Version bump and removed old ebuilds.

Package-Manager: portage-2.2_rc1/cvs/Linux 2.6.25-SENTINEL-4 i686

7 files changed, 118 insertions, 260 deletions

diff --git a/sci-libs/blas-atlas/ChangeLog b/sci-libs/blas-atlas/ChangeLog
index e99e520ef3b9..312d9c0ac98f 100644
--- a/sci-libs/blas-atlas/ChangeLog
+++ b/sci-libs/blas-atlas/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for sci-libs/blas-atlas
 # Copyright 2002-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/blas-atlas/ChangeLog,v 1.80 2008/06/07 16:42:26 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/blas-atlas/ChangeLog,v 1.81 2008/07/21 13:42:28 markusle Exp $
+
+*blas-atlas-3.9.0 (20 Jul 2008)
+
+  20 Jul 2008; Markus Dittrich <markusle@gentoo.org>
+  -files/blas-atlas-3.8.1-gemm-fix.patch,
+  -files/blas-atlas-3.8.1-gemm-perf-fix.patch,
+  +files/atlas-3.9.0-decl-fix.patch,
+  +files/atlas-3.9.0-upstream-fixes.patch, -blas-atlas-3.8.1.ebuild,
+  -blas-atlas-3.8.1-r1.ebuild, +blas-atlas-3.9.0.ebuild:
+  Version bump and removed old ebuilds.
 
 *blas-atlas-3.8.2 (07 Jun 2008)
 
diff --git a/sci-libs/blas-atlas/blas-atlas-3.8.1.ebuild b/sci-libs/blas-atlas/blas-atlas-3.8.1.ebuild
deleted file mode 100644
index 1da4be168708..000000000000
--- a/sci-libs/blas-atlas/blas-atlas-3.8.1.ebuild
+++ /dev/null
@@ -1,221 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/blas-atlas/blas-atlas-3.8.1.ebuild,v 1.6 2008/06/04 13:09:55 markusle Exp $
-
-inherit eutils toolchain-funcs fortran multilib
-
-PATCH_V="3.7.39"
-
-DESCRIPTION="Automatically Tuned Linear Algebra Software BLAS implementation"
-HOMEPAGE="http://math-atlas.sourceforge.net/"
-MY_PN=${PN/blas-/}
-SRC_URI="mirror://sourceforge/math-atlas/${MY_PN}${PV}.tar.bz2
-	mirror://gentoo/${MY_PN}-${PATCH_V}-shared-libs.patch.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86"
-IUSE="doc"
-
-RDEPEND="app-admin/eselect-blas
-	app-admin/eselect-cblas
-	doc? ( app-doc/blas-docs )"
-DEPEND="app-admin/eselect-blas
-	app-admin/eselect-cblas
-	>=sys-devel/libtool-1.5"
-
-S="${WORKDIR}/ATLAS"
-
-pkg_setup() {
-	# icc won't compile (as of icc-10.0.026)
-	# and will blow out $PORTAGE_TMPDIR
-	if [[ $(tc-getCC) = icc* ]]; then
-		eerror "icc compiler is not supported with sci-libs/blas-atlas"
-		die "blas-atlas won't compile with icc"
-	fi
-
-	FORTRAN="g77 gfortran ifc"
-	fortran_pkg_setup
-	echo
-	ewarn "Please make sure to disable CPU throttling completely"
-	ewarn "during the compile of blas-atlas. Otherwise, all atlas"
-	ewarn "generated timings will be completely random and the"
-	ewarn "performance of the resulting libraries will be degraded"
-	ewarn "considerably."
-	echo
-	ewarn "For users of <=gcc-4.1.1 only:"
-	ewarn "If you experience failing SANITY tests during"
-	ewarn "atlas' compile please try passing -mfpmath=387; this"
-	ewarn "option might also result in much better performance"
-	ewarn "than using then sse instruction set depending on your"
-	ewarn "CPU."
