f4bc1201162b9dce21254e2f9497bbc391dd3ad7bba30fd5cec8fd9376e587b
+MD5 26accaf55746435d81fb5c55d1f41114 ccp4-6.0.2.ebuild 13483
+RMD160 20043e32b6a1aae3e9431c2c5f793816ee754b7e ccp4-6.0.2.ebuild 13483
+SHA256 0f4bc1201162b9dce21254e2f9497bbc391dd3ad7bba30fd5cec8fd9376e587b ccp4-6.0.2.ebuild 13483
+MISC ChangeLog 2216 RMD160 cbdef48f6f45064fa21a7a1e57b580e3899dc108 SHA1 d4fb0a46ab1a6ef736be031530329fcbae78d583 SHA256 3afb703e3805ab9c3830fa4d468fda79c16094311602fa859e2ee089580b3410
+MD5 2ebc390cdd05eabb3257b6a7b77d2309 ChangeLog 2216
+RMD160 cbdef48f6f45064fa21a7a1e57b580e3899dc108 ChangeLog 2216
+SHA256 3afb703e3805ab9c3830fa4d468fda79c16094311602fa859e2ee089580b3410 ChangeLog 2216
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
@@ -81,3 +94,6 @@ SHA256 52ebe8c93194a9140171ac2e0d80b4750913b3e97ac1ee0f37c34ad9137deda8 files/di
 MD5 42c7b9d83453a9015d474ef4eaea76c1 files/digest-ccp4-6.0.1-r1 3286
 RMD160 9c65d5658b463f2aa751cb59c63d954c0b69568a files/digest-ccp4-6.0.1-r1 3286
 SHA256 3ccb5d939d1f0386093758fe8c5cfbb54be329869df7a77b85c0653d613f0a86 files/digest-ccp4-6.0.1-r1 3286
+MD5 4197e0ed0288c715e184aa7df8a4dbd6 files/digest-ccp4-6.0.2 265
+RMD160 b7b82a63b44e956b19cd49241a49565cac594d25 files/digest-ccp4-6.0.2 265
+SHA256 a9d7f019b604fd193ac9797e76d5c3058771a16866134bdbe9b94ca137405946 files/digest-ccp4-6.0.2 265

diff --git a/sci-chemistry/ccp4/ccp4-6.0.2.ebuild b/sci-chemistry/ccp4/ccp4-6.0.2.ebuild
new file mode 100644 (file)
index 0000000..092ff62
--- /dev/null
+++ b/sci-chemistry/ccp4/ccp4-6.0.2.ebuild
@@ -0,0 +1,423 @@
+# Copyright 1999-2006 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.ebuild,v 1.1 2006/11/24 10:45:41 dberkholz Exp $
+
+inherit fortran eutils gnuconfig toolchain-funcs
+
+FORTRAN="g77 gfortran ifc"
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+PATCH_TOT="0"
+#PATCH1=( src/mmdb_app_
+#      chainsaw.cpp-11May2006.diff )
+#PATCH2=( src
+#      anisoanl.f-r1.22-r1.24.diff )
+
+DESCRIPTION="Protein X-ray crystallography toolkit"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+RESTRICT="mirror stricter"
+SRC_URI="${SRC}/${PV}/source/${P}-core-src.tar.gz"
+for i in $(seq $PATCH_TOT); do
+       NAME="PATCH${i}[1]"
+       SRC_URI="${SRC_URI}
+               ${SRC}/${PV}/patches/${!NAME}"
+done
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~ppc ~x86"
+IUSE="X"
+# app-office/sc overlaps sc binary and man page
+# We can't rename ours since the automated ccp4i interface expects it there,
+# as do many scripts. app-office/sc can't rename its because that's the name
+# of the package.
