Drop package masked for removal.

12 files changed, 0 insertions, 1262 deletions

diff --git a/sci-mathematics/Macaulay2/ChangeLog b/sci-mathematics/Macaulay2/ChangeLog
deleted file mode 100644
index 6190b424c8e4..000000000000
--- a/sci-mathematics/Macaulay2/ChangeLog
+++ /dev/null
@@ -1,52 +0,0 @@
-# ChangeLog for sci-mathematics/Macaulay2
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/Macaulay2/ChangeLog,v 1.17 2008/01/16 11:28:47 markusle Exp $
-
-  16 Jan 2008; Markus Dittrich <markusle@gentoo.org> Macaulay2-1.0.ebuild:
-  Fixed problem with the version detection of boehm-gc (bug #206057).
-
-*Macaulay2-1.0 (06 Jan 2008)
-
-  06 Jan 2008; Markus Dittrich <markusle@gentoo.org>
-  -files/gentoo-libfac-0.3.2.include.diff,
-  +files/Macaulay2-1.0-example-fix.patch, 
-  -files/gentoo-factory-1.3b.diff,
-  -Macaulay2-0.9.2.ebuild, -Macaulay2-0.9.95.ebuild, 
-  +Macaulay2-1.0.ebuild:
-  Version bump and removed old versions. The tarball for
-  Macaulay2-1.0 was extracted from upstream's svn release
-  branch since no sources were posted.
-
-  31 May 2007; Markus Dittrich <markusle@gentoo.org>
-  Macaulay2-0.9.95-r2.ebuild:
-  More cleanup.
-
-*Macaulay2-0.9.95-r2 (30 May 2007)
-
-  30 May 2007; Markus Dittrich <markusle@gentoo.org>
-  +Macaulay2-0.9.95-r2.ebuild:
-  This revision includes a cleaned up ebuild which now properly
-  builds on amd64 (see bug #179700).
-
-  25 May 2007; Markus Dittrich <markusle@gentoo.org>
-  Macaulay2-0.9.95-r1.ebuild:
-  Changed ebuild to adhere to multilib (see bug #179700).
-
-  14 Mar 2007; Christian Faulhammer <opfer@gentoo.org>
-  Macaulay2-0.9.95-r1.ebuild:
-  stable x86, bug 196576
-
-  06 Mar 2007; Christian Faulhammer <opfer@gentoo.org>
-  Macaulay2-0.9.95-r1.ebuild:
-  no, pkg_postinstall does not exist, so change it to pkg_postinst
-
-  06 Mar 2007; Christian Faulhammer <opfer@gentoo.org>
-  Macaulay2-0.9.95-r1.ebuild:
-  correct site file handling
-
-*Macaulay2-0.9.95-r1 (06 Mar 2007)
-
-  06 Mar 2007; Christian Faulhammer <opfer@gentoo.org>
-  +files/70Macaulay2-gentoo.el, +Macaulay2-0.9.95-r1.ebuild:
-  revision bump, enabling emacs when requested; added some quotes
-
diff --git a/sci-mathematics/Macaulay2/Macaulay2-0.9.95-r1.ebuild b/sci-mathematics/Macaulay2/Macaulay2-0.9.95-r1.ebuild
deleted file mode 100644
index e3e5386b3ca3..000000000000
--- a/sci-mathematics/Macaulay2/Macaulay2-0.9.95-r1.ebuild
+++ /dev/null
@@ -1,91 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/Macaulay2/Macaulay2-0.9.95-r1.ebuild,v 1.7 2008/01/06 15:51:17 markusle Exp $
-
-inherit elisp-common eutils flag-o-matic toolchain-funcs autotools
-
-IUSE="emacs"
-
-DESCRIPTION="research tool for commutative algebra and algebraic geometry"
-SRC_URI="http://www.math.uiuc.edu/Macaulay2/Downloads/${P}-src.tar.gz
-	ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Factory/factory-3-0-2.tar.gz \
-	ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/libfac-3-0-2.tar.gz"
-
-HOMEPAGE="http://www.math.uiuc.edu/Macaulay2/"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="x86"
-
-DEPEND="sys-libs/gdbm
-	dev-libs/gmp
-	dev-libs/ntl
-	dev-libs/boehm-gc
-	virtual/blas
-	virtual/lapack
-	dev-util/ctags
-	sys-libs/ncurses
-	emacs? ( virtual/emacs )"
-
-SITEFILE=70Macaulay2-gentoo.el
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${P}-etags-gentoo.patch
-	epatch "${FILESDIR}"/${P}-cpp-fix.patch
-	epatch "${FILESDIR}"/${P}-test-fix.patch
-}
-
-src_compile() {
-	cd "${WORKDIR}/factory"
-	econf --enable-NTL --prefix="${WORKDIR}" || \
-		die "failed to configure factory"
-	emake || die "failed to build factory"
-	make install || die "failed to install factory"
-
-	cd "${WORKDIR}/libfac"
-	CPPFLAGS="-I${WORKDIR}/include" ./configure --with-NOSTREAMIO \
-		--prefix="${WORKDIR}" || die "failed to configure libfac"
-	make DEFS=-DHAVE_SINGULAR_ERROR || die "failed to build libfac"
-	make install || die "failed to install libfac"
-
-	CXXFLAGS="${CXXFLAGS} -Wno-deprecated"
-	cd "${S}"
-	sed -e "/^docm2RelDir/s:Macaulay2:${P}:" \
-		-i include/config.Makefile.in || \
-		die "failed to fix makefile"
-	make && CPPFLAGS="-I/usr/include/gc -I${WORKDIR}/include" \
-		LDFLAGS="-L${WORKDIR}/$(get_libdir)" \
-		./configure --prefix="${D}/usr" --disable-encap \
-		--with-lapacklibs="-llapack -lblas" || \
-		die "failed to configure Macaulay"
-	# fix install paths
-	make || die "failed to build Macaulay"
-}
-
-src_test() {
-	make check || die "tests failed"
-}
-
-src_install () {
-	make install || die "install failed"
-
-	# nothing in here, get rid of it
-	rm -fr "${D}"/usr/$(get_libdir) || \
-		die "failed to remove empty /usr/lib"
-
-	use emacs && elisp-site-file-install "${FILESDIR}/${SITEFILE}"
-}
-
-pkg_postinst() {
-	if use emacs; then
-		elisp-site-regen
-		elog "If you want to set a hot key for Macaulay2 in Emacs add a line similar to"
-		elog "(global-set-key [ f12 ] 'M2)"
-		elog "in order to set it to F12 (or choose a different one."
-	fi
-}
-pkg_postrm() {
-	use emacs && elisp-site-regen
-}
diff --git a/sci-mathematics/Macaulay2/Macaulay2-0.9.95-r2.ebuild b/sci-mathematics/Macaulay2/Macaulay2-0.9.95-r2.ebuild
deleted file mode 100644
index aff91f51d1b4..000000000000
--- a/sci-mathematics/Macaulay2/Macaulay2-0.9.95-r2.ebuild
+++ /dev/null
@@ -1,91 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/Macaulay2/Macaulay2-0.9.95-r2.ebuild,v 1.3 2008/01/06 15:51:17 markusle Exp $
-
-inherit elisp-common eutils flag-o-matic toolchain-funcs autotools
-
-IUSE="emacs"
-
-DESCRIPTION="research tool for commutative algebra and algebraic geometry"
-SRC_URI="http://www.math.uiuc.edu/Macaulay2/Downloads/${P}-src.tar.gz
-	ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Factory/factory-3-0-2.tar.gz \
-	ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/libfac-3-0-2.tar.gz"
-
-HOMEPAGE="http://www.math.uiuc.edu/Macaulay2/"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~x86"
-
-DEPEND="sys-libs/gdbm
-	dev-libs/gmp
-	dev-libs/ntl
-	dev-libs/boehm-gc
-	virtual/blas
-	virtual/lapack
-	dev-util/ctags
-	sys-libs/ncurses
-	emacs? ( virtual/emacs )"
-
-SITEFILE=70Macaulay2-gentoo.el
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${P}-etags-gentoo.patch
-	epatch "${FILESDIR}"/${P}-cpp-fix.patch
-	epatch "${FILESDIR}"/${P}-test-fix.patch
-}
-
-src_compile() {
-	cd "${WORKDIR}/factory"
-	econf --enable-NTL --prefix="${WORKDIR}" || \
-		die "failed to configure factory"
-	emake || die "failed to build factory"
-	make install || die "failed to install factory"
-
-	cd "${WORKDIR}/libfac"
-	CPPFLAGS="-I${WORKDIR}/include" econf --with-NOSTREAMIO \
-		--prefix="${WORKDIR}" || die "failed to configure libfac"
-	emake DEFS=-DHAVE_SINGULAR_ERROR || die "failed to build libfac"
-	make install || die "failed to install libfac"
-
-	cd "${S}"
-	sed -e "/^docm2RelDir/s:Macaulay2:${P}:" \
-		-i include/config.Makefile.in || \
-		die "failed to fix makefile"
-
-	CXXFLAGS="${CXXFLAGS} -Wno-deprecated"
-	append-ldflags "-L${WORKDIR}/$(get_libdir)"
-	emake -j1 && CPPFLAGS="-I/usr/include/gc -I${WORKDIR}/include" \
-		./configure --prefix="${D}/usr" --disable-encap \
-		--with-lapacklibs="-llapack -lblas" || \
-		die "failed to configure Macaulay"
-	emake -j1 || die "failed to build Macaulay"
-}
-
-src_test() {
-	make check || die "tests failed"
-}
-
-src_install () {
-	make install || die "install failed"
-
-	# nothing in here, get rid of it
-	rm -fr "${D}"/usr/$(get_libdir) || \
-		die "failed to remove empty /usr/lib"
-
-	use emacs && elisp-site-file-install "${FILESDIR}/${SITEFILE}"
-}
-
-pkg_postinst() {
-	if use emacs; then
-		elisp-site-regen
-		elog "If you want to set a hot key for Macaulay2 in Emacs add a line similar to"
-		elog "(global-set-key [ f12 ] 'M2)"
-		elog "in order to set it to F12 (or choose a different one."
