broken

Signed-off-by: Justin Lecher <jlec@gentoo.org>

7 files changed, 0 insertions, 379 deletions

diff --git a/sci-chemistry/phaser/ChangeLog b/sci-chemistry/phaser/ChangeLog
deleted file mode 100644
index bc908bd4b..000000000
--- a/sci-chemistry/phaser/ChangeLog
+++ /dev/null
@@ -1,21 +0,0 @@
-# ChangeLog for sci-chemistry/phaser
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  25 Oct 2011; Justin Lecher <jlec@gentoo.org> metadata.xml:
-  Removed no-herd from herd tag in metadata.xml
-
-  10 Jul 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de>
-  phaser-2.1.4.ebuild, phaser-2.1.4-r1.ebuild:
-  Silence repoman.
-
-*phaser-2.1.4-r1 (29 May 2009)
-*phaser-2.1.4 (29 May 2009)
-
-  29 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +files/2.1.4-sadf.patch, +phaser-2.1.4.ebuild, +phaser-2.1.4-r1.ebuild,
-  +metadata.xml:
-  version 2.1.4 written by me 
-  2.1.4-r1 seperatly written by Johan Hattne Thanks!
-  builds phaser staticaly against bundled cctbx.
-
diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest
deleted file mode 100644
index eb8b8c568..000000000
--- a/sci-chemistry/phaser/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST phaser-2.1.4-cctbx-src.tar.gz 22388206 SHA256 594829cc82cb3c57e223ded99faf1fe86b192f2b48a935f93d2a4b89b9018970
diff --git a/sci-chemistry/phaser/files/2.1.4-sadf.patch b/sci-chemistry/phaser/files/2.1.4-sadf.patch
deleted file mode 100644
index ee1abe375..000000000
--- a/sci-chemistry/phaser/files/2.1.4-sadf.patch
+++ /dev/null
@@ -1,64 +0,0 @@
---- ccp4-6.1.1/src/phaser/source/phaser/src/RefineSADf.cc	2009-02-05 19:03:10.000000000 +0100
-+++ ccp4-6.1.1/src/phaser/source/phaser/src/RefineSADf.cc.new	2008-07-14 15:25:47.000000000 +0200
-@@ -161,7 +161,8 @@
-     if (atoms_extra[a].REJECTED) PHASER_ASSERT(atoms[a].occupancy == 0);
-   }
- 
--  cctbx::xray::fast_gradients<dFloatType> fast_gradients(
-+  typedef cctbx::xray::fast_gradients<dFloatType> fast_gradients_t;
-+  fast_gradients_t fast_gradients(
-       cctbxUC,
-       atoms.const_ref(),
-       scattering_type_registry,
-@@ -206,9 +205,9 @@
-     sc.flags.set_tan_u_iso(false);
-   }
- 
--  af::const_ref<dCmplxType, cctbx::maptbx::c_grid_padded_p1<3> > gradmap_const_ref(
--    gradmap_fft_ref.begin(),
--    cctbx::maptbx::c_grid_padded_p1<3>(cfft.n(), cfft.n()));
-+  typedef fast_gradients_t::accessor_type fgat;
-+  af::const_ref<dCmplxType, fgat>
-+    gradmap_const_ref(gradmap_fft_ref.begin(), fgat(cfft.n(), cfft.n()));
-   bool sampled_density_must_be_positive(true);
-   fast_gradients.sampling(
-       atoms.const_ref(),
---- ccp4-6.1.1/src/phaser/source/phaser/io/Errors.cc      2007-11-14 15:46:41.000000000 +0100
-+++ ccp4-6.1.1/src/phaser/source/phaser/io/Errors.cc.new      2007-11-14 15:46:41.000000000 +0100
-@@ -1,6 +1,7 @@
- //(c) 2000-2007 Cambridge University Technical Services Ltd
- //All rights reserved
- #include <phaser/io/Errors.h>
-+#include <cstdio>
- 
- namespace phaser {
- 
-@@ -20,7 +21,7 @@
-     sfile.erase(sfile.begin(),sfile.begin()+i+1);
-     std::string::size_type j = sfile.rfind("\\"); //microsoft file separator
-     sfile.erase(sfile.begin(),sfile.begin()+j+1);
--    sprintf(buf, "%ld", line);
-+    std::sprintf(buf, "%ld", line);
-     msg_ =   std::string("Program") + s + " error in source file "
-               + sfile + " (line " + buf + ")\n";
-     if (msg.size()) msg_ += "*** "+ msg + " ***";
---- ccp4-6.1.1/src/phaser/source/phaser/SConscript        2008-06-19 11:57:30.000000000 +0200
-+++ ccp4-6.1.1/src/phaser/source/phaser/SConscript.new        2008-06-19 11:57:30.000000000 +0200
-@@ -12,13 +12,15 @@
- 
- cxxflags = env_etc.cxxflags_base
- print "Compiling distributed version of phaser"
-+ccp4io_lib = getattr(env_etc, "ccp4io_lib", "cmtz")
-+  # XXX backward compatibility 2008-09-10
- env_etc.phaser_common_libs = [
-   "phaserrun",
-   "phasersrc",
-   "phaserio",
-   "phaserkey",
-   "phaserlib",
--  "cmtz",
-+  ccp4io_lib,
-   "cctbx",
- ]
- env_etc.phaser_common_includes = [
-
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 ecc98490c..000000000
--- a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-6.1.1/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py.orig	2009-05-27 16:55:30.712547511 -0500
-+++ ccp4-6.1.1/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py	2009-05-27 16:55:44.446546721 -0500
-@@ -802,8 +802,6 @@
-     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 deb55d19f..000000000
--- a/sci-chemistry/phaser/metadata.xml
+++ /dev/null
@@ -1,30 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<!-- 
-$Header: $
-
-This is the example metadata file.
