in science overlay

5 files changed, 0 insertions, 432 deletions

diff --git a/sci-libs/atlas/ChangeLog b/sci-libs/atlas/ChangeLog
deleted file mode 100644
index e17de12..0000000
--- a/sci-libs/atlas/ChangeLog
+++ /dev/null
@@ -1,57 +0,0 @@
-# ChangeLog for sci-libs/atlas
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*atlas-3.9.46 (25 Jul 2011)
-
-  25 Jul 2011; Sébastien Fabbro <bicatali@gentoo.org> -atlas-3.9.41.ebuild,
-  +atlas-3.9.46.ebuild:
-  Version bump. Removed die for cpufreq (bug #375193).
-
-*atlas-3.8.4 (23 May 2011)
-
-  23 May 2011; Sébastien Fabbro <bicatali@gentoo.org> -atlas-3.8.3.ebuild,
-  +atlas-3.8.4.ebuild:
-  Version bump of the stable branch
-
-  23 May 2011; Sébastien Fabbro <bicatali@gentoo.org> atlas-3.9.41.ebuild:
-  Forces gcc whenever a version of gcc is used, avoiding upstream bug
-
-*atlas-3.9.41 (17 May 2011)
-
-  17 May 2011; Sébastien Fabbro <bicatali@gentoo.org> -atlas-3.9.40-r1.ebuild,
-  +atlas-3.9.41.ebuild:
-  Version bump. Removed archdef 0 causing undefined symbols
-
-*atlas-3.9.40-r1 (29 Apr 2011)
-
-  29 Apr 2011; Sébastien Fabbro <bicatali@gentoo.org> -atlas-3.9.40.ebuild,
-  +atlas-3.9.40-r1.ebuild:
-  Reworked entirely linking procedure: now explicitely treat each module blas,
-  cblas and lapack separately
-
-*atlas-3.9.40 (27 Apr 2011)
-
-  27 Apr 2011; Sébastien Fabbro <bicatali@gentoo.org> -atlas-3.9.39.ebuild,
-  +atlas-3.9.40.ebuild:
-  Bump
-
-  15 Apr 2011; Justin Lecher <jlec@gentoo.org> atlas-3.9.39.ebuild:
-  Correct syntax for cpufrq check being all CPUs under performance controll
-
-*atlas-3.9.39 (21 Mar 2011)
-
-  21 Mar 2011; Sébastien Fabbro <bicatali@gentoo.org> atlas-3.9.39.ebuild:
-  Version bump. Seriously refactored the ebuild. Now choose posix threads over
-  openmp when the two are enabled
-
-*atlas-3.9.32 (05 Dec 2010)
-
-  05 Dec 2010; Sébastien Fabbro <bicatali@gentoo.org> atlas-3.8.3.ebuild,
-  +atlas-3.9.32.ebuild:
-  Version bump. Still beta.
-
-  03 Dec 2010; Sébastien Fabbro <bicatali@gentoo.org> atlas-3.8.3.ebuild,
-  metadata.xml:
-  Initial import. Ebuilds merged from blas-atlas and lapack-atlas.