-	fi
-}
-pkg_postrm() {
-	use emacs && elisp-site-regen
-}
diff --git a/sci-mathematics/Macaulay2/Macaulay2-1.0.ebuild b/sci-mathematics/Macaulay2/Macaulay2-1.0.ebuild
deleted file mode 100644
index bf8714ad0163..000000000000
--- a/sci-mathematics/Macaulay2/Macaulay2-1.0.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/Macaulay2/Macaulay2-1.0.ebuild,v 1.3 2008/01/16 11:28:47 markusle Exp $
-
-inherit elisp-common eutils flag-o-matic toolchain-funcs autotools
-
-IUSE="emacs"
-
-DESCRIPTION="research tool for commutative algebra and algebraic geometry"
-SRC_URI="mirror://gentoo/${P}-src.tar.bz2
-	ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Factory/factory-3-0-3.tar.gz \
-	ftp://www.mathematik.uni-kl.de/pub/Math/Singular/Libfac/libfac-3-0-3.tar.gz"
-
-HOMEPAGE="http://www.math.uiuc.edu/Macaulay2/"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~x86 ~amd64"
-
-DEPEND="sys-libs/gdbm
-	dev-libs/gmp
-	dev-libs/ntl
-	dev-libs/boehm-gc
-	virtual/blas
-	virtual/lapack
-	dev-util/ctags
-	sys-libs/ncurses
-	emacs? ( virtual/emacs )"
-
-SITEFILE=70Macaulay2-gentoo.el
-
-pkg_setup() {
-
-	# boehm-gc currently is broken with USE='threads'
-	# (see bug #195335) causing Macaulay2 to fail
-	if built_with_use "dev-libs/boehm-gc" "threads" \
-		&& has_version "=dev-libs/boehm-gc-7*"; then
-		echo
-		eerror "dev-libs/boehm-gc-7* with USE=\"threads\" is"
-		eerror "currently broken (see bug #195335) causing"
-		eerror "Macaulay to fail building. Please re-emerge"
-		eerror "dev-libs/boehm-gc-7* with USE=\"-threads\"!"
-		die "boehm-gc setup error"
-		echo
-	fi
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${P}-example-fix.patch
-
-	sed -e "s:\$docdirtail/${PN}:\$docdirtail/${P}:" \
-		-i configure.ac \
-		|| die "Failed to fix doc install directory."
-}
-
-src_compile() {
-	cd "${WORKDIR}/factory-3.0.3"
-	econf --enable-NTL --prefix="${WORKDIR}" || \
-		die "failed to configure factory"
-	emake || die "failed to build factory"
-	make install || die "failed to install factory"
-
-	cd "${WORKDIR}/libfac"
-	CPPFLAGS="-I${WORKDIR}/include" econf --with-NOSTREAMIO \
-		--prefix="${WORKDIR}" || die "failed to configure libfac"
-	emake || die "failed to build libfac"
-	make install || die "failed to install libfac"
-
-	cd "${S}"
-	sed -e "/^docm2RelDir/s:Macaulay2:${P}:" \
-		-i include/config.Makefile.in \
-		|| die "failed to fix makefile"
-
-	CXXFLAGS="${CXXFLAGS} -Wno-deprecated"
-	append-ldflags "-L${WORKDIR}/$(get_libdir)"
-	emake -j1 && CPPFLAGS="-I/usr/include/gc -I${WORKDIR}/include" \
-		./configure --prefix="${D}/usr" --disable-encap \
-		--with-lapacklibs="$(pkg-config lapack --libs)" \
-		|| die "failed to configure Macaulay"
-
-	emake -j1 || die "failed to build Macaulay"
-}
-
-# checks are currently very broken
-#src_test() {
-#	cd "${S}"
-#	make check || die "tests failed"
-#}
-
-src_install () {
-	make install || die "install failed"
-
-	# nothing useful in here, get rid of it
-	# NOTE: Macaulay installs into lib even on amd64 hence don't
-	# replace lib with $(get_libdir) below!
-	rm -fr "${D}"/usr/lib \
-		|| die "failed to remove empty /usr/lib"
-
-	use emacs && elisp-site-file-install "${FILESDIR}/${SITEFILE}"
-}
-
-pkg_postinst() {
-	if use emacs; then
-		elisp-site-regen
-		elog "If you want to set a hot key for Macaulay2 in Emacs add a line similar to"
-		elog "(global-set-key [ f12 ] 'M2)"
-		elog "in order to set it to F12 (or choose a different one."
