mgorny 15/01/18 19:04:16 Modified: ChangeLog Added: ccp4-apps-6.1.3-r13.ebuild Log: Convert to python-single-r1. (Portage version: 2.2.15/cvs/Linux x86_64, signed Manifest commit with key EFB4464E!)
Revision Changes Path 1.43 sci-chemistry/ccp4-apps/ChangeLog file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog?rev=1.43&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog?rev=1.43&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog?r1=1.42&r2=1.43 Index: ChangeLog =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v retrieving revision 1.42 retrieving revision 1.43 diff -u -r1.42 -r1.43 --- ChangeLog 27 Oct 2014 14:25:40 -0000 1.42 +++ ChangeLog 18 Jan 2015 19:04:16 -0000 1.43 @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/ccp4-apps -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.42 2014/10/27 14:25:40 jlec Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.43 2015/01/18 19:04:16 mgorny Exp $ + +*ccp4-apps-6.1.3-r13 (18 Jan 2015) + + 18 Jan 2015; Michał Górny <mgo...@gentoo.org> +ccp4-apps-6.1.3-r13.ebuild: + Convert to python-single-r1. 27 Oct 2014; Justin Lecher <j...@gentoo.org> ccp4-apps-6.1.3-r11.ebuild, ccp4-apps-6.1.3-r12.ebuild: @@ -206,4 +211,3 @@ +files/6.1.3-rename-rapper.patch, +files/6.1.3-rename-truncate.patch, +files/6.1.3-setup.patch, +ccp4-apps-6.1.3.ebuild, +metadata.xml: Splitted apps from ccp4 - 1.1 sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild?rev=1.1&content-type=text/plain Index: ccp4-apps-6.1.3-r13.ebuild =================================================================== # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild,v 1.1 2015/01/18 19:04:16 mgorny Exp $ EAPI=5 PYTHON_COMPAT=( python2_7 ) inherit autotools eutils fortran-2 flag-o-matic gnuconfig python-single-r1 toolchain-funcs MY_P="${PN/-apps}-${PV}" #UPDATE="04_03_09" #PATCHDATE="090511" PATCH_TOT="0" DESCRIPTION="Protein X-ray crystallography toolkit" HOMEPAGE="http://www.ccp4.ac.uk/"; SRC="ftp://ftp.ccp4.ac.uk/ccp4"; SRC_URI=" ${SRC}/${PV}/${MY_P}-core-src.tar.gz http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"; # 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/${!NAME}" done LICENSE="ccp4" SLOT="0" KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" IUSE="examples X" X11DEPS=" x11-libs/libX11 x11-libs/libXaw x11-libs/libXt x11-libs/libxdl_view" TKDEPS=" >=dev-lang/tk-8.3 >=dev-tcltk/blt-2.4 dev-tcltk/iwidgets dev-tcltk/itcl dev-tcltk/itk >=dev-tcltk/tdom-0.8 dev-tcltk/tktreectrl" SCILIBS=" ~sci-libs/ccp4-libs-${PV} >=sci-libs/ccp4-libs-${PV}-r7 sci-libs/clipper sci-libs/fftw:2.1 sci-libs/mmdb:0 sci-libs/ssm virtual/blas virtual/lapack" SCIAPPS=" sci-chemistry/pdb-extract sci-chemistry/pymol sci-chemistry/rasmol >=sci-chemistry/oasis-4.0-r1" RDEPEND=" ${TKDEPS} ${SCILIBS} app-shells/tcsh dev-python/pyxml dev-libs/libxml2:2 dev-libs/libjwc_c dev-libs/libjwc_f dev-libs/boehm-gc !app-office/sc !<sci-chemistry/ccp4-6.1.3 X? ( ${X11DEPS} )" DEPEND="${RDEPEND} X? ( x11-misc/imake x11-proto/inputproto x11-proto/xextproto )" PDEPEND="${SCIAPPS}" RESTRICT="mirror" S="${WORKDIR}/${MY_P}" pkg_setup() { fortran-2_pkg_setup python-single-r1_pkg_setup } src_prepare() { tc-export PKG_CONFIG 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 # We already have sci-chemistry/rasmol # Also remember to create the bindir. ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch # libraries come from sci-libs/ccp4-libs ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch # We have seperate ebuilds for those for bin in molref xia scala imosflm balbes; do ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch done # don't configure what is not build ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch # Set python paths correctly ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch # Set python paths correctly ccp_patch "${FILESDIR}"/${PV}-pisa.patch # Set python paths correctly ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch # Fix upstreams code ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch # Not renaming, but unbundling libs ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch # Use pkg-config to detect BLAS/LAPCK ccp_patch "${FILESDIR}"/${PV}-lapack.patch # unbundle libs ccp_patch "${FILESDIR}"/${PV}-unbundle.patch # tcl-8.6 ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch # Update things for oasis 4 usage epatch "${WORKDIR}"/${PV}-oasis4.0.patch sed 's: oasis : :g' -i src/Makefile.in || die einfo "Done." # done applying Gentoo patches echo find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete sed \ -e "s:/usr:${EPREFIX}/usr:g" \ -e 's:-Wl,-rpath,$CLIB::g' \ -e 's: -rpath $CLIB::g' \ -e 's: -I${srcdir}/include/cpp_c_headers::g' \ -e 's:sleep 1:sleep .2:g' \ -e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \ -e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \ -e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \ -e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \ -i configure || die sed \ -e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \ -i src/Makefile* || die find "${S}" -name "Makefile.