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-rw-r--r--sci-chemistry/phaser/Manifest1
-rw-r--r--sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch13
-rw-r--r--sci-chemistry/phaser/metadata.xml9
-rw-r--r--sci-chemistry/phaser/phaser-2.1.4.ebuild115
4 files changed, 0 insertions, 138 deletions
diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest
deleted file mode 100644
index deb3ba972a75..000000000000
--- a/sci-chemistry/phaser/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ccp4-6.1.13-phaser-cctbx-src.tar.gz 22021353 SHA256 e6c4365cb34da5ce2dd5f1e74b8927258064016194446163418c8a3139a4b804 SHA512 cdf36572613a6e400af0f29da501ccfd2a9f1a7e2d89162aad3fe14929816b41790bb57ba1e77976b9046c6e06a29df2748999db93a2cd0a4d1fde95ac1f9e8b WHIRLPOOL 5aa1a1c6520be90ef02be0e9de9c111a9835cda05a3549c390f62ceef7e68c8392670d91941b823c0ee94f29e6aab9d34a61b90e8bd3d4820a83daa547463fdb
diff --git a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch
deleted file mode 100644
index 5311cb332785..000000000000
--- a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
-index 3b1bd3a..8939a74 100755
---- a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
-+++ b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py
-@@ -802,8 +802,6 @@ class environment:
- else:
- action = self.write_bin_sh_dispatcher
- ext = ""
-- try: os.chmod(source_file, 0755)
-- except OSError: pass
- target_file_ext = target_file + ext
- remove_or_rename(target_file_ext)
- try: action(source_file, target_file_ext)
diff --git a/sci-chemistry/phaser/metadata.xml b/sci-chemistry/phaser/metadata.xml
deleted file mode 100644
index 6b4826474daa..000000000000
--- a/sci-chemistry/phaser/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-chemistry</herd>
- <maintainer>
- <email>jlec@gentoo.org</email>
- <description>ccp4 maintainer</description>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild
deleted file mode 100644
index 86fa57f52603..000000000000
--- a/sci-chemistry/phaser/phaser-2.1.4.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic python-single-r1 toolchain-funcs
-
-CCP4VER="6.1.13"
-
-DESCRIPTION="A program for phasing macromolecular crystal structures"
-HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser"
-SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-${PN}-cctbx-src.tar.gz"
-
-LICENSE="|| ( phaser phaser-com ccp4 )"
-SLOT="0"
-#KEYWORDS="~amd64 ~x86"
-KEYWORDS=""
-IUSE="openmp"
-
-RDEPEND=""
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}"/ccp4-${CCP4VER}
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/phaser-2.1.4-chmod.patch \
- "${FILESDIR}"/phaser-2.1.4-ldflags.patch
-
- use openmp && append-flags -fopenmp
-
- for i in ${CXXFLAGS}; do
- OPTS="${OPTS} \"${i}\","
- done
-
- OPTS=${OPTS%,}
-
- sed -i \
- -e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \
- "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die
-
- for i in ${LDFLAGS}; do
- OPTSLD="${OPTSLD} \"${i}\","
- done
-
- sed -i \
- -e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\"\]:g" \
- -e "s:\[\"-static:\[${OPTSLD} \"-static:g" \
- "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die
-
-}
-
-src_configure() {
- local compiler
- local mtype
- local mversion
- local nproc
-
- # Valid compilers are win32_cl, sunos_CC, unix_gcc, unix_ecc,
- # unix_icc, unix_icpc, tru64_cxx, hp_ux11_aCC, irix_CC,
- # darwin_c++, darwin_gcc. The build systems seems to prepend
- # unix_ all by itself. Can this be derived from $(tc-getCC)?
- compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-
- # Breaks cross compilation.
- mtype=$(src/${PN}/bin/machine_type)
- mversion=$(src/${PN}/bin/machine_version)
-
- einfo "Creating build directory"
- mkdir build
- cd build
- ln -sf "${S}/lib/cctbx/cctbx_sources/scons" scons
- ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx
-
- einfo "Configuring phaser components"
- $(PYTHON) "libtbx/configure.py" \
- --build=release \
- --compiler=${compiler} \
- --repository="${S}"/src/${PN}/source \
- --repository="${S}"/lib/cctbx/cctbx_sources \
- --static_libraries \
- ccp4io="${S}" \
- mmtbx \
- phaser || die "configure.py failed"
-}
-
-src_compile() {
- nproc=`echo "-j1 ${MAKEOPTS}" \
- | sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"`
-
- cd build
- einfo "Setting up build environment"
- source setpaths.sh
-
- einfo "Compiling phaser components"
- libtbx.scons -j ${nproc} || die "libtbx.scons failed"
-}
-
-src_install() {
- dobin build/exe/phaser || die
-
- cat >> "${T}"/53${PN} <<- EOF
- PHASER="${EPREFIX}/usr/bin"
- PHASER_ENVIRONMENT="1"
- PHASER_MTYPE="${mtype}"
- PHASER_MVERSION="${mversion}"
- PHASER_VERSION="${PV}"
- EOF
-
- doenvd "${T}"/53${PN} || die
-}