+RDEPEND="X? (
+                               x11-libs/libX11
+                               x11-libs/libXt
+                               x11-libs/libXaw
+               )
+               >=dev-lang/tcl-8.3
+               >=dev-lang/tk-8.3
+               >=dev-tcltk/blt-2.4
+               virtual/lapack
+               virtual/blas
+               =sci-libs/fftw-2*
+               sci-chemistry/pdb-extract
+               sci-chemistry/rasmol
+               sci-libs/mccp4
+               || ( app-shells/tcsh app-shells/csh )
+               !app-office/sc"
+# >=sys-apps/portage-2.1.1_pre1 for RESTRICT=stricter
+# Otherwise portage dies instead of fixing RPATHs
+DEPEND="${RDEPEND}
+               X? (
+                               x11-misc/imake
+                               x11-proto/inputproto
+                               x11-proto/xextproto
+               )
+               >=sys-apps/portage-2.1.1_pre1"
+
+S="${WORKDIR}/${PN}-${PV}"
+
+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
+
+       # We already have sci-chemistry/rasmol
+       ccp_patch ${FILESDIR}/dont-build-rasmol.patch
+
+       # We already have sci-chemistry/pdb-extract
+# Use configure option instead
+#      ccp_patch ${FILESDIR}/dont-build-pdb-extract.patch
+
+       ccp_patch ${FILESDIR}/create-mosflm-bindir.patch
+       ccp_patch ${FILESDIR}/make-mosflm-libdir.patch
+       ccp_patch ${FILESDIR}/make-mosflm-index-libdir.patch
+       ccp_patch ${FILESDIR}/make-mosflm-cbf-libdir.patch
+       ccp_patch ${FILESDIR}/make-ipmosflm-dir.patch
+
+# Don't use these when we aren't building phaser
+#      ccp_patch ${FILESDIR}/make-phaser-bindir.patch
+#      ccp_patch ${FILESDIR}/no-phaser-ld-assume-kernel.patch
+#      # scons config.py tries to chmod python on live system
+#      ccp_patch ${FILESDIR}/dont-chmod-python-binary.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
+       ccp_patch ${FILESDIR}/clipper-find-mccp4-includes.patch
+
+       # Default to firefox browser, not 'netscape'
+       ccp_patch ${FILESDIR}/ccp4i-default-to-firefox.patch
+
+       # Also use -lpthread when linking blas and lapack
+       # We may need more fixing to use libcblas for the C files
+       ccp_patch ${FILESDIR}/check-blas-lapack-pthread.patch
+
+       # gerror_ gets defined twice on ppc if you're using gfortran/g95
+       ccp_patch ${FILESDIR}/${PV}-ppc-double-define-gerror.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 \
+               $(use_enable X x) \
+               --with-shared-libs \
+               --with-fftw=/usr \
+               --with-warnings \
+               --disable-pdb_extract \
+               --disable-cctbx \
+               --disable-phaser \
+               --tmpdir="${TMPDIR}" \
+               ${GENTOO_OSNAME} || die "econf failed"
+       emake -j1 || 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"
+
+       # Fix env
+       sed -i \
+               -e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
+               -e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
+               -e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
+               -e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
+               -e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
+               -e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \
+               -e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \
+               -e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
+               ${S}/include/ccp4.setup*
+
+       # Get rid of S instances
+       # Also the main clipper library is built as libclipper-core, not libclipper
+       sed -i \
+               -e "s:${S}:${ROOT}usr:g" \
+               -e "s:lclipper :lclipper-core :g" \
+               ${S}/bin/clipper-config
+#      sed -i \
+#              -e "s:${S}:${ROOT}usr:g" \
+#              ${S}/$(get_libdir)/cctbx/cctbx_build/setpaths*
+
+       # Bins
+       EXEDESTTREE="/usr/bin" doexe ${S}/bin/*
+
+       # Libs
+       for file in ${S}/lib/*; do
+               if [[ -d ${file} ]]; then
+                       continue
+               elif [[ -x ${file} ]]; then
+                       dolib.so ${file}
+               else
+                       INSDESTTREE="/usr/$(get_libdir)" doins ${file}
+               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
+               libjwc_c.so.0.1.1
+               libjwc_f.so.0.1.1
+               libssm.so.0.0.0
+               libxdl_viewextra.so.0.0.0
+               libxdl_view.so.2.0.0"
+
+       for LIBNAME in ${LIBNAMES}; do
+               library_dosym ${LIBNAME}
+       done
+
+#      dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so
+#      dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0
+#      dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0.0
+#
+#      dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so
+#      dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0
+#      dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0.0
+#
+#      dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so
+#      dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0
+#      dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0.0
+#
+#      dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so
+#      dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0
+#      dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0.0
+#
+#      dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so
+#      dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0
+#      dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0.0
+#
+#      dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so
+#      dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0
+#      dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0.0
+#
+#      dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so
+#      dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0
+#      dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0.0
+#
+#      dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so
+#      dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1
+#      dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1.0
+#
+#      dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so
+#      dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0
+#      dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0.0
+#
+#      dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so
+#      dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0
+#      dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0.1
+#
+#      dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so
+#      dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0
+#      dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0.1
+#
+#      dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so
+#      dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0
+#      dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0.0
+#
+#      dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so
+#      dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0
+#      dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0.0
+#
+#      dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so
+#      dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2
+#      dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2.0
+
+       # Environment files, setup scripts, etc.