-	fi
-}
-pkg_postrm() {
-	use emacs && elisp-site-regen
-}
diff --git a/sci-mathematics/Macaulay2/Manifest b/sci-mathematics/Macaulay2/Manifest
deleted file mode 100644
index aaadf1928116..000000000000
--- a/sci-mathematics/Macaulay2/Manifest
+++ /dev/null
@@ -1,17 +0,0 @@
-AUX 70Macaulay2-gentoo.el 57 RMD160 07b266ed45b28e5ebe7ee8e46ea73571a401dea3 SHA1 877ac4fd55e2b42922212bce587c2aa68e010bf2 SHA256 427d14300a958b0970837191006641f5e1c9952cf3492c640bc1e8c223b221f5
-AUX Macaulay2-0.9.95-cpp-fix.patch 519 RMD160 0b06c11bb534ae8b1367c1339a9515d514d619b8 SHA1 4d238ea61a64374927e5908595078ade568df047 SHA256 9a3a2e4bc96559381f2f96dc161a55cdb9a7237d78a4cf8f37c62d58c96fcee2
-AUX Macaulay2-0.9.95-etags-gentoo.patch 3807 RMD160 384eb18029577238343507430a6191ce6bd82cbe SHA1 b68f32567b72bd926fd6de97fa5ad10736b1a362 SHA256 5b2eb9d87159fce19ad21551c66c92c55749bebf64760621e9fdbe77daa8fd0e
-AUX Macaulay2-0.9.95-test-fix.patch 16184 RMD160 35cc11256a4fad4d0f512d60b90beb2a36263020 SHA1 a9d093921fb9bfa6f0031e45c7da3e25f4167905 SHA256 5926b4c5e96a8b5a90f409aef588ffea79cab8ff752a5d23acf233ae15269195
-AUX Macaulay2-1.0-example-fix.patch 4914 RMD160 a19e96d54fc599d3a84854e8e85d7f708c9a51be SHA1 c094aecd7e21ff3cab3bf5680bceb23f6c894813 SHA256 23233f37c4edc3ab66c7cb8cd732cc25a650099eaa5fda43e06e81b1b4a65c15
-AUX gentoo-Macaulay2-0.9.2.diff 10410 RMD160 0e22513f9beca1aae5e0061e6767c0203096db2f SHA1 13b1ff7ed39884fcd16e671b30084783774b1a96 SHA256 11982820a82d78b0721971dcae2e05090b6c0178e9faf4f0b1536227ed6ceca7
-DIST Macaulay2-0.9.95-src.tar.gz 2875836 RMD160 f3c5ad889e89d238ca3ede40e692bc42744861a8 SHA1 dbcbc93b0d3f0a43ad947dc704d7ae7427a7c8d2 SHA256 3fd4698d82de76a8356d24dfdba2775794231b5723ee3fda232ce2f0d1e6360a
-DIST Macaulay2-1.0-src.tar.bz2 4570637 RMD160 9662a67d16a604566b4385e2e45387de610f7074 SHA1 8318976c201bbe5f9e34d1e8a7c2d0a45dc375a9 SHA256 19f537b41d361edcd4d328da4d79d047c95c627e5711180424948c40b9ea14aa
-DIST factory-3-0-2.tar.gz 503712 RMD160 3cfaa7e438af75fb1c00501099c0d6c88fbfdd8b SHA1 5cce5050fe559a18a076709bf220bddb16914414 SHA256 463a29232f9e187014bd53bb726cf1628f929ee830fa63d445dcc9a45403d8ed
-DIST factory-3-0-3.tar.gz 376442 RMD160 ddce30badddbafd74ce9679424d4d092eb08ce88 SHA1 0989d80972dd58b792fce5c1327eb33e5fca979a SHA256 1baac37529b4c24a6b05bb96fc44773daea56892881836d1537d7f756ebfb05b
-DIST libfac-3-0-2.tar.gz 87369 RMD160 847103ae3fcc870188630028965086c3933a2009 SHA1 fbe2c51559dc439022d4a05afc70691e69210fdc SHA256 3fae688d7471e137834e9f89e5677e2ded4d578942b54ce7efa536817799fa74
-DIST libfac-3-0-3.tar.gz 90384 RMD160 92b8da7365014555104280151821a3a203bd0158 SHA1 19a23900f01539294aab197546cce6fade8439f9 SHA256 a0bb87cecd64f26045d11ba57b56abf1dd8b32bfd5ec8aa83b616e8f4a4f145a
-EBUILD Macaulay2-0.9.95-r1.ebuild 2595 RMD160 93162a178674b996b2f12106820b05fa0d80a457 SHA1 f3c98de4841af03e607fbba40eed9bda5cd624fd SHA256 c78af0fbeeca81fade77cda8e173d15674d58cb0b04a4fa0fc2d35cb0782b712
-EBUILD Macaulay2-0.9.95-r2.ebuild 2585 RMD160 0e3f5ae790ace6765f39f6e5478f2d2df9616e14 SHA1 91c2219176f2f33fbe963fa159289aff92fa80c0 SHA256 cc1f3285af68621cf74576f5537532be967ce0c48fb23e398973514be55538b7
-EBUILD Macaulay2-1.0.ebuild 3218 RMD160 dbb4fc0202ff9b4831260c683a99742745466a78 SHA1 414da1c0219cc8636e7ea4e24a517ea7049910fc SHA256 c72c37954589c3a62c52f4a53c2e42d74880d2433cedd97c53ec8724a204c132
-MISC ChangeLog 1872 RMD160 5d84080e0d92032a6191fcecd93af0f4c7efe755 SHA1 2aa1aa3b5e47cdbda19f703a5b19f1c6d1f2dafe SHA256 5b212411431af29644a9407fbac646266a9f1d8eae2884e0e33cd007b4025c22
-MISC metadata.xml 467 RMD160 55a9d3716d9efee869202e289dbae72403a6dd1b SHA1 0e5160029c89907b18624b95285472007542f52b SHA256 3f550d75544118b43295756f3246bc13f7f7505ae1c864bbad1eab6c98bc95d4
diff --git a/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el b/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el
deleted file mode 100644
index 84c0a8c8c3d0..000000000000
--- a/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el
+++ /dev/null
@@ -1,3 +0,0 @@
-;; sci-mathematics/Macaulay2 init file
-
-(load "M2-init")
diff --git a/sci-mathematics/Macaulay2/files/Macaulay2-0.9.95-cpp-fix.patch b/sci-mathematics/Macaulay2/files/Macaulay2-0.9.95-cpp-fix.patch
deleted file mode 100644
index 48667771bbb8..000000000000
--- a/sci-mathematics/Macaulay2/files/Macaulay2-0.9.95-cpp-fix.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-diff -Naur Macaulay2-0.9.95.old/Macaulay2/e/comp.hpp Macaulay2-0.9.95/Macaulay2/e/comp.hpp
---- Macaulay2-0.9.95.old/Macaulay2/e/comp.hpp	2007-03-01 09:11:04.000000000 -0500
-+++ Macaulay2-0.9.95/Macaulay2/e/comp.hpp	2007-03-01 09:12:09.000000000 -0500
-@@ -4,7 +4,16 @@
- #define _comp_hpp_
- 
- extern char system_interruptedFlag;
-+
-+#if defined(__cplusplus)
-+extern "C" {
-+#endif
- extern int gbTrace;
-+#if defined(__cplusplus)
-+}
-+#endif
-+
-+
- 
- #include "engine.h"
- /* engine.h includes definitions of the stop conditions
diff --git a/sci-mathematics/Macaulay2/files/Macaulay2-0.9.95-etags-gentoo.patch b/sci-mathematics/Macaulay2/files/Macaulay2-0.9.95-etags-gentoo.patch
deleted file mode 100644
index 47e97185854d..000000000000
--- a/sci-mathematics/Macaulay2/files/Macaulay2-0.9.95-etags-gentoo.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-diff -Naur Macaulay2-0.9.95/Macaulay2/c/Makefile.in Macaulay2-0.9.95-new/Macaulay2/c/Makefile.in
---- Macaulay2-0.9.95/Macaulay2/c/Makefile.in	2006-07-06 11:16:05.000000000 -0400
-+++ Macaulay2-0.9.95-new/Macaulay2/c/Makefile.in	2006-11-11 10:13:07.000000000 -0500
-@@ -30,7 +30,7 @@
- ############################## tags
- all :: tags
- tags : @srcdir@/TAGS
--@srcdir@/TAGS: $(SRCFILES); cd @srcdir@ && etags $(SRCFILES)
-+@srcdir@/TAGS: $(SRCFILES); cd @srcdir@ && exuberant-ctags $(SRCFILES)
- ############################## cleaning
- clean :
- 	rm -f *.o scc1 scc.a grammar.output grammar.tab.h \
-diff -Naur Macaulay2-0.9.95/Macaulay2/d/Makefile.in Macaulay2-0.9.95-new/Macaulay2/d/Makefile.in
---- Macaulay2-0.9.95/Macaulay2/d/Makefile.in	2006-07-15 18:35:12.000000000 -0400
-+++ Macaulay2-0.9.95-new/Macaulay2/d/Makefile.in	2006-11-11 10:13:07.000000000 -0500
-@@ -314,7 +314,7 @@
- tags: @srcdir@/TAGS
- clean::; rm -f TAGS @srcdir@/TAGS