*" \ -exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \; # Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die # Rapper bundles libxml2 and boehm-gc. Don't build, use or install those. pushd src/rapper 2>/dev/null eautoreconf popd 2>/dev/null gnuconfig_update python_fix_shebang -f . } src_configure() { # Build system is broken if we set LDFLAGS export GENTOOLDFLAGS="${LDFLAGS}" unset LDFLAGS # These are broken with ./src/procheck/ps.f filter-flags "-floop-*" # GENTOO_OSNAME can be one of: # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd # linux_compaq_compilers linux_intel_compilers generic Darwin # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers if [[ "$(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 || die # Fix up variables -- need to reset CCP4_MASTER at install-time sed -i \ -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ "${S}"/include/ccp4.setup* || die # Set up variables for build source "${S}"/include/ccp4.setup-sh export CC=$(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=${FFLAGS:- -O2} export BINSORT_SCR="${T}" export CCP4_MASTER="${WORKDIR}" export CCP4I_TCLTK="${EPREFIX}/usr/bin" export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}" # Can't use econf, configure rejects unknown options like --prefix ./configure \ $(use_enable X x) \ --with-shared-libs \ --with-fftw="${EPREFIX}/usr" \ --with-warnings \ --disable-pdb_extract \ --disable-cctbx \ --disable-phaser \ --disable-diffractionImg \ --disable-clipper \ --disable-ssm \ --disable-mosflm \ --disable-mrbump \ --tmpdir="${TMPDIR}" \ ${GENTOO_OSNAME} || die "configure failed" # We do this manually, since disabling the clipper libraries also # disables the clipper programs pushd src/clipper_progs 2>/dev/null econf \ --prefix="${S}" \ --bindir="${ED}"/usr/libexec/ccp4/bin \ --with-ccp4="${S}" \ --with-clipper="${EPREFIX}/usr" \ --with-fftw="${EPREFIX}/usr" \ --with-mmdb="${EPREFIX}/usr" \ CXX=$(tc-getCXX) popd 2>/dev/null } src_compile() { # fsplit is required for the programs pushd lib/src 2>/dev/null emake fsplit -j1 || die popd 2>/dev/null # We do this manually, since disabling the clipper libraries also # disables the clipper programs pushd src/clipper_progs 2>/dev/null emake || die popd 2>/dev/null emake -j1 || die "emake failed" } src_install() { # Set up variables for build source "${S}"/include/ccp4.setup-sh # if we don't make this, a ton of programs fail to install mkdir "${S}"/bin || die # We do this manually, since disabling the clipper libraries also # disables the clipper programs pushd "${S}"/src/clipper_progs 2>/dev/null emake install || die popd 2>/dev/null einstall || die "install failed" # Collision with sci-chemistry/mrbump rm -f "${S}"/bin/{mrbump,pydbviewer} || die # Bins exeinto /usr/libexec/ccp4/bin/ doexe "${S}"/bin/* || die # Libs for file in "${S}"/lib/*; do if [[ -d ${file} ]]; then continue elif [[ -x ${file} ]]; then dolib.so ${file} || die else insinto /usr/$(get_libdir) doins ${file} || die fi done rm -f "${S}"/include/ccp4.setup* # smartie -- log parsing insinto /usr/share/ccp4 doins -r "${S}"/share/smartie || die # Install docs and examples local _man pushd "${S}"/man/cat1 > /dev/null for _man in *; do newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2} done popd > /dev/null mv "${S}"/manual/README "${S}"/manual/README-manual dodoc manual/* README CHANGES doc/* examples/README || die rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.* rm "${ED}"/usr/share/doc/${PF}/COPYING.* dohtml -r "${S}"/html/* if use examples; then for i in data rnase toxd; do docinto examples/${i} dodoc "${S}"/examples/${i}/* done docinto examples/tutorial dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css for i in data results; do docinto examples/tutorial/${i} dodoc "${S}"/examples/tutorial/${i}/* done for i in non-runnable runnable; do docinto examples/unix/${i} dodoc "${S}"/examples/unix/${i}/* done fi # Needed for ccp4i docs to work dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die cat >> "${T}"/baubles <<- EOF #!${EPREFIX}/bin/bash exec "${EPYTHON}" "\${CCP4}/share/ccp4/smartie/baubles.py" EOF exeinto /usr/libexec/ccp4/bin/ doexe "${T}"/baubles || die } # Epatch wrapper for bulk patching ccp_patch() { EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} }