-	echo
-	epause 10
-}
-
-src_unpack() {
-	unpack ${A}
-
-	cd "${S}"
-	epatch "${DISTDIR}"/${MY_PN}-${PATCH_V}-shared-libs.patch.bz2
-	epatch "${FILESDIR}"/${MY_PN}-asm-gentoo.patch
-	epatch "${FILESDIR}"/${MY_PN}-${PATCH_V}-decl-fix.patch
-	epatch "${FILESDIR}"/${P}-gemm-fix.patch
-
-	BLD_DIR="${S}"/gentoo-build
-	mkdir "${BLD_DIR}" || die "failed to generate build directory"
-	cd "${BLD_DIR}"
-	cp "${FILESDIR}"/war . && chmod a+x war || die "failed to install war"
-
-	local archselect=
-	if use amd64 || use ppc64; then
-		archselect="-b 64"
-	elif use alpha; then
-		archselect=""
-	else
-		archselect="-b 32"
-	fi
-
-	../configure \
-		--cc="$(tc-getCC)" \
-		--cflags="${CFLAGS}" \
-		--prefix="${D}/${DESTTREE}" \
-		--libdir="${D}/${DESTTREE}"/$(get_libdir)/atlas \
-		--incdir="${D}/${DESTTREE}"/include \
-		-C ac "$(tc-getCC)" -F ac "${CFLAGS}" \
-		-C if ${FORTRANC} -F if "${FFLAGS:-'-O2'}" \
-		-Ss pmake "\$(MAKE) ${MAKEOPTS}" \
-		-Si cputhrchk 0 ${archselect} \
-		|| die "configure failed"
-}
-
-src_compile() {
-	cd "${BLD_DIR}"
-
-	# atlas does its own parallel builds
-	emake -j1 || die "emake failed"
-
-	RPATH="${DESTTREE}"/$(get_libdir)/blas
-	make \
-		LIBDIR=$(get_libdir) \
-		RPATH="${RPATH}"/atlas \
-		shared || die "failed to build shared libraries"
-
-	# build shared libraries of threaded libraries if applicable
-	if [[ -d gentoo/libptcblas.a ]]; then
-		make \
-			LIBDIR=$(get_libdir) \
-			RPATH="${RPATH}"/threaded-atlas \
-			ptshared || die "failed to build threaded shared libraries"
-	fi
-}
-
-src_test() {
-	# make check does not work because
-	# we don't build lapack libs
-	for i in F77 C; do
-		einfo "Testing ${i} interface"
-		cd "${BLD_DIR}"/interfaces/blas/${i}/testing
-		make sanity_test || die "emake tests for ${i} failed"
-		if [[ -d "${BLD_DIR}"/gentoo/libptf77blas.a ]]; then
-			make ptsanity_test || die "emake tests threaded for ${i}failed"
-		fi
-	done
-	echo "Timing ATLAS"
-	cd "${BLD_DIR}"
-	emake time || die "emake time failed"
-}
-
-src_install () {
-	dodir "${RPATH}"/atlas
-	cd "${BLD_DIR}"/gentoo/libs
-	cp -P libatlas* "${D}/${DESTTREE}"/$(get_libdir) \
-		|| die "Failed to install libatlas"
-
-	# pkgconfig files
-	local extlibs="-lm"
-	local threadlibs
-	[[ ${FORTRANC} == gfortran ]] && extlibs="${extlibs} -lgfortran"
-	[[ ${FORTRANC} == g77 ]] && extlibs="${extlibs} -lg2c"
-	cp "${FILESDIR}"/blas.pc.in blas.pc
-	cp "${FILESDIR}"/cblas.pc.in cblas.pc
-	sed -i \
-		-e "s:@LIBDIR@:$(get_libdir):" \
-		-e "s:@PV@:${PV}:" \
-		-e "s:@EXTLIBS@:${extlibs}:g" \
-		-e "s:@THREADLIBS@:${threadlibs}:g" \
-		*blas.pc || die "sed *blas.pc failed"
-
-	cp -P *blas* "${D}/${RPATH}"/atlas \
-		|| die "Failed to install blas/cblas"
-
-	ESELECT_PROF=atlas
-	eselect blas add $(get_libdir) "${FILESDIR}"/eselect.blas.atlas ${ESELECT_PROF}
-	eselect cblas add $(get_libdir) "${FILESDIR}"/eselect.cblas.atlas ${ESELECT_PROF}
-
-	if [[ -d "${BLD_DIR}"/gentoo/threaded-libs ]];	then
-		dodir "${RPATH}"/threaded-atlas
-		cd "${BLD_DIR}"/gentoo/threaded-libs