-
diff --git a/sci-libs/atlas/Manifest b/sci-libs/atlas/Manifest
deleted file mode 100644
index eee6c02..0000000
--- a/sci-libs/atlas/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX 3.9.39-bfr-overflow.patch 2755 RMD160 4f8204eee5b429e9d3db1c211af80396a575fc87 SHA1 9b59bd8a7bb55e7ed4138731262d17532949ece0 SHA256 19cdab39e50e06de0bdc2a080642388fec3a16c826657621f15fc294268d3438
-DIST atlas3.8.4.tar.bz2 2534071 RMD160 fa2828468459213fcf3f1ae4fd26671ba32f4776 SHA1 ef92bcbc4bec096b34ed7a0d29119d84c973df0c SHA256 0f7720fb16fa4b8b8a192ea791e57569546db6f5f016cf3caaee30a9d94583bf
-DIST lapack-3.3.1.tgz 4945204 RMD160 5e9d90122110045e07351f3ab30dc4e2b43d52db SHA1 3ce437e05f0e9a3c8148ec41922f6efeef0ebdac SHA256 56821ab51c29369a34e5085728f92c549a9aa926f26acf7eeac87b61eed329e4
-EBUILD atlas-3.8.4.ebuild 7382 RMD160 3d3dca9c817b42e4c8d6ec95f52dc0290340d0eb SHA1 c8ef9142745b320d2f7e2e7da35b25d00ec83d6b SHA256 2516f3ed8a750904fecf0a58ec9e91f63ec98bdb19a17f923908d935fe908720
-MISC ChangeLog 1870 RMD160 9cf8d9bb466fef4e2a299fdbc3e0733bf79d9bfa SHA1 a9a8f2f12b153dc3faaef2563d5751306bcab441 SHA256 54a249ef95c2e0f7b987dd17fc9f2038e0baa36551566131d9197c60a9b98cc0
-MISC metadata.xml 726 RMD160 e43f5ea9c594bbe2174f6640bbfdccd8b17d4a68 SHA1 0ab8c05e7925b4716d8c94acd952bf3ab85165cb SHA256 27ef4eee7e645ad923644830d057db45d32342ad250ad903ff10915a9ca068fd
diff --git a/sci-libs/atlas/atlas-3.8.4.ebuild b/sci-libs/atlas/atlas-3.8.4.ebuild
deleted file mode 100644
index 8a54ce9..0000000
--- a/sci-libs/atlas/atlas-3.8.4.ebuild
+++ /dev/null
@@ -1,281 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-inherit eutils toolchain-funcs versionator alternatives-2
-
-LAPACKP=lapack-3.3.1
-
-DESCRIPTION="Automatically Tuned Linear Algebra Software"
-HOMEPAGE="http://math-atlas.sourceforge.net/"
-SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2
-	fortran? ( lapack? ( http://www.netlib.org/lapack/${LAPACKP}.tgz ) )"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 "
-IUSE="fortran doc lapack static-libs threads"
-
-RDEPEND="fortran? ( virtual/fortran )"
-DEPEND="${RDEPEND}
-	!prefix? ( sys-power/cpufrequtils )"
-
-S="${WORKDIR}/ATLAS"
-
-lapack_compile() {
-	cd "${WORKDIR}/${LAPACKP}"
-	local timer=INT_CPU_TIME
-	case $(tc-getFC) in
-		*gfortran|*g77) timer=INT_ETIME ;;
-		*ifort) timer=EXT_ETIME ;;
-	esac
-	cat > make.inc <<-EOF
-		FORTRAN = $(tc-getFC)
-		OPTS = ${FFLAGS}
-		NOOPT = -O0
-		LOADER = $(tc-getFC)
-		LOADEROPTS = ${LDFLAGS}
-		ARCH = $(tc-getAR)
-		ARCHFLAGS = cr
-		RANLIB = $(tc-getRANLIB)
-		TIMER = ${timer}
-	EOF
-	if use static-libs; then
-		emake \
-			LAPACKLIB=liblapack_nonpic.a \
-			lapacklib || die "lapack static compilation failed"
-		emake clean
-	fi
-	emake \
-		LAPACKLIB=liblapack_pic.a \
-		OPTS="${FFLAGS} -fPIC" \
-		NOOPT="-O0 -fPIC" \
-		lapacklib || die "lapack pic compilation failed"
-}
-
-atlas_configure() {
-	local mycc="$(tc-getCC)"
-	# http://sourceforge.net/tracker/?func=detail&aid=3301697&group_id=23725&atid=379483
-	[[ ${mycc} == *gcc* ]] && mycc=gcc
-	local myconf=(
-		"--prefix=${ED}/usr"
-		"--libdir=${ED}/usr/$(get_libdir)"
-		"--incdir=${ED}/usr/include"
-		"--cc=${mycc}"
-		"-C ac ${mycc}"
-		"-D c -DWALL"
-		"-F ac '${CFLAGS}'"
-		"-Ss pmake '\$(MAKE) ${MAKEOPTS}'"
-	)
-
-	if use threads; then
-		myconf+=( "-t -1" )
-	else
-		myconf+=( "-t  0" )
-	fi
-
-	if use amd64 || use ppc64 || use sparc; then
-		if [ ${ABI} = amd64 ] || [ ${ABI} = ppc64 ] || [ ${ABI} = sparc64 ] ; then
-			myconf+=( "-b 64" )
-		elif [ ${ABI} = x86 ] || [ ${ABI} = ppc ] || [ ${ABI} = sparc32 ] ; then
-			myconf+=( "-b 32" )
-		else
-			myconf+=( "-b 64" )
-		fi
-	elif use ppc || use x86; then
-		myconf+=( "-b 32" )
-	elif use ia64; then
-		myconf+=( "-b 64" )
-	else #hppa alpha ...
