5 files changed, 0 insertions, 238 deletions
diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
deleted file mode 100644
index 7ce467c81..000000000
--- a/sci-chemistry/apbs/ChangeLog
+++ /dev/null
@@ -1,10 +0,0 @@
-# ChangeLog for sci-chemistry/apbs
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*apbs-9999 (01 May 2014)
-
-  01 May 2014; Justin Lecher <jlec@gentoo.org> +apbs-9999.ebuild,
-  +files/apbs-9999-manip.patch, +files/apbs-9999-prll.patch, +metadata.xml:
-  Add live ebuild
-
diff --git a/sci-chemistry/apbs/apbs-9999.ebuild b/sci-chemistry/apbs/apbs-9999.ebuild
deleted file mode 100644
index dcbc0f98a..000000000
--- a/sci-chemistry/apbs/apbs-9999.ebuild
+++ /dev/null
@@ -1,91 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.3-r3.ebuild,v 1.5 2013/05/02 15:16:35 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils flag-o-matic git-r3 multilib python-single-r1 toolchain-funcs
-
-DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
-HOMEPAGE="http://www.poissonboltzmann.org/apbs/"
-SRC_URI=""
-EGIT_REPO_URI="git://git.code.sf.net/p/apbs/code"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS=""
-IUSE="debug examples +fetk mpi +openmp +tools"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-libs/maloc[mpi=]
-	virtual/blas
-	sys-libs/readline
-	fetk? (
-		sci-libs/fetk
-		sci-libs/amd
-		sci-libs/umfpack
-		sci-libs/superlu )
-	mpi? ( virtual/mpi )"
-DEPEND="${DEPEND}
-	virtual/pkgconfig"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-manip.patch
-	"${FILESDIR}"/${P}-prll.patch
-)
-
-DOCS=(
-	doc/{APBS-1.4-README.txt,ChangeLog,README}
-)
-
-src_prepare() {
-	local _examples
-
-	use examples || examples=$(ls examples/*)
-
-	rm -rf \
-		contrib/maloc* include/Eigen/* \
-		doc/{license,release_procedure.txt,programmer,CMakeLists.txt} \
-		${examples} \
-		|| die
-
-	append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
-
-	sed \
-		-e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \
-		-e 's:-lg2c::g' \
-		-i CMakeLists.txt || die
-
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir)
-		-DLIBRARY_INSTALL_PATH=$(get_libdir)
-		-DFETK_PATH="${EPREFIX}"/usr/
-		-DBUILD_SHARED_LIBS=ON
-		-DENABLE_PYTHON=ON
-		$(cmake-utils_use_build tools)
-		$(cmake-utils_use_enable debug)
-# Not acitve in the code yet
-#		$(cmake-utils_use_enable fast)
-		$(cmake-utils_use_enable fetk)
-		$(cmake-utils_use_enable mpi)
-		$(cmake-utils_use_enable openmp)
-	)
-	cmake-utils_src_configure
-}
-
-src_test() {
-	cd tests || die
-	"${PYTHON}" apbs_tester.py -l log || die
-	grep -q 'FAILED' log && die "Tests failed"
-}
-
-src_install() {
-	cmake-utils_src_install
-	python_optimize "${ED}"
-}
diff --git a/sci-chemistry/apbs/files/apbs-9999-manip.patch b/sci-chemistry/apbs/files/apbs-9999-manip.patch
deleted file mode 100644
index fd5c1a299..000000000
--- a/sci-chemistry/apbs/files/apbs-9999-manip.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- tools/CMakeLists.txt | 1 -
- 1 file changed, 1 deletion(-)
-
-diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
-index 1982a3c..30ab17a 100644
---- a/tools/CMakeLists.txt
-+++ b/tools/CMakeLists.txt
-@@ -1,7 +1,6 @@
- set(EXECUTABLE_OUTPUT_PATH ${TOOLS_PATH}/bin)
- 
- add_subdirectory(mesh)
--add_subdirectory(manip)
- 
- if(ENABLE_PYTHON)
-     add_subdirectory(manip)
diff --git a/sci-chemistry/apbs/files/apbs-9999-prll.patch b/sci-chemistry/apbs/files/apbs-9999-prll.patch
deleted file mode 100644
index 99e1845bb..000000000
--- a/sci-chemistry/apbs/files/apbs-9999-prll.patch
+++ /dev/null
@@ -1,101 +0,0 @@
- CMakeLists.txt          | 16 ++++++++--------
- src/CMakeLists.txt      |  1 -
- src/fem/CMakeLists.txt  |  2 +-
- src/pmgc/CMakeLists.txt |  2 +-
- 4 files changed, 10 insertions(+), 11 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index e3f720c..6b7db4c 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -61,7 +61,7 @@ set(LIBRARY_OUTPUT_PATH ${APBS_ROOT}/lib)
- set(TOOLS_PATH ${APBS_ROOT}/tools)
- set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs)
- 