+       INSDESTTREE="/usr/share/ccp4/include" doins ${S}/include/*
+
+       # CCP4Interface - GUI
+       INSDESTTREE="/usr/$(get_libdir)/ccp4" doins -r ${S}/ccp4i
+       EXEDESTTREE="/usr/$(get_libdir)/ccp4/ccp4i/bin" doexe ${S}/ccp4i/bin/*
+
+       # Data
+       INSDESTTREE="/usr/share/ccp4" doins -r ${S}/lib/data
+
+       # Include files
+       for i in ccp4 clipper mmdb ssm; do
+               INSDESTTREE="/usr/include" doins -r ${S}/include/${i}
+       done
+
+       # Install docs and examples
+
+       doman ${S}/man/cat1/*
+
+       mv ${S}/manual/README ${S}/manual/README-manual
+       dodoc ${S}/manual/*
+
+       dodoc ${S}/README ${S}/CHANGES
+
+       dodoc ${S}/doc/*
+       rm ${D}/usr/share/doc/${PF}/GNUmakefile.gz
+       rm ${D}/usr/share/doc/${PF}/COPYING.gz
+
+       dohtml -r ${S}/html/*
+       dodoc ${S}/examples/README
+
+       # Fix wrongly installed HTML pages from clipper
+       dohtml "${D}"/usr/html/*
+       rm -rf "${D}"/usr/html
+
+       for i in data rnase toxd; do
+               DOCDESTTREE="examples/${i}" dodoc ${S}/examples/${i}/*
+       done
+
+       DOCDESTTREE="examples/tutorial" dohtml -r ${S}/examples/tutorial/html
+       DOCDESTTREE="examples/tutorial" dohtml examples/tutorial/tut.css
+       for i in data results; do
+               DOCDESTTREE="examples/tutorial/${i}" dodoc ${S}/examples/tutorial/${i}/*
+       done
+
+       for i in non-runnable runnable; do
+               DOCDESTTREE="examples/unix/${i}" dodoc ${S}/examples/unix/${i}
+       done
+
+       # Needed for ccp4i docs to work
+       dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples
+       dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
+
+       # Fix overlaps with other packages
+       rm ${D}/usr/share/man/man1/rasmol.1.gz
+}
+
+pkg_postinst() {
+       einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
+       einfo "in /usr/share/ccp4/include/ccp4.setup* to modify this."
+
+       ewarn "Set your .bashrc or other shell login file to source"
+       ewarn "one of the ccp4.setup* files in ${ROOT}usr/share/ccp4/include."
+       ewarn "CCP4 will not work without this."
+}
+
+# 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 .${LIB_MAJOR} .${LIB_MAJOR}.${LIB_MINOR} ""; do
+               einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}"
+               dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX}
+       done
+}

diff --git a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch
new file mode 100644 (file)
index 0000000..1420419
--- /dev/null
+++ b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch
@@ -0,0 +1,87 @@
+--- ccp4-6.0.1.orig/configure  2006-06-10 17:30:02.000000000 -0700
++++ ccp4-6.0.1/configure       2006-06-10 17:45:43.000000000 -0700
+@@ -623,45 +623,45 @@
+ #     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 $i."
+-       badvar=1
+-     fi
+-   done
+-
+-   for i in libdir bindir; do
+-     if ( eval test -d \$$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 ./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 $i."
++#       badvar=1
++#     fi
++#   done
++#
++#   for i in libdir bindir; do
++#     if ( eval test -d \$$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 ./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-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch
new file mode 100644 (file)
index 0000000..a77d949
--- /dev/null
+++ b/sci-chemistry/ccp4/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-chemistry/ccp4/files/digest-ccp4-6.0.2 b/sci-chemistry/ccp4/files/digest-ccp4-6.0.2
new file mode 100644 (file)
index 0000000..2f4e81e
--- /dev/null
+++ b/sci-chemistry/ccp4/files/digest-ccp4-6.0.2
@@ -0,0 +1,3 @@
+MD5 a47ae8b8e6fa76eef7f17baa85e8dc16 ccp4-6.0.2-core-src.tar.gz 62286123
+RMD160 159c71c5079422d6e540e4678fb8e4f9f83fc99d ccp4-6.0.2-core-src.tar.gz 62286123
+SHA256 b8716198b4d5c1ad3aea190180a5c56e0e80eda0386e5c99542d169da6960875 ccp4-6.0.2-core-src.tar.gz 62286123