- @srcdir@/TAGS: Makefile $(SRCFILES)
--	cd @srcdir@ && etags $(shell ../util/echoout -r $(SRCFILES))
-+	cd @srcdir@ && exuberant-ctags $(shell ../util/echoout -r $(SRCFILES))
- 
- clean ::; rm -f *.log a.out *.o *.sym *.a *.oo *.sig *.sg *.dep *.dp core gmon.out mapfile restart.tmp
- distclean : clean; rm -f Makefile
-diff -Naur Macaulay2-0.9.95/Macaulay2/dumpdata/Makefile.in Macaulay2-0.9.95-new/Macaulay2/dumpdata/Makefile.in
---- Macaulay2-0.9.95/Macaulay2/dumpdata/Makefile.in	2006-05-30 15:16:42.000000000 -0400
-+++ Macaulay2-0.9.95-new/Macaulay2/dumpdata/Makefile.in	2006-11-11 10:13:07.000000000 -0500
-@@ -14,7 +14,7 @@
- gdb: checkit; gdb checkit
- all:: tags
- tags: @srcdir@/TAGS
--@srcdir@/TAGS: Makefile @srcdir@/*.h @srcdir@/*.c ; cd @srcdir@ && etags *.h *.c
-+@srcdir@/TAGS: Makefile @srcdir@/*.h @srcdir@/*.c ; cd @srcdir@ && exuberant-ctags *.h *.c
- clean::; rm -f *.o checkit core check-data *.a libdump.a
- EXTRAOBJS :=
- # EXTRAOBJS += mmap.o
-diff -Naur Macaulay2-0.9.95/Macaulay2/e/Makefile.in Macaulay2-0.9.95-new/Macaulay2/e/Makefile.in
---- Macaulay2-0.9.95/Macaulay2/e/Makefile.in	2006-06-20 16:26:04.000000000 -0400
-+++ Macaulay2-0.9.95-new/Macaulay2/e/Makefile.in	2006-11-11 10:13:07.000000000 -0500
-@@ -71,7 +71,7 @@
- 		 @srcdir@/linalgGB/*.hpp @srcdir@/linalgGB/*.cpp \
- 		 @srcdir@/f4/*.hpp @srcdir@/f4/*.cpp \
- 		 statuscodes
--	cd @srcdir@ && etags $(patsubst @srcdir@/%, %, $^)
-+	cd @srcdir@ && exuberant-ctags $(patsubst @srcdir@/%, %, $^)
- 
- # the target 'initialize' is used by the Makefile in the parent directory
- initialize all :: $(addsuffix .hpp, $(GENERATED_H))
-diff -Naur Macaulay2-0.9.95/Macaulay2/html-check-links/Makefile.in Macaulay2-0.9.95-new/Macaulay2/html-check-links/Makefile.in
---- Macaulay2-0.9.95/Macaulay2/html-check-links/Makefile.in	2004-04-03 14:43:21.000000000 -0500
-+++ Macaulay2-0.9.95-new/Macaulay2/html-check-links/Makefile.in	2006-11-11 10:13:07.000000000 -0500
-@@ -34,7 +34,7 @@
- ifneq ($(DEPENDS),no)
- include $(CFILES:.c=.dep)
- endif
--TAGS: $(SRC); etags $^
-+TAGS: $(SRC); exuberant-ctags $^
- lex.o : grammar.fixed.c
- clean:; rm -f	*.o html-check-links *.dep y.tab.h lex.yy.c TAGS y.output \
- 		core grammar.c grammar.tab.* lex.c grammar.fixed.* grammar.output
-diff -Naur Macaulay2-0.9.95/Macaulay2/regex/Makefile.in Macaulay2-0.9.95-new/Macaulay2/regex/Makefile.in
---- Macaulay2-0.9.95/Macaulay2/regex/Makefile.in	2005-08-08 14:06:05.000000000 -0400
-+++ Macaulay2-0.9.95-new/Macaulay2/regex/Makefile.in	2006-11-11 10:13:07.000000000 -0500
-@@ -33,7 +33,7 @@
- 	@ echo " ** creating $@ from $<"
- 	@ $(CC)  -MM $(CPPFLAGS) $< >$*-tmp.dep && <$*-tmp.dep sed 's/\($*\)\.o[ :]*/\1.o $@ : /' >$@ && rm $*-tmp.dep
- 
--@srcdir@/TAGS: $(CFILES); cd @srcdir@ && etags $(CFILES)
-+@srcdir@/TAGS: $(CFILES); cd @srcdir@ && exuberant-ctags $(CFILES)
- DEPENDS = yes
- ifeq "$(DEPENDS)" "yes"
- include $(CFILES:.c=.dep) $(CCFILES:.cpp=.dep)
diff --git a/sci-mathematics/Macaulay2/files/Macaulay2-0.9.95-test-fix.patch b/sci-mathematics/Macaulay2/files/Macaulay2-0.9.95-test-fix.patch
deleted file mode 100644
index d372090769c5..000000000000
--- a/sci-mathematics/Macaulay2/files/Macaulay2-0.9.95-test-fix.patch
+++ /dev/null
@@ -1,436 +0,0 @@
-diff -Naur Macaulay2-0.9.95/Macaulay2/dumpdata/Makefile.in Macaulay2-0.9.95.new/Macaulay2/dumpdata/Makefile.in
---- Macaulay2-0.9.95/Macaulay2/dumpdata/Makefile.in	2006-05-30 15:16:42.000000000 -0400
-+++ Macaulay2-0.9.95.new/Macaulay2/dumpdata/Makefile.in	2007-03-02 10:25:10.000000000 -0500
-@@ -28,7 +28,7 @@
- libdump.a: libdump.a(file.o warning.o map.o dumpdata.o maputil.o printmaps.o $(EXTRAOBJS)); ranlib libdump.a
- all:: libdump.a
- check:: checkit
--	./checkit dump "hi there" && ./checkit load "look!"
-+#	./checkit dump "hi there" && ./checkit load "look!"
- #	LD_DEBUG=$(LD_DEBUG) LOADDATA_DEBUG=true; export LD_DEBUG LOADDATA_DEBUG; set -x; ./checkit dump "hi there" && ./checkit load "look!"
- debug1:; gdb --args ./checkit dump "hi there"
- debug2:; gdb --args ./checkit load "look!"
-diff -Naur Macaulay2-0.9.95/Macaulay2/m2/html.m2 Macaulay2-0.9.95.new/Macaulay2/m2/html.m2
---- Macaulay2-0.9.95/Macaulay2/m2/html.m2	2006-11-03 23:52:15.000000000 -0500
-+++ Macaulay2-0.9.95.new/Macaulay2/m2/html.m2	2007-03-02 10:25:10.000000000 -0500
-@@ -398,7 +398,7 @@
-      args := "--silent --print-width 77 --stop --int" | (if usermode then "" else " -q") | " " | ldpkg;
-      cmdname := commandLine#0;
-      if ulimit === null then (
--	  ulimit = utest " -t 80" | utest " -m 200000"| utest " -v 200000";
-+	  ulimit = utest " -t 80" | utest " -m 500000"| utest " -v 500000";
- 	  );
-      tmpf << "-- -*- M2-comint -*-" << endl << close;
-      cmd := ulimit | "cd " | rundir | "; time " | cmdname | " " | args | " <" | format inf | " >>" | format tmpf | " 2>&1";
-diff -Naur Macaulay2-0.9.95/Macaulay2/packages/ComputationsBook/Makefile.chapter Macaulay2-0.9.95.new/Macaulay2/packages/ComputationsBook/Makefile.chapter
---- Macaulay2-0.9.95/Macaulay2/packages/ComputationsBook/Makefile.chapter	2006-11-03 11:43:27.000000000 -0500
-+++ Macaulay2-0.9.95.new/Macaulay2/packages/ComputationsBook/Makefile.chapter	2007-03-02 10:25:10.000000000 -0500
-@@ -6,7 +6,7 @@
- check: test.out.expected.trim test.out.trim
- 	diff -u -b $^
- 
--ULIMIT := ulimit -v 380000; ulimit -t 3000
-+ULIMIT := ulimit -v 500000; ulimit -m 500000; ulimit -t 3000
- PATHJOIN := 'path = join({"./","$(chapter_srcdir)/"},path)'
- M2CMD := time nice -18 ../../../bin/M2$(EXE) --stop -q -e $(PATHJOIN)
- EXIT := -e "exit 0"
-diff -Naur Macaulay2-0.9.95/Macaulay2/packages/LLLBases.m2 Macaulay2-0.9.95.new/Macaulay2/packages/LLLBases.m2
---- Macaulay2-0.9.95/Macaulay2/packages/LLLBases.m2	2006-10-30 13:07:46.000000000 -0500
-+++ Macaulay2-0.9.95.new/Macaulay2/packages/LLLBases.m2	2007-03-02 16:21:23.000000000 -0500
-@@ -1020,18 +1020,18 @@
- under certain circumstances even be better.",
- SUBSECTION "Examples",
- EXAMPLE {
--	  "m1 = map(ZZ^50, ZZ^50, (j,i) -> (i+1)^8 * (j+1)^4 + i + j + 2);",
--	  "m = syz m1;",
--	  "time LLL m;",
--	  "time LLL(m, Strategy=>CohenEngine);",
--	  "time LLL(m, Strategy=>CohenTopLevel);",
--	  "time LLL(m, Strategy=>{Givens,RealFP});",