-The root element of this file is <pkgmetadata>. Within this element a 
-number of subelements are allowed: herd, maintainer, and 
-longdescription. herd is a required subelement.
-
-For a full description look at:
-http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=4
-
-
-Before committing, please remove the comments from this file. They are 
-not relevant for general metadata.xml files.
--->
-<pkgmetadata>
-	<maintainer>
-		<email>jlec@gentoo.org</email>
-		<!--  <description>coding for fun</description> -->
-	</maintainer>
-	<!-- <longdescription>Long description of the package</longdescription> -->
-	<!--
-<use>
-  <flag name='flag'>Description of how USE='flag' affects this package.</flag>
-  <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this package.</flag>
-</use>
--->
-</pkgmetadata>
diff --git a/sci-chemistry/phaser/phaser-2.1.4-r1.ebuild b/sci-chemistry/phaser/phaser-2.1.4-r1.ebuild
deleted file mode 100644
index 2f8cafac4..000000000
--- a/sci-chemistry/phaser/phaser-2.1.4-r1.ebuild
+++ /dev/null
@@ -1,138 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit base flag-o-matic python
-
-DESCRIPTION="A program for phasing macromolecular crystal structures"
-HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser"
-SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/${PN}-${PV}-cctbx-src.tar.gz"
-
-LICENSE="|| ( phaser phaser-com ccp4 )"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="openmp"
-RDEPEND=""
-DEPEND="${RDEPEND}
-		  app-shells/tcsh"
-
-S="${WORKDIR}"/ccp4-6.1.1
-
-PATCHES=(
-	"${FILESDIR}"/phaser-2.1.4-chmod.patch
-	)
-
-src_prepare() {
-	base_src_prepare
-
-	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" \
-		"${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die
-
-}
-
-src_compile() {
-	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)
-	nproc=`echo "-j1 ${MAKEOPTS}" \
-		| sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"`
-
-	einfo "Creating build directory $nproc "
-	mkdir build
-	cd    build
-	ln -sf "${S}/lib/cctbx/cctbx_sources/scons"  scons
-	ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx
-
-	# It is difficult to rely on sci-libs/cctbx for the cctbx
-	# dependency, because upstream releases new versions quite
-	# frequently.  Perhaps better to link statically to the bundled
-	# cctbx.
-	einfo "Configuring phaser components"
-	python_version
-	${python} "libtbx/configure.py" \
-		--build=release \
-		--compiler=${compiler} \
-		--repository="${S}"/src/${PN}/source \
-		--repository="${S}"/lib/cctbx/cctbx_sources \
-		--static_libraries \
-		ccp4io="${S}" \
-		mmtbx \
-		phaser || die "configure.py failed"
-
-	einfo "Setting up build environment"
-	source setpaths.sh
-
-	einfo "Compiling phaser components"
-	libtbx.scons -j ${nproc} || die "libtbx.scons failed"
-
-	# Hardcoded /usr/bin does not look nice.  Should these files,
-	# perhaps, be installed somewhere?