-
-		# pkgconfig files
-		cp "${FILESDIR}"/blas.pc.in blas.pc
-		cp "${FILESDIR}"/cblas.pc.in cblas.pc
-		threadlibs="-lpthread"
-		sed -i \
-			-e "s:@LIBDIR@:$(get_libdir):" \
-			-e "s:@PV@:${PV}:" \
-			-e "s:@EXTLIBS@:${extlibs}:g" \
-			-e "s:@THREADLIBS@:${threadlibs}:g" \
-			*blas.pc || die "sed *blas.pc failed"
-
-		cp -P * "${D}/${RPATH}"/threaded-atlas \
-			|| die "Failed to install threaded atlas"
-		ESELECT_PROF=atlas-threads
-
-		eselect blas add $(get_libdir) "${FILESDIR}"/eselect.blas.threaded-atlas ${ESELECT_PROF}
-		eselect cblas add $(get_libdir) "${FILESDIR}"/eselect.cblas.threaded-atlas ${ESELECT_PROF}
-	fi
-
-	insinto "${DESTTREE}"/include/atlas
-	doins \
-		"${S}"/include/cblas.h \
-		"${S}"/include/atlas_misc.h \
-		"${S}"/include/atlas_enum.h \
-		|| die "failed to install headers"
-
-	# These headers contain the architecture-specific
-	# optimizations determined by ATLAS. The atlas-lapack build
-	# is much shorter if they are available, so save them:
-	doins "${BLD_DIR}"/include/*.h \
-		|| die "failed to install timing headers"
-
-	# some docs
-	cd "${S}"/doc
-	dodoc INDEX.txt AtlasCredits.txt ChangeLog || die "dodoc failed"
-	# atlas specific doc (blas generic docs installed by blas-docs)
-	if use doc; then
-		insinto /usr/share/doc/${PF}
-		doins atlas*pdf cblasqref.pdf || die "doins docs failed"
-	fi
-}
-
-pkg_postinst() {
-	for p in blas cblas; do
-		local current_p=$(eselect ${p} show | cut -d' ' -f2)
-		# this snippet works around the eselect bug #189942 and makes
-		# sure that users upgrading from a previous blas-atlas
-		# version pick up the new pkg-config files
-		if [[ ${current_p} == ${ESELECT_PROF} \
-			  || ${current_p} == "threaded-atlas" \
-			  || -z ${current_p} ]]; then
-			local configfile="${ROOT}"/etc/env.d/${p}/$(get_libdir)/config
-			[[ -e ${configfile} ]] && rm -f ${configfile}
-			eselect ${p} set ${ESELECT_PROF}
-			elog "${p} has been eselected to ${ESELECT_PROF}"
-		else
-			elog "Current eselected ${p} is ${current_p}"
-			elog "To use the ${p} ${ESELECT_PROF} implementation, you have to issue (as root):"
-			elog "\t eselect ${p} set ${ESELECT_PROF}"
-		fi
-	done
-}
diff --git a/sci-libs/blas-atlas/blas-atlas-3.8.1-r1.ebuild b/sci-libs/blas-atlas/blas-atlas-3.9.0.ebuild
index f8b38b1f4d26..6029a1c0ebf9 100644
--- a/sci-libs/blas-atlas/blas-atlas-3.8.1-r1.ebuild
+++ b/sci-libs/blas-atlas/blas-atlas-3.9.0.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/blas-atlas/blas-atlas-3.8.1-r1.ebuild,v 1.1 2008/06/06 22:35:16 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/blas-atlas/blas-atlas-3.9.0.ebuild,v 1.1 2008/07/21 13:42:28 markusle Exp $
 
 inherit eutils toolchain-funcs fortran multilib
 
-PATCH_V="3.7.39"
+PATCH_V="3.9.0"
 
 DESCRIPTION="Automatically Tuned Linear Algebra Software BLAS implementation"
 HOMEPAGE="http://math-atlas.sourceforge.net/"
@@ -43,7 +43,7 @@ pkg_setup() {
 	ewarn "performance of the resulting libraries will be degraded"
 	ewarn "considerably."