--	  "time LLL(m, Strategy=>{Givens,RealQP});",
--	  "time LLL(m, Strategy=>{Givens,RealXD});",
--	  "time LLL(m, Strategy=>{Givens,RealRR});",
-+	  --"m1 = map(ZZ^50, ZZ^50, (j,i) -> (i+1)^8 * (j+1)^4 + i + j + 2);",
-+	  --"m = syz m1;",
-+	  --"time LLL m;",
-+	  --"time LLL(m, Strategy=>CohenEngine);",
-+	  --"time LLL(m, Strategy=>CohenTopLevel);",
-+	  --"time LLL(m, Strategy=>{Givens,RealFP});",
-+	  --"time LLL(m, Strategy=>{Givens,RealQP});",
-+	  --"time LLL(m, Strategy=>{Givens,RealXD});",
-+	  --"time LLL(m, Strategy=>{Givens,RealRR});",
-      	  -- this one takes too long:
- 	  -- "time LLL(m, Strategy=>{BKZ,Givens,RealFP});",
--	  "time LLL(m, Strategy=>{BKZ,Givens,RealQP});",
-+	  --"time LLL(m, Strategy=>{BKZ,Givens,RealQP});",
-      	  -- this one takes too long:
- 	  -- "time LLL(m, Strategy=>{BKZ,Givens,RealXD});",
-      	  -- maybe this one takes too long:
-@@ -1063,7 +1063,7 @@
- 	  "m = matrix {{1, 0}, {1, 1}, {1, 2}, {1, 3}}",
- 	  "isLLL m",
- 	  "n = LLL m",
--	  "isLLL n"
-+	  --"isLLL n"
- 	  },
-      "If the optional argument Threshold is given, the conditions are checked using that value.",
-      EXAMPLE {
-@@ -1119,9 +1119,9 @@
-      PARA{},
-      "For an example,",
-      EXAMPLE {
--	  "s = apply(5,i->372*(random 1000000))",
--	  "(g,z) = gcdLLL s",
--	  "matrix{s} * z"
-+	 "s = apply(5,i->372*(random 1000000))",
-+	  --"(g,z) = gcdLLL s",
-+	  -- "matrix{s} * z"
- 	  },
-      SeeAlso => {LLLBases, LLL, kernelLLL, hermite}
-      }
-@@ -1186,9 +1186,9 @@
-      EXAMPLE {
- 	  ///
- 	  A = map(ZZ^10, ZZ^7, (i,j) -> if random 1.0 > .2 then random 1000 else 0)
--	  hermite A
--	  (B,U) = hermite(A, ChangeMatrix=>true)
--	  A*U == B
-+	  --hermite A
-+	  --(B,U) = hermite(A, ChangeMatrix=>true)
-+	  --A*U == B
- 	  ///
- 	  },
-      Caveat => {},
-diff -Naur Macaulay2-0.9.95/Macaulay2/packages/Makefile.in Macaulay2-0.9.95.new/Macaulay2/packages/Makefile.in
---- Macaulay2-0.9.95/Macaulay2/packages/Makefile.in	2006-08-27 18:24:06.000000000 -0400
-+++ Macaulay2-0.9.95.new/Macaulay2/packages/Makefile.in	2007-03-02 10:25:45.000000000 -0500
-@@ -68,7 +68,7 @@
- clean::; rm -rf tmp *.installed
- 
- distclean::clean
--clean check distclean ::; $(MAKE) -C ComputationsBook $@
-+clean check distclean ::; 
- Makefile: Makefile.in; cd ../..; ./config.status Macaulay2/packages/Makefile
- distclean::; rm -f Makefile
- 
-diff -Naur Macaulay2-0.9.95/Macaulay2/test/Makefile.test Macaulay2-0.9.95.new/Macaulay2/test/Makefile.test
---- Macaulay2-0.9.95/Macaulay2/test/Makefile.test	2006-05-10 01:58:54.000000000 -0400
-+++ Macaulay2-0.9.95.new/Macaulay2/test/Makefile.test	2007-03-02 15:50:36.000000000 -0500
-@@ -4,8 +4,8 @@
- 
- DOTS ?= ..
- TLIMIT ?= 40
--MLIMIT ?= 90000
--VLIMIT ?= 90000
-+MLIMIT ?= 500000
-+VLIMIT ?= 500000
- LIMIT  = ulimit -t $(TLIMIT) -m $(MLIMIT) -v $(VLIMIT) 2>/dev/null
- 
- RESULTS := $(notdir $(patsubst %.m2, %.out, $(wildcard $(SRCDIR)/*.m2))) \
-@@ -27,7 +27,7 @@
- 	@ $(LIMIT); \
- 		echo "--*- compilation -*-" >$*.errors; \
- 		if (echo 'input "$<"'; echo 'collectGarbage()'; echo exit 0) | \
--		   time $(DOTS)/bin/M2$(EXE) $(ARGS) >>$*.errors 2>&1 ; \
-+		   $(DOTS)/bin/M2$(EXE) $(ARGS) >>$*.errors 2>&1 ; \
- 		then mv $*.errors $@ ; \
- 		else a=$$?; \
- 		     echo "$*.errors:0: error output left here; some errors follow" >&2 ; \
-@@ -38,7 +38,7 @@
- 	@ echo testing: $<
- 	@ $(LIMIT); \
- 		echo "--*- compilation -*-" >$*.errors; \
--		if time $(DOTS)/bin/M2$(EXE) $(ARGS) <$< >>$*.errors 2>&1 ; \
-+		if $(DOTS)/bin/M2$(EXE) $(ARGS) <$< >>$*.errors 2>&1 ; \
- 		then mv $*.errors $@ ; \
- 		else a=$$?; \
- 		     echo "$*.errors:0: error output left here; some errors follow" >&2 ; \
-diff -Naur Macaulay2-0.9.95/Macaulay2/test/engine/LU.m2 Macaulay2-0.9.95.new/Macaulay2/test/engine/LU.m2
---- Macaulay2-0.9.95/Macaulay2/test/engine/LU.m2	2006-06-21 16:24:13.000000000 -0400
-+++ Macaulay2-0.9.95.new/Macaulay2/test/engine/LU.m2	1969-12-31 19:00:00.000000000 -0500
-@@ -1,95 +0,0 @@
--------------------------------
---- Test of LU decomposition --
--------------------------------
--permutationMatrix = (p) -> (
--     M := mutableZero(ZZ, #p, #p, Dense=>false);
--     for i from 0 to #p-1 do
--       M_(i,p#i) = 1;
--     matrix M)
--
--M = matrix {{1.0, 3.0, 4.0, 5.0},{2.0, 3.0, 0.0, 1.0}}
--(P,L,U) = LU mutableMatrix(M, Dense=>true)
--permutationMatrix {0,2,1}
--assert(0 == (permutationMatrix P) * (matrix L) * (matrix U) - M)
--
--
--time m = mutableMatrix(random(RR^7, RR^8), Dense=>true)
--time (P,L,U) = LU m;
--
--collectGarbage()
--
--assert(0 == (permutationMatrix P) * (matrix L) * (matrix U) - (matrix m) )
--
--time m = mutableMatrix(random(RR^40, RR^100), Dense=>true);
--time (P,L,U) = LU m;
--
--collectGarbage()
--
--(permutationMatrix P) * (matrix L) * (matrix U) - (matrix m) 
--
--time m = mutableMatrix(random(RR^600, RR^600), Dense=>true);
--time randomMutableMatrix
--time (P,L,U) = LU m;
--
---- Over ZZ/p
--K = ZZ/7
--M = matrix(K, {{1,2,3,4},{0,3,1,2}})
--(P,L,U) = LU mutableMatrix(M,Dense=>true)
--assert(0 == (permutationMatrix P) * (matrix L) * (matrix U) - M )
--rowSwap(U,0,1)
--U
--(P,L,U2) = LU mutableMatrix(U,Dense=>true)
--assert(0 == (permutationMatrix P) * (matrix L) * (matrix U2) - matrix U )
--
---- over QQ
--R = QQ
--m = matrix(R, {{1,2,3,4,5},
--	  {2,3,4,5,1},
--	  {3,4,5,1,2},
--	  {4,5,1,2,3},
--	  {5,1,2,3,4}})
--m1 = mutableMatrix(m, Dense=>false)
--print "LU over QQ not defined yet"
----(P,L,U) = LU m1
--
--R = ZZ/32003
--m = matrix(R, {{1,2,3,4,5},
--	  {2,3,4,5,1},
--	  {3,4,5,1,2},
--	  {4,5,1,2,3},
--	  {5,1,2,3,4}})
--m1 = mutableMatrix(m, Dense=>true)
--(P,L,U) = LU m1
--assert(0 == (permutationMatrix P) * (matrix L) * (matrix U) - m )
--
--print "rawFFLU seems to be non-functional? next part commented out"
--///
--debug Core
--rawFFLU raw m1
--m1
--
--debug Core
--R = ZZ
--m = matrix(R, {{1,2,3,4,5},
--	  {2,3,4,5,1},
--	  {3,4,5,1,2},
--	  {4,5,1,2,3},
--	  {5,1,2,3,4}})
--m1 = mutableMatrix(m, Dense=>false)
--rawFFLU raw m1
--m1
--det matrix m1
--det m
--factor det m
--
--R = ZZ[vars(0..8)]
--m = genericMatrix(R,a,3,3)
--m1 = mutableMatrix m
--rawFFLU raw m1
--m1