--set(LIBRARY_INSTALL_PATH lib)
-+set(LIBRARY_INSTALL_PATH ${CMAKE_INSTALL_LIBDIR})
- set(HEADER_INSTALL_PATH include/apbs)
- set(EXECUTABLE_INSTALL_PATH bin)
- set(SHARE_INSTALL_PATH share/apbs)
-@@ -93,8 +93,6 @@ set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}")
- list(APPEND CMAKE_INCLUDE_PATH /usr/include)
- list(APPEND CMAKE_INCLUDE_PATH /usr/local/include)
- 
--set(APBS_LIBS "-L${APBS_ROOT}/lib -lapbs_geoflow")
--
- ################################################################################
- # Enable ansi pedantic compiling                                               #
- ################################################################################
-@@ -202,9 +200,11 @@ if(ENABLE_BEM)
-     else()
-         set(TABI_LIBRARY_BASENAME ${CMAKE_STATIC_LIBRARY_PREFIX}${TABI}${CMAKE_STATIC_LIBRARY_SUFFIX})
-     endif()
--    
-+	
-+	file(GLOB MODS ${LIBRARY_OUTPUT_PATH}/*.mod)    
-+
-     install(
--        FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${LIBRARY_OUTPUT_PATH}/*.mod
-+        FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${MODS}
-         DESTINATION ${LIBRARY_INSTALL_PATH}
-     )
-     set(TABI_LIBRARY ${APBS_ROOT}/${LIBRARY_INSTALL_PATH}/${TABI_LIBRARY_BASENAME})
-@@ -219,7 +219,7 @@ if(ENABLE_BEM)
-     endif()
-     get_filename_component(LIBGFORTRANPATH ${LIBGFORTRANPATH} PATH)
-     find_path(LIBGFORTRAN_PATH ${LIBGFORTRAN_NAME} PATH ${LIBGFORTRANPATH})
--    list(APPEND APBS_LIBS "-L${APBS_ROOT}/${LIBRARY_INSTALL_PATH} -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" )
-+    list(APPEND APBS_LIBS "-L${APBS_ROOT}/lib -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" )
- endif()
- 
- find_file( # this should be find path...
-@@ -237,7 +237,7 @@ endif()
- 
- 
- find_library(MALOC_LIBRARY  "maloc"
--    PATHS ${FETK_PATH}/lib ${CONTRIB_PATH}
-+    PATHS ${FETK_PATH}/${CMAKE_INSTALL_LIBDIR} ${CONTRIB_PATH}
-     DOC   "The fetk/maloc library"
- )
- if(MALOC_LIBRARY)
-@@ -295,7 +295,7 @@ if(ENABLE_FETK)
-     set(FETK_ENALBED 1)
- 
-     list(APPEND APBS_LIBS "-lstdc++")
--    list(APPEND APBS_LIBS "-L${FETK_PATH}/lib")
-+    list(APPEND APBS_LIBS "-L${FETK_PATH}/${CMAKE_INSTALL_LIBDIR}")
-     list(APPEND APBS_LIBS -lamd -lpunc -lmc -lgamer -lsuperlu -lumfpack
- -lblas -lvf2c -ltetgen -ltriangle -lg2c -lreadline )
-     
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index 44d20fa..5d5150b 100644
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -23,7 +23,6 @@ macro(add_items TYPE)
- endmacro()
- 
- 
--
- macro(add_sublibrary LIBRARY)
-     set(LIBRARY_NAME "apbs_${LIBRARY}")
-     set(LIBRARY_DEPENDENCIES ${APBS_LIBS} ${ARGN})
-diff --git a/src/fem/CMakeLists.txt b/src/fem/CMakeLists.txt
-index 5a950c2..dc37f48 100644
---- a/src/fem/CMakeLists.txt
-+++ b/src/fem/CMakeLists.txt
-@@ -12,4 +12,4 @@ add_items(
-     vpee.h
- )
- 
--add_sublibrary(fem)
-+add_sublibrary(fem apbs_geoflow)
-diff --git a/src/pmgc/CMakeLists.txt b/src/pmgc/CMakeLists.txt
-index 85b0c1e..97c95f0 100644
---- a/src/pmgc/CMakeLists.txt
-+++ b/src/pmgc/CMakeLists.txt
-@@ -42,4 +42,4 @@ add_items(
-     mgfasd.h
- )
- 
--add_sublibrary(pmgc)
-+add_sublibrary(pmgc apbs_geoflow)
diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml
deleted file mode 100644
index b8e509525..000000000
--- a/sci-chemistry/apbs/metadata.xml
+++ /dev/null
@@ -1,21 +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>
-    <name>Justin Lecher</name>
-    <description>Ebuild Crasher</description>
-  </maintainer>
-  <use>
-    <flag name="fetk">Include support for FeTK</flag>
-    <flag name="tools">Install optional tools</flag>
-  </use>
-  <longdescription>
-APBS is a software package for modeling biomolecular solvation through solution 
-of the Poisson-Boltzmann equation (PBE), one of the most popular continuum 
-models for describing electrostatic interactions between molecular solutes in 
-salty, aqueous media. Continuum electrostatics plays an important role in 
-several areas of biomolecular simulation
-</longdescription>
-</pkgmetadata>