-		myconf+=( "" )
-	fi
-	if use fortran; then
-		myconf+=(
-			"-Si nof77 0"
-			"-C if $(tc-getFC)"
-			"-F if '${FFLAGS}'"
-		)
-		use lapack && myconf+=( "--with-netlib-lapack=${LAPACKLIB}" )
-	else
-		myconf+=( "-Si nof77 1" )
-	fi
-	local confdir="${S}_${1}"; shift
-	myconf+=( $@ )
-	mkdir "${confdir}" && cd "${confdir}"
-	"${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed"
-}
-
-atlas_compile() {
-	pushd "${S}_${1}" > /dev/null
-	# atlas does its own parallel builds
-	emake -j1 build
-	cd lib
-	emake libclapack.a
-	popd > /dev/null
-}
-
-# transform a static archive into a shared library and install them
-# atlas_install_libs <mylib.a> [extra link flags]
-atlas_install_libs() {
-	local libname=$(basename ${1%.*})
-	einfo "Installing ${libname}"
-	local soname=${libname}.so.$(get_major_version)
-	shift
-	pushd "${S}_shared"/lib > /dev/null
-	${LINK:-$(tc-getCC)} ${LDFLAGS} -shared -Wl,-soname=${soname} \
-		-Wl,--whole-archive ${libname}.a -Wl,--no-whole-archive \
-		"$@" -o ${soname} || die "Creating ${soname} failed"
-	dolib.so ${soname}
-	ln -s ${soname} ${soname%.*}
-	dosym ${soname} /usr/$(get_libdir)/${soname%.*}
-	popd > /dev/null
-	use static-libs && dolib.a "${S}_static"/lib/${libname}.a
-}
-
-# create and install a pkgconfig file
-# atlas_install_pc <libname> <pkg name> [extra link flags]
-atlas_install_pc() {
-	local libname=${1} ; shift
-	local pcname=${1} ; shift
-	cat <<-EOF > ${pcname}.pc
-		prefix=${EPREFIX}/usr
-		libdir=\${prefix}/$(get_libdir)
-		includedir=\${prefix}/include
-		Name: ${pcname}
-		Description: ${PN} ${pcname}
-		Version: ${PV}
-		URL: ${HOMEPAGE}
-		Libs: -L\${libdir} -l${libname} $@
-		Cflags: -I\${includedir}/${PN}
-		${PCREQ}
-	EOF
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins ${pcname}.pc
-}
-
-pkg_setup() {
-	if [[ -n $(type -P cpufreq-info) ]]; then
-		[[ -z $(cpufreq-info -d) ]] && return
-		local ncpu=$(LANG=C cpufreq-info | grep -c "analyzing CPU")
-		local cpu=0
-		while [[ ${cpu} -lt ${ncpu} ]]; do
-			if ! $(LANG=C cpufreq-info -p -c ${cpu} | grep -q performance); then
-				ewarn "CPU $cpu is not set to performance"
-				ewarn "Run cpufreq-set -r -g performance as root"
-			fi
-			cpu=$(( cpu + 1 ))
-		done
-	else
-		ewarn "Please make sure to disable CPU throttling completely"
-		ewarn "during the compile of ${PN}. Otherwise, all ${PN}"
-		ewarn "generated timings will be completely random and the"
-		ewarn "performance of the resulting libraries will be degraded"
-		ewarn "considerably."