--///
--
---- Local Variables:
---- compile-command: "make -C $M2BUILDDIR/Macaulay2/test/engine LU.out"
---- End:
--
-diff -Naur Macaulay2-0.9.95/Macaulay2/test/engine-div.m2 Macaulay2-0.9.95.new/Macaulay2/test/engine-div.m2
---- Macaulay2-0.9.95/Macaulay2/test/engine-div.m2	2006-11-03 23:19:39.000000000 -0500
-+++ Macaulay2-0.9.95.new/Macaulay2/test/engine-div.m2	2007-03-02 10:25:10.000000000 -0500
-@@ -113,7 +113,7 @@
- checkremquot((y^2+x)^3,y^2+x)
- 
- -- Polynomials in a Laurent polynomial ring
--R = ZZ[x,y,z,Inverses=>true] -- ERROR
-+-- R = ZZ[x,y,z,Inverses=>true] -- ERROR
- R = ZZ[x,y,z,Inverses=>true, MonomialOrder=>RevLex]
- f = 1 - x^-1
- g = x-1
-@@ -126,11 +126,11 @@
- g = quot(g,1-x)
- rem(g,1-x)
- checkremquot(f,1-x^-1)
--checkremquot(f,1-x^-1-y^-1) -- HANGS
-+-- checkremquot(f,1-x^-1-y^-1) -- HANGS
- 
- f % (1-x^-1)
- f == (1-x^-1) * (f // (1-x^-1))
--f % (1-x^-1-y^-1)
-+-- f % (1-x^-1-y^-1)
- 
- R = QQ[t,u,Inverses => true, MonomialOrder=>RevLex]
- 
-diff -Naur Macaulay2-0.9.95/Macaulay2/test/overflow.m2 Macaulay2-0.9.95.new/Macaulay2/test/overflow.m2
---- Macaulay2-0.9.95/Macaulay2/test/overflow.m2	2006-11-03 10:58:21.000000000 -0500
-+++ Macaulay2-0.9.95.new/Macaulay2/test/overflow.m2	2007-03-02 10:25:10.000000000 -0500
-@@ -11,18 +11,18 @@
- 
- R = QQ[x,MonomialSize => 8]
- assert ( degree x^15^15 == {15*15} )
--assert ( degree x^16^16 == {16*16} )
-+-- assert ( degree x^16^16 == {16*16} )
- 
--x^127 * x -- this has an error
-+-- x^127 * x -- this has an error
- x^127
- oo^2 -- too large...
- 
- R = QQ[x,Weights=>{2^16}]
- assert( x^(2^13) > x^40 )
- assert( x^(2^14) > x^40 )
--assert( x^(2^15) > x^40 )
--assert( x^(2^16) > x^40 )
--assert( x^(2^17) > x^40 )
-+-- assert( x^(2^15) > x^40 )
-+-- assert( x^(2^16) > x^40 )
-+-- assert( x^(2^17) > x^40 )
- 
- end
- -- Local Variables:
-diff -Naur Macaulay2-0.9.95/Macaulay2/test/prune2.m2 Macaulay2-0.9.95.new/Macaulay2/test/prune2.m2
---- Macaulay2-0.9.95/Macaulay2/test/prune2.m2	2006-07-10 23:14:54.000000000 -0400
-+++ Macaulay2-0.9.95.new/Macaulay2/test/prune2.m2	1969-12-31 19:00:00.000000000 -0500
-@@ -1,48 +0,0 @@
--for i to 5 do (
--     N = prune (M = coker ( random (ZZ^11, ZZ^3) * matrix "2,,;,3,;,,7" ) ) ;
--     assert (numgens source presentation N < 6);
--     assert isIsomorphism N.cache.pruningMap ;
--     )
--
----
--inc = random(ZZ^11, ZZ^3, MaximalRank => true)
--f = inc * matrix "2,,;,5,;,,3"
--g = inc * matrix "0,,;,385,;,,21"
--M = subquotient(
--     f * random(ZZ^3,ZZ^4,MaximalRank => true),
--     g * random(ZZ^3,ZZ^4,MaximalRank => true)
--     )	-- isomorphic to ZZ ++ ZZ/77 ++ ZZ/7
--N = prune M
--factor M
--assert ( ideal(0) == fittingIdeal_0 N)
--assert ( ideal(7*7*11) == fittingIdeal_1 N)
--assert ( ideal(7) == fittingIdeal_2 N)
--assert ( ideal(1) == fittingIdeal_3 N)
--assert ( rank M == 1 )
----
--R = ZZ/101[x,MonomialOrder => {Position => Up}]
--inc = random(R^6, R^3, MaximalRank => true)
--f = inc * diagonalMatrix{x, x-1          ,x^2-2         }
--g = inc * diagonalMatrix{0,(x-1)*(x-3),(x^2-2)*(x-3)*(x^2-7)}
--M = subquotient(
--     f * random(R^3,R^4,MaximalRank => true),
--     g * random(R^3,R^4,MaximalRank => true)
--     )	-- isomorphic to R ++ R/(x-3) ++ R/(x-3)(x^2-7)
--N = prune M
--factor M
--assert ( ideal(0_R) == fittingIdeal_0 N)
--assert ( ideal((x-3)^2*(x^2-7)) == fittingIdeal_1 N)
--assert ( ideal(x-3) == fittingIdeal_2 N)
--assert ( ideal(1_R) == fittingIdeal_3 N)
--assert ( rank M == 1 )
--factor M
--
---- 
--
--
--R = QQ[x,y]
--assert ( R^0 == prune coker id_(R^3) )
--
--R = ZZ[x,y]
--assert ( R^0 == prune coker id_(R^3) )
--
-diff -Naur Macaulay2-0.9.95/Macaulay2/test/randommat.m2 Macaulay2-0.9.95.new/Macaulay2/test/randommat.m2
---- Macaulay2-0.9.95/Macaulay2/test/randommat.m2	2006-07-08 16:16:23.000000000 -0400
-+++ Macaulay2-0.9.95.new/Macaulay2/test/randommat.m2	2007-03-02 10:25:10.000000000 -0500
-@@ -16,9 +16,9 @@
- 
- -- check random isomorphisms are isomorphisms
- 
--assert isIsomorphism random(ZZ^6,ZZ^6,MaximalRank=>true)
--assert isInjective random(ZZ^6,ZZ^3,MaximalRank=>true)
--assert isSurjective random(ZZ^3,ZZ^6,MaximalRank=>true)
-+-- assert isIsomorphism random(ZZ^6,ZZ^6,MaximalRank=>true)
-+-- assert isInjective random(ZZ^6,ZZ^3,MaximalRank=>true)
-+-- assert isSurjective random(ZZ^3,ZZ^6,MaximalRank=>true)
- 
- R = ZZ/101[x,y]
- assert isIsomorphism random(R^4,R^4,MaximalRank=>true)
-diff -Naur Macaulay2-0.9.95/Macaulay2/test/rank.m2 Macaulay2-0.9.95.new/Macaulay2/test/rank.m2
---- Macaulay2-0.9.95/Macaulay2/test/rank.m2	2006-07-08 17:33:03.000000000 -0400
-+++ Macaulay2-0.9.95.new/Macaulay2/test/rank.m2	1969-12-31 19:00:00.000000000 -0500
-@@ -1,12 +0,0 @@
--assert ( 8 == rank coker (random (ZZ^11, ZZ^3, MaximalRank => true) * matrix "2,,;,5,;,,11" * random(ZZ^3,ZZ^5,MaximalRank => true)))
--assert ( 8 == rank coker (random (QQ^11, QQ^3, MaximalRank => true) * matrix "2,,;,5,;,,11" * random(QQ^3,QQ^5,MaximalRank => true)))
--assert ( 3 == rank (random (ZZ^11, ZZ^3, MaximalRank => true) * matrix "2,,;,5,;,,11" * random(ZZ^3,ZZ^5,MaximalRank => true)))
--assert ( 3 == rank (random (QQ^11, QQ^3, MaximalRank => true) * matrix "2,,;,5,;,,11" * random(QQ^3,QQ^5,MaximalRank => true)))
--
--
--end
--
--
--R = QQ[x,y]
--r = rank coker (random (R^11, R^3, MaximalRank => true) * matrix "x3+2,,;,5,;,,x+1" * random(R^3,R^5,MaximalRank => true))
--assert ( 3 == r )
-diff -Naur Macaulay2-0.9.95/Macaulay2/test/res11.m2 Macaulay2-0.9.95.new/Macaulay2/test/res11.m2
---- Macaulay2-0.9.95/Macaulay2/test/res11.m2	2006-07-12 16:32:03.000000000 -0400
-+++ Macaulay2-0.9.95.new/Macaulay2/test/res11.m2	1969-12-31 19:00:00.000000000 -0500
-@@ -1,23 +0,0 @@
--inc = random(ZZ^11, ZZ^4, MaximalRank => true)
--M = subquotient(
--     inc * diagonalMatrix {4,2,5     ,3  } * random(ZZ^4,ZZ^5,MaximalRank => true),
--     inc * diagonalMatrix {0,0,5*7*11,3*7} * random(ZZ^4,ZZ^5,MaximalRank => true)
--     )	-- isomorphic to ZZ^2 ++ ZZ/77 ++ ZZ/7
--C = res M
--assert (length C <= 1)
--assert isIsomorphism map(M,HH_0 C,id_(cover M))
--assert ( HH_1 C == 0 )
--
--
----
--R = QQ[x]
--M = coker matrix(R, {{1},{0}})
--C = res(M, Strategy=>2)  -- this one fails too...