-#	einfo "Creating env.csh"
-#	cat >> "${T}"/env.csh <<- EOF
-#	#! /bin/csh
-#
-#	setenv PHASER             /usr/bin
-#	setenv PHASER_ENVIRONMENT 1
-#	setenv PHASER_MTYPE       ${mtype}
-#	setenv PHASER_MVERSION    ${mversion}
-#	setenv PHASER_VERSION     ${PV}
-#	EOF
-
-#	einfo "Creating env.sh"
-	cat >> "${T}"/53${PN} <<- EOF
-
-	PHASER="/usr/bin"
-	PHASER_ENVIRONMENT="1"
-	PHASER_MTYPE="${mtype}"
-	PHASER_MVERSION="${mversion}"
-	PHASER_VERSION="${PV}"
-	EOF
-
-	doenvd "${T}"/53${PN}
-}
-
-# Why do some tests say that CNS and SHELX is not available?  Same for
-# cctbx ebuild tests.
-src_test() {
-	cd "${S}//build" && \
-	source setpaths.sh && \
-	csh ./run_tests.csh || die "run_test.csh failed"
-}
-
-# This is a bit thin.  Maybe install other files from the distribution
-# as well?
-src_install() {
-	dobin build/exe/phaser || die
-}
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 73f18f4ee..000000000
--- a/sci-chemistry/phaser/phaser-2.1.4.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit eutils python toolchain-funcs
-
-DESCRIPTION="Phasing macromolecular crystal structures with maximum likelihood methods"
-SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/${P}-cctbx-src.tar.gz"
-HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser/"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~x86 ~amd64"
-IUSE="openmp"
-
-DEPEND="dev-util/scons"
-RDEPEND="sci-libs/cctbx"
-
-S="${WORKDIR}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	rm -rf lib/*
-	cp -rf $CCP4/lib/cctbx/cctbx_sources/libtbx "${WORKDIR}"
-
-	mkdir -p "${WORKDIR}"/scons/src/
-	ln -sf /usr/$(get_libdir)/scons-1.2.0 "${WORKDIR}"/scons/src/engine || die
-
-	epatch "${FILESDIR}"/${PV}-sadf.patch
-}
-
-src_compile(){
-	python_version
-
-	local MYCONF
-	local MAKEOPTS_EXP
-	local OPTS
-	local OPTSLD
-
-	MYCONF="${S}/libtbx/configure.py"
-
-	MYCONF="${MYCONF} --repository ${S}/ccp4-6.1.1/src/${PN}/source --repository /usr/$(get_libdir)/cctbx/cctbx_sources/ \
-	--build=release ccp4io=${CCP4}/$(get_libdir)/cctbx/cctbx_sources/ccp4io/"
-
-	MAKEOPTS_EXP=${MAKEOPTS/j/j }
-	MAKEOPTS_EXP=${MAKEOPTS_EXP%-l[0-9]*}
-
-	# Get CXXFLAGS in format suitable for substitition into SConscript
-	for i in ${CXXFLAGS}; do
-	OPTS="${OPTS} \"${i}\","
-	done
-
-	# Strip off the last comma
-	OPTS=${OPTS%,}
-
-	# Fix CXXFLAGS
-	sed -i \
-	-e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \
-	"${S}"/libtbx/SConscript
-
-	# Get LDFLAGS in format suitable for substitition into SConscript
-	for i in ${LDFLAGS}; do
-	OPTSLD="${OPTSLD} \"${i}\","
-	done
-
-	# Fix LDFLAGS which should be as-needed ready
-	sed -i \
-	-e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\":g" \
-	"${S}"/libtbx/SConscript
-
-	# Get compiler in the right way
-	COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-	MYCONF="${MYCONF} --compiler=${COMPILER}"
-
-	# Additional USE flag usage
-	check_use openmp
-	MYCONF="${MYCONF} --enable-openmp-if-possible=${USE_openmp}"
-	use threads && USEthreads="--enable-boost-threads" && \
-	ewarn "If using boost threads openmp support is disabled"
-
-	MYCONF="${MYCONF} ${USE_threads} --scan-boost"
-
-	MYCONF="${MYCONF} phaser"
-	einfo "configuring with ${python} ${MYCONF}"
-
-	${python} ${MYCONF} \
-	|| die "configure failed"
-
-	source setpaths_all.sh
-
-	einfo "compiling with libtbx.scons ${MAKEOPTS_EXP}"
-	libtbx.scons ${MAKEOPTS_EXP} .|| die "make failed"
-}
-
-src_install() {
-	rm lib/libboost*
-	dolib.so lib/*.so || die
-	dolib.a lib/*.a || die
-	dobin exe/phaser || die
-}
-
-check_use() {
-
-	for var in $@; do
-	if use ${var}; then
-	printf -v "USE_$var" True
-	else
-	printf -v "USE_$var" False
-
-	fi
-	shift
-	done
-}