 	echo
-	ewarn "For users of <=gcc-4.1.1 only:"
+	ewarn "For users of <=gcc-4.1 only:"
 	ewarn "If you experience failing SANITY tests during"
 	ewarn "atlas' compile please try passing -mfpmath=387; this"
 	ewarn "option might also result in much better performance"
@@ -60,8 +60,7 @@ src_unpack() {
 	epatch "${DISTDIR}"/${MY_PN}-${PATCH_V}-shared-libs.patch.bz2
 	epatch "${FILESDIR}"/${MY_PN}-asm-gentoo.patch
 	epatch "${FILESDIR}"/${MY_PN}-${PATCH_V}-decl-fix.patch
-	epatch "${FILESDIR}"/${P}-gemm-fix.patch
-	epatch "${FILESDIR}"/${P}-gemm-perf-fix.patch
+	epatch "${FILESDIR}"/${MY_PN}-${PV}-upstream-fixes.patch
 
 	BLD_DIR="${S}"/gentoo-build
 	mkdir "${BLD_DIR}" || die "failed to generate build directory"
@@ -77,13 +76,22 @@ src_unpack() {
 		archselect="-b 32"
 	fi
 
+	# unfortunately, atlas-3.9.0 chokes when passed
+	# x86_64-pc-linux-gnu-gcc and friends instead of
+	# plain gcc. Hence, we'll have to workaround this
+	# until it is fixed by upstream
+	local c_compiler=$(tc-getCC)
+	if [[ "${c_compiler}" == *gcc* ]]; then
+		c_compiler="gcc"
+	fi
+
 	../configure \
-		--cc="$(tc-getCC)" \
+		--cc="${c_compiler}" \
 		--cflags="${CFLAGS}" \
 		--prefix="${D}/${DESTTREE}" \
 		--libdir="${D}/${DESTTREE}"/$(get_libdir)/atlas \
 		--incdir="${D}/${DESTTREE}"/include \
-		-C ac "$(tc-getCC)" -F ac "${CFLAGS}" \
+		-C ac "${c_compiler}" -F ac "${CFLAGS}" \
 		-C if ${FORTRANC} -F if "${FFLAGS:-'-O2'}" \
 		-Ss pmake "\$(MAKE) ${MAKEOPTS}" \
 		-Si cputhrchk 0 ${archselect} \
diff --git a/sci-libs/blas-atlas/files/atlas-3.9.0-decl-fix.patch b/sci-libs/blas-atlas/files/atlas-3.9.0-decl-fix.patch
new file mode 100644
index 000000000000..1ec44fcf7884
--- /dev/null
+++ b/sci-libs/blas-atlas/files/atlas-3.9.0-decl-fix.patch
@@ -0,0 +1,71 @@
+diff -Naur ATLAS/bin/atlas_waitfile.c ATLAS-new/bin/atlas_waitfile.c
+--- ATLAS/bin/atlas_waitfile.c	2007-10-07 09:48:56.000000000 -0400
++++ ATLAS-new/bin/atlas_waitfile.c	2007-10-09 10:57:13.000000000 -0400
+@@ -1,3 +1,4 @@
++#include <stdlib.h>
+ #include <stdio.h>
+ 
+ void PrintUsage(char *nam)
+diff -Naur ATLAS/src/auxil/ATL_buildinfo.c ATLAS-new/src/auxil/ATL_buildinfo.c
+--- ATLAS/src/auxil/ATL_buildinfo.c	2007-10-07 09:49:03.000000000 -0400
++++ ATLAS-new/src/auxil/ATL_buildinfo.c	2007-10-09 10:56:10.000000000 -0400
+@@ -1,3 +1,4 @@
++#include <stdio.h>
+ #include "atlas_buildinfo.h"
+ #include "atlas_cacheedge.h"