--C = res M
--HH_0 C
--assert ( M == HH_0 C )
--
--M = coker matrix(R, {{0},{1}})
--C = res M
--HH_0 C
--assert ( M == HH_0 C )
-diff -Naur Macaulay2-0.9.95/Macaulay2/test/slow/ker8.m2 Macaulay2-0.9.95.new/Macaulay2/test/slow/ker8.m2
---- Macaulay2-0.9.95/Macaulay2/test/slow/ker8.m2	2006-11-03 13:00:57.000000000 -0500
-+++ Macaulay2-0.9.95.new/Macaulay2/test/slow/ker8.m2	2007-03-02 10:25:10.000000000 -0500
-@@ -51,7 +51,7 @@
-       x33*y12+x32*y22+x33*y22+x31*y32+x32*y32+x33*y32,
-       x33*y13+x32*y23+x33*y23+x31*y33+x32*y33+x33*y33});
- 
--time kernel(f);
-+-- time kernel(f);
- 
- -- 
- -- 
-diff -Naur Macaulay2-0.9.95/Macaulay2/test/smith.m2 Macaulay2-0.9.95.new/Macaulay2/test/smith.m2
---- Macaulay2-0.9.95/Macaulay2/test/smith.m2	2006-07-11 12:26:34.000000000 -0400
-+++ Macaulay2-0.9.95.new/Macaulay2/test/smith.m2	2007-03-02 10:25:10.000000000 -0500
-@@ -19,7 +19,7 @@
- assert ( t*f*s == g )
- 
- 
--(g,t,s) = smithNormalForm ( f = random(ZZ^15,ZZ^3,MaximalRank=>true) * matrix "14,,;,140,;,,1260" * random(ZZ^3,ZZ^20,MaximalRank=>true) );
-+-- (g,t,s) = smithNormalForm ( f = random(ZZ^15,ZZ^3,MaximalRank=>true) * matrix "14,,;,140,;,,1260" * random(ZZ^3,ZZ^20,MaximalRank=>true) );
- g
--assert ( t*f*s == g )
--assert ( # pivots g == 3 )
-+-- assert ( t*f*s == g )
-+-- assert ( # pivots g == 3 )
diff --git a/sci-mathematics/Macaulay2/files/Macaulay2-1.0-example-fix.patch b/sci-mathematics/Macaulay2/files/Macaulay2-1.0-example-fix.patch
deleted file mode 100644
index f0fa82c87a08..000000000000
--- a/sci-mathematics/Macaulay2/files/Macaulay2-1.0-example-fix.patch
+++ /dev/null
@@ -1,110 +0,0 @@
-diff -Naur Macaulay2-1.0/Macaulay2/Makefile.in Macaulay2-1.0.new/Macaulay2/Makefile.in
---- Macaulay2-1.0/Macaulay2/Makefile.in	2008-01-04 08:43:50.000000000 -0500
-+++ Macaulay2-1.0.new/Macaulay2/Makefile.in	2008-01-05 11:49:14.000000000 -0500
-@@ -10,13 +10,11 @@
- VPATH = @srcdir@
- ################################# .
- install install-others install-Macaulay2 :: @encapdir@/@docpackagesdirtail@ @encapdir@/@docpackagesdirtail@ \
--	   @encapdir@/@docpackagesdirtail@/COPYING \
- 	   @encapdir@/@docpackagesdirtail@/README \
- 	   @encapdir@/@docpackagesdirtail@/CHANGES \
- 	   @encapdir@/@docpackagesdirtail@/LAYOUT
- 
- @encapdir@/@docpackagesdirtail@:; @MKDIR_P@ "$@"
--@encapdir@/@docpackagesdirtail@/COPYING : COPYING ; @INSTALL_DATA@ $< "$@"
- @encapdir@/@docpackagesdirtail@/CHANGES : CHANGES ; @INSTALL_DATA@ $< "$@"
- @encapdir@/@docpackagesdirtail@/LAYOUT  : LAYOUT  ; @INSTALL_DATA@ $< "$@"
- @encapdir@/@docpackagesdirtail@/README  : README  ; @INSTALL_DATA@ $< "$@"
-diff -Naur Macaulay2-1.0/Macaulay2/packages/LLLBases.m2 Macaulay2-1.0.new/Macaulay2/packages/LLLBases.m2
---- Macaulay2-1.0/Macaulay2/packages/LLLBases.m2	2008-01-04 08:43:50.000000000 -0500
-+++ Macaulay2-1.0.new/Macaulay2/packages/LLLBases.m2	2008-01-05 08:48:07.000000000 -0500
-@@ -812,11 +812,8 @@
- 	  "LLL m"
- 	  },
-      "It is also possible to get the change of basis 
--     matrix from the original basis to the LLL basis.  For example,",
--     EXAMPLE {
--	  "(n,c) = LLL(m, Strategy => NTL, ChangeMatrix=>true)",
--	  "m * c == n"
--	  },
-+     matrix from the original basis to the LLL basis.  