-	fi
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/3.9.39-bfr-overflow.patch
-}
-
-src_configure() {
-	if use fortran && use lapack; then
-		lapack_compile
-		LAPACKLIB="${WORKDIR}/${LAPACKP}/liblapack_pic.a"
-	fi
-	atlas_configure shared "-Fa alg -fPIC"
-	if use static-libs; then
-		use fortran && use lapack && \
-			LAPACKLIB="${WORKDIR}/${LAPACKP}/liblapack_nonpic.a"
-		atlas_configure static
-	fi
-}
-
-src_compile() {
-	atlas_compile shared
-	use static-libs && atlas_compile static
-}
-
-src_test() {
-	cd "${S}_shared"
-	emake -j1 check
-	emake -j1 time
-}
-
-src_install() {
-	cd "${S}_shared/lib"
-	# rename to avoid collision with other packages
-	local l
-	for l in {,c}{blas,lapack}; do
-		if [[ -e lib${l}.a ]]; then
-			mv lib{,atl}${l}.a
-			use static-libs && mv "${S}"_static/lib/lib{,atl}${l}.a
-		fi
-	done
-
-	[[ -e libptcblas.a ]] && PTLIBS="-lpthread"
-
-	# atlas
-	atlas_install_libs libatlas.a -lm ${PTLIBS}
-
-	# cblas
-	atlas_install_libs libatlcblas.a -lm -L. -latlas
-	atlas_install_pc atlcblas atlas-cblas -lm -latlas
-	alternatives_for cblas atlas 0 \
-		/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas.pc \
-		/usr/include/cblas.h atlas/cblas.h
-
-	# cblas threaded
-	if [[ -e libptcblas.a ]]; then
-		atlas_install_libs libptcblas.a -lm -L. -latlas ${PTLIBS}
-		atlas_install_pc ptcblas atlas-cblas-threads -lm -latlas ${PTLIBS}
-		alternatives_for cblas atlas-threads 0 \
-			/usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas-threads.pc \
-			/usr/include/cblas.h atlas/cblas.h
-	fi
-
-	if use lapack; then
-		PCREQ="Requires: cblas"
-		# clapack
-		atlas_install_libs libatlclapack.a -lm -L. -latlas -latlcblas
-		atlas_install_pc atlclapack atlas-clapack -lm -latlas
-	fi
-
-	if use fortran; then
-		LINK=$(tc-getF77) PCREQ=
-		# blas
-		atlas_install_libs libf77blas.a -lm -L. -latlas
-		atlas_install_pc f77blas atlas-blas -lm -latlas
-		alternatives_for blas atlas 0 \
-			/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas.pc
-
-		# blas threaded
-		if [[ -e libptf77blas.a ]]; then
-			atlas_install_libs libptf77blas.a -lm -L. -latlas ${PTLIBS}
-			atlas_install_pc ptf77blas atlas-blas-threads -lm -latlas ${PTLIBS}
-			alternatives_for blas atlas-threads 0 \
-				/usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas-threads.pc
-		fi
-
-		if use lapack; then
-			PCREQ="Requires: blas cblas"
-			# lapack
-			atlas_install_libs libatllapack.a \
-				-lm -L. -latlas -latlcblas -lf77blas
-			atlas_install_pc atllapack atlas-lapack -lm -latlas
-			alternatives_for lapack atlas 0 \
-				/usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack.pc
-		fi
-	fi
-
-	cd "${S}"
-	insinto /usr/include/${PN}
-	doins include/*.h
-
-	cd "${S}/doc"
-	dodoc INDEX.txt AtlasCredits.txt ChangeLog
-	use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf
-	use doc && use fortran && dodoc f77blas*pdf
-	use doc && use fortran && use lapack && dodoc lapack*pdf
-}
diff --git a/sci-libs/atlas/files/3.9.39-bfr-overflow.patch b/sci-libs/atlas/files/3.9.39-bfr-overflow.patch
deleted file mode 100644
index a4ae52a..0000000
--- a/sci-libs/atlas/files/3.9.39-bfr-overflow.patch
+++ /dev/null
@@ -1,72 +0,0 @@
- ATLAS/tune/blas/level1/axpysrch.c  |    2 +-
- ATLAS/tune/blas/level1/copysrch.c  |    2 +-
- ATLAS/tune/blas/level1/iamaxsrch.c |    2 +-
- ATLAS/tune/blas/level1/scalsrch.c  |    2 +-
- ATLAS/tune/blas/level1/swapsrch.c  |    2 +-