+ 
+diff -Naur ATLAS/tune/blas/gemm/usercomb.c ATLAS-new/tune/blas/gemm/usercomb.c
+--- ATLAS/tune/blas/gemm/usercomb.c	2007-10-07 09:49:39.000000000 -0400
++++ ATLAS-new/tune/blas/gemm/usercomb.c	2007-10-09 10:58:53.000000000 -0400
+@@ -29,6 +29,7 @@
+  */
+ #include <stdio.h>
+ #include <stdlib.h>
++#include <string.h>
+ #include <assert.h>
+ 
+ int LineIsCont(char *ln)
+diff -Naur ATLAS/tune/blas/gemv/gemvtune.c ATLAS-new/tune/blas/gemv/gemvtune.c
+--- ATLAS/tune/blas/gemv/gemvtune.c	2007-10-07 09:49:39.000000000 -0400
++++ ATLAS-new/tune/blas/gemv/gemvtune.c	2007-10-09 11:00:29.000000000 -0400
+@@ -36,6 +36,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <assert.h>
++#include <string.h>
+ 
+ struct FA_allocs
+ {
+diff -Naur ATLAS/tune/blas/gemv/mvsearch.c ATLAS-new/tune/blas/gemv/mvsearch.c
+--- ATLAS/tune/blas/gemv/mvsearch.c	2007-10-07 09:49:39.000000000 -0400
++++ ATLAS-new/tune/blas/gemv/mvsearch.c	2007-10-09 10:59:56.000000000 -0400
+@@ -32,6 +32,7 @@
+ #include <stdlib.h>
+ #include <ctype.h>
+ #include <assert.h>
++#include <string.h>
+ #include "atlas_fopen.h"
+ 
+ #define ATL_MVIsMM(iflag_) ( ((iflag_) | 8) == (iflag_) )
+diff -Naur ATLAS/tune/blas/ger/ger1tune.c ATLAS-new/tune/blas/ger/ger1tune.c
+--- ATLAS/tune/blas/ger/ger1tune.c	2007-10-07 09:49:39.000000000 -0400
++++ ATLAS-new/tune/blas/ger/ger1tune.c	2007-10-09 11:01:15.000000000 -0400
+@@ -36,6 +36,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <assert.h>
++#include <string.h>
+ 
+ struct FA_allocs
+ {
+diff -Naur ATLAS/tune/blas/ger/r1search.c ATLAS-new/tune/blas/ger/r1search.c
+--- ATLAS/tune/blas/ger/r1search.c	2007-10-07 09:49:39.000000000 -0400
++++ ATLAS-new/tune/blas/ger/r1search.c	2007-10-09 11:00:58.000000000 -0400
+@@ -31,6 +31,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <ctype.h>
++#include <string.h>
+ #include <assert.h>
+ #include "atlas_fopen.h"
+ 
diff --git a/sci-libs/blas-atlas/files/atlas-3.9.0-upstream-fixes.patch b/sci-libs/blas-atlas/files/atlas-3.9.0-upstream-fixes.patch
new file mode 100644
index 000000000000..a0e548f10d73
--- /dev/null
+++ b/sci-libs/blas-atlas/files/atlas-3.9.0-upstream-fixes.patch
@@ -0,0 +1,21 @@
+diff -Naur ATLAS/src/auxil/ATL_ptflushcache.c ATLAS.new/src/auxil/ATL_ptflushcache.c
+--- ATLAS/src/auxil/ATL_ptflushcache.c	2008-07-17 21:24:53.000000000 -0400
++++ ATLAS.new/src/auxil/ATL_ptflushcache.c	2008-07-18 18:40:37.000000000 -0400
+@@ -88,7 +88,7 @@
+      }
+      fct[i].N = N;
+      fct[i].dp = cache+i*N;
+-     ATL_ptCF(fct+i);
++     ATL_ptCF(fct+i-1);
+      dret = fct[i].dret;
+      for (i=0; i < ATL_NTHREADS-1; i++)
+      {
+@@ -133,7 +133,7 @@
+    {
+       ATL_assert(!pthread_create(tp+i, &attr, ATL_ptCLF, fp));
+    }
+-   ATL_FlushAreaByCL(fp);   /* should be redundant, do to be safe */
++   ATL_FlushAreasByCL(fp);   /* should be redundant, do to be safe */
+    for (i=0; i < ATL_NTHREADS; i++)
+    {
+       ATL_assert(!pthread_join(tp[i], NULL));
diff --git a/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-fix.patch b/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-fix.patch
deleted file mode 100644
index 9409f90c8a07..000000000000
--- a/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-fix.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff -Naur ATLAS/src/blas/gemm/ATL_cmmJITcp.c ATLAS.new/src/blas/gemm/ATL_cmmJITcp.c
---- ATLAS/src/blas/gemm/ATL_cmmJITcp.c	2008-02-22 11:38:58.000000000 -0500
-+++ ATLAS.new/src/blas/gemm/ATL_cmmJITcp.c	2008-05-23 18:07:34.000000000 -0400
-@@ -264,8 +264,11 @@
-       NBmm1 = Mjoin(PATLU,pMBmm_b1);
-       NBmmX = Mjoin(PATLU,pMBmm_bX);
-    }
--   else  /* two or more dim < NB, requires generated cleanup */
--      NBmm0 = NBmm1 = NBmmX = Mjoin(PATLU,pKBmm);
-+   else 
-+   { 
-+     NBmm0 = NBmm1 = NBmmX = Mjoin(PATLU,pKBmm);
-+     if (SCALAR_IS_ZERO(beta)) Mjoin(PATL,gezero)(M, N, C, ldc); 
-+   }
-    if (nblk)
-    {
-       if (B)
diff --git a/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-perf-fix.patch b/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-perf-fix.patch
deleted file mode 100644
index 8afa7c7692c9..000000000000
--- a/sci-libs/blas-atlas/files/blas-atlas-3.8.1-gemm-perf-fix.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff -Naur ATLAS/src/blas/gemm/ATL_gemmXX.c ATLAS.new/src/blas/gemm/ATL_gemmXX.c
---- ATLAS/src/blas/gemm/ATL_gemmXX.c	2008-02-22 11:38:58.000000000 -0500
-+++ ATLAS.new/src/blas/gemm/ATL_gemmXX.c	2008-06-06 16:32:31.000000000 -0400
-@@ -188,10 +188,6 @@
-             mm2 = mm1;
-             mm1 = Mjoin(PATL,mmJITcp);
-          }
--         {
--            mm2 = mm1;
--            mm1 = Mjoin(PATL,mmJITcp);
--         }
-    #endif
-    #ifdef SMALLK_MM
-       if (ATL_OOM Mjoin(PATL,mmJKI)(ETA, ETB, M, N, K, alpha, A, lda, B, ldb,