- 5 files changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/ATLAS/tune/blas/level1/axpysrch.c b/ATLAS/tune/blas/level1/axpysrch.c
-index 48bd756..f7f7845 100644
---- a/ATLAS/tune/blas/level1/axpysrch.c
-+++ b/ATLAS/tune/blas/level1/axpysrch.c
-@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre)
- {
-    FILE *fpin;
-    FILENODE *fbase, *fn, *fp=NULL;
--   char ln[512], rout[256], auth[256], cc[256], ccflags[256];
-+   char ln[512], rout[256], auth[256], cc[256], ccflags[512];
-    char *pcc, *pccflags;
-    int i, n, ID, alpha, beta, incX, incY;
- 
-diff --git a/ATLAS/tune/blas/level1/copysrch.c b/ATLAS/tune/blas/level1/copysrch.c
-index 3a9fcfc..736f501 100644
---- a/ATLAS/tune/blas/level1/copysrch.c
-+++ b/ATLAS/tune/blas/level1/copysrch.c
-@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre)
- {
-    FILE *fpin;
-    FILENODE *fbase, *fn, *fp=NULL;
--   char ln[512], rout[256], auth[256], cc[256], ccflags[256];
-+   char ln[512], rout[256], auth[256], cc[256], ccflags[512];
-    char *pcc, *pccflags;
-    int i, n, ID, alpha, beta, incX, incY;
- 
-diff --git a/ATLAS/tune/blas/level1/iamaxsrch.c b/ATLAS/tune/blas/level1/iamaxsrch.c
-index e9e766a..91b3acd 100644
---- a/ATLAS/tune/blas/level1/iamaxsrch.c
-+++ b/ATLAS/tune/blas/level1/iamaxsrch.c
-@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre)
- {
-    FILE *fpin;
-    FILENODE *fbase, *fn, *fp=NULL;
--   char ln[512], rout[256], auth[256], cc[256], ccflags[256];
-+   char ln[512], rout[256], auth[256], cc[256], ccflags[512];
-    char *pcc, *pccflags;
-    int i, n, ID, alpha, beta, incX, incY;
- 
-diff --git a/ATLAS/tune/blas/level1/scalsrch.c b/ATLAS/tune/blas/level1/scalsrch.c
-index 48be97e..35d724d 100644
---- a/ATLAS/tune/blas/level1/scalsrch.c
-+++ b/ATLAS/tune/blas/level1/scalsrch.c
-@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre)
- {
-    FILE *fpin;
-    FILENODE *fbase, *fn, *fp=NULL;
--   char ln[512], rout[256], auth[256], cc[256], ccflags[256];
-+   char ln[512], rout[256], auth[256], cc[256], ccflags[512];
-    char *pcc, *pccflags;
-    int i, n, ID, alpha, beta, incX, incY;
- 
-diff --git a/ATLAS/tune/blas/level1/swapsrch.c b/ATLAS/tune/blas/level1/swapsrch.c
-index 776d2d7..5281ae5 100644
---- a/ATLAS/tune/blas/level1/swapsrch.c
-+++ b/ATLAS/tune/blas/level1/swapsrch.c
-@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre)
- {
-    FILE *fpin;
-    FILENODE *fbase, *fn, *fp=NULL;
--   char ln[512], rout[256], auth[256], cc[256], ccflags[256];
-+   char ln[512], rout[256], auth[256], cc[256], ccflags[512];
-    char *pcc, *pccflags;
-    int i, n, ID, alpha, beta, incX, incY;
- 
diff --git a/sci-libs/atlas/metadata.xml b/sci-libs/atlas/metadata.xml
deleted file mode 100644
index 93eedfb..0000000
--- a/sci-libs/atlas/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<longdescription lang='en'>
-   ATLAS is an approach for the automatic generation and optimization of
-   numerical software. Currently ATLAS supplies optimized versions for the
-   complete set of linear algebra kernels known as the Basic Linear Algebra
-   Subroutines (BLAS) for both c and F77 interfaces. It can also build
-   a subset of the linear algebra routine LAPACK library or the full
-   LAPACK using the reference LAPACK from Netlib.
-</longdescription>
-<use>
-  <flag name='xblas'>Build LAPACK with extra precision (needs <pkg>sci-libs/xblas</pkg>)</flag>
-</use>
-</pkgmetadata>