-+     **** examples disabled due to segmentation fault *****",
-      Caveat => {"If the strategy given is not an NTL strategy, then the columns of the matrix m must be linearly independent.",
- 	  "In any case, the matrix must be defined over the ring ZZ."},
-      SeeAlso => {isLLL, gcdLLL, kernelLLL, hermite}
-@@ -1021,16 +1018,17 @@
- EXAMPLE {
- 	  "m1 = map(ZZ^50, ZZ^50, (j,i) -> (i+1)^8 * (j+1)^4 + i + j + 2);",
- 	  "m = syz m1;",
--	  "time LLL m;",
--	  "time LLL(m, Strategy=>CohenEngine);",
--	  "time LLL(m, Strategy=>CohenTopLevel);",
--	  "time LLL(m, Strategy=>{Givens,RealFP});",
--	  "time LLL(m, Strategy=>{Givens,RealQP});",
--	  "time LLL(m, Strategy=>{Givens,RealXD});",
--	  "time LLL(m, Strategy=>{Givens,RealRR});",
-+	  -- "time LLL m;"
-+	  -- these ones are broken
-+	  -- "time LLL(m, Strategy=>CohenEngine);",
-+	  -- "time LLL(m, Strategy=>CohenTopLevel);",
-+	  -- "time LLL(m, Strategy=>{Givens,RealFP});",
-+	  -- "time LLL(m, Strategy=>{Givens,RealQP});",
-+	  -- "time LLL(m, Strategy=>{Givens,RealXD});",
-+	  -- "time LLL(m, Strategy=>{Givens,RealRR});",
-      	  -- this one takes too long:
- 	  -- "time LLL(m, Strategy=>{BKZ,Givens,RealFP});",
--	  "time LLL(m, Strategy=>{BKZ,Givens,RealQP});",
-+	  -- "time LLL(m, Strategy=>{BKZ,Givens,RealQP});",
-      	  -- this one takes too long:
- 	  -- "time LLL(m, Strategy=>{BKZ,Givens,RealXD});",
-      	  -- maybe this one takes too long:
-@@ -1062,7 +1060,8 @@
- 	  "m = matrix {{1, 0}, {1, 1}, {1, 2}, {1, 3}}",
- 	  "isLLL m",
- 	  "n = LLL m",
--	  "isLLL n"
-+	  -- doesn't work
-+	  -- "isLLL n"
- 	  },
-      "If the optional argument Threshold is given, the conditions are checked using that value.",
-      EXAMPLE {
-@@ -1118,9 +1117,10 @@
-      PARA{},
-      "For an example,",
-      EXAMPLE {
--	  "s = apply(5,i->372*(random 1000000))",
--	  "(g,z) = gcdLLL s",
--	  "matrix{s} * z"
-+	  "s = apply(5,i->372*(random 1000000))"
-+	  -- don't work
-+	  -- "(g,z) = gcdLLL s",
-+	  -- "matrix{s} * z"
- 	  },
-      SeeAlso => {LLLBases, LLL, kernelLLL, hermite}
-      }
-diff -Naur Macaulay2-1.0/Macaulay2/packages/Macaulay2/doc.m2 Macaulay2-1.0.new/Macaulay2/packages/Macaulay2/doc.m2
---- Macaulay2-1.0/Macaulay2/packages/Macaulay2/doc.m2	2008-01-04 08:43:50.000000000 -0500
-+++ Macaulay2-1.0.new/Macaulay2/packages/Macaulay2/doc.m2	2008-01-04 23:30:22.000000000 -0500
-@@ -1821,8 +1821,6 @@
-      Outputs => {"f" => {"a random, graded, degree ", TT "0", " map, from ", TT "G", " to ", TT "F"}},
-      EXAMPLE lines ///
- 	  R = ZZ/101[x,y];
--      	  random(R^{1,2,3},R^{1,2,3})
--	  random(ZZ^3,ZZ^6,MaximalRank=>true)
- 	  ///,
-      Caveat => {
- 	  "Over a polynomial ring, specifying ", TT "MaximalRank=>true", " will yield a non-homogeneous matrix."
-diff -Naur Macaulay2-1.0/Macaulay2/packages/Macaulay2/functions/lift-doc.m2 Macaulay2-1.0.new/Macaulay2/packages/Macaulay2/functions/lift-doc.m2
---- Macaulay2-1.0/Macaulay2/packages/Macaulay2/functions/lift-doc.m2	2008-01-04 08:43:44.000000000 -0500
-+++ Macaulay2-1.0.new/Macaulay2/packages/Macaulay2/functions/lift-doc.m2	2008-01-04 23:31:09.000000000 -0500
-@@ -95,10 +95,6 @@
- 	  "A continued fraction method is used to lift a real number to a rational number.",
- 	  },
-      EXAMPLE lines ///
--	  12/127.
--	  lift(oo,QQ)
--          ///,
--     EXAMPLE lines ///
- 	  setPrecision 15
-           z = lift(.2341124,RRR)
-           ///,
diff --git a/sci-mathematics/Macaulay2/files/gentoo-Macaulay2-0.9.2.diff b/sci-mathematics/Macaulay2/files/gentoo-Macaulay2-0.9.2.diff
deleted file mode 100644
index 358705c770ec..000000000000
--- a/sci-mathematics/Macaulay2/files/gentoo-Macaulay2-0.9.2.diff
+++ /dev/null
@@ -1,245 +0,0 @@
-diff -U 4 -H -d -r -N -- Macaulay2-0.9.2-org/Macaulay2/c/Makefile.in Macaulay2-0.9.2/Macaulay2/c/Makefile.in
---- Macaulay2-0.9.2-org/Macaulay2/c/Makefile.in	2001-08-16 00:52:01.000000000 +0200
-+++ Macaulay2-0.9.2/Macaulay2/c/Makefile.in	2004-04-27 21:00:55.529735512 +0200
-@@ -11,9 +11,9 @@
- 	rm -f y.tab.h y.output
- ############################################################
- .PHONY : clean all install
- YFLAGS := -vdlt
--LOADLIBES += -lm -lgc
-+LOADLIBES += -lm -lgc -ldl
- CNAMES := scc1.c readfile.c error.c dictionary.c list.c cprint.c type.c chk.c compat.c
- HFILES := $(CNAMES:.c=.h) scc.h grammar.h
- OFILES := $(CNAMES:.c=.o) grammar.o
- SRCFILES := $(HFILES) $(CNAMES) grammar.y
-diff -U 4 -H -d -r -N -- Macaulay2-0.9.2-org/Macaulay2/d/Makefile.in Macaulay2-0.9.2/Macaulay2/d/Makefile.in
---- Macaulay2-0.9.2-org/Macaulay2/d/Makefile.in	2002-01-10 17:46:37.000000000 +0100
-+++ Macaulay2-0.9.2/Macaulay2/d/Makefile.in	2004-04-27 21:20:55.014386128 +0200
-@@ -349,9 +349,9 @@
- endif
- 
- ../libexec/Macaulay2$(EXE) : $(ALLOBJ) $(LIBRARYFILES)
- 	rm -f $@
--	time $(PURIFYCMD) $(CC) $(LDFLAGS) $(ALLOBJ) $(LOADLIBES) $(LDLIBS) $(LINK_OUTPUT_OPTION)
-+	$(PURIFYCMD) $(CC) $(LDFLAGS) $(ALLOBJ) $(LOADLIBES) -ldl -lpthread $(LDLIBS) $(LINK_OUTPUT_OPTION)
- 	$(STRIPCMD) $@
- 
- t_main.o : types.h
- t : t_main.o gmp.o stdio.o strings.o system.o varstrin.o nets.o scclib.o C.o t.o
-diff -U 4 -H -d -r -N -- Macaulay2-0.9.2-org/Macaulay2/e/x_factor.cpp Macaulay2-0.9.2/Macaulay2/e/x_factor.cpp
---- Macaulay2-0.9.2-org/Macaulay2/e/x_factor.cpp	2001-08-08 03:15:34.000000000 +0200
-+++ Macaulay2-0.9.2/Macaulay2/e/x_factor.cpp	2004-04-27 21:05:20.549446392 +0200
-@@ -3,9 +3,9 @@
- //#if !defined(__MWERKS__)
- #if 1
- #include <assert.h>
- #include <iostream.h>
--#define divides ignore_this_symbol /* bits/stl_function.h contains a generic one, sigh, gcc 3.0 */
-+//#define divides ignore_this_symbol /* bits/stl_function.h contains a generic one, sigh, gcc 3.0 */
- #include "interp.hpp"
- #undef divides
- #include "matrix.hpp"
- #include "z_mod_p.hpp"
-diff -U 4 -H -d -r -N -- Macaulay2-0.9.2-org/Macaulay2/m2/Makefile.in Macaulay2-0.9.2/Macaulay2/m2/Makefile.in
---- Macaulay2-0.9.2-org/Macaulay2/m2/Makefile.in	2001-08-15 22:46:13.000000000 +0200
-+++ Macaulay2-0.9.2/Macaulay2/m2/Makefile.in	2004-04-27 21:11:14.595623192 +0200
-@@ -102,9 +102,9 @@
- phase1 :: ../$(DUMPDATAFILE)
- ../$(DUMPDATAFILE) : $(DUMPEDM2FILES) ../libexec/Macaulay2
- 	 # phase 1: read *.m2 and dump data
- 	rm -f ../$(DUMPDATAFILE)
--	time env M2HOME=.. ../libexec/Macaulay2 -q -silent -tty '-ephase=1' \
-+	env M2HOME=.. ../libexec/Macaulay2 -q -silent -tty '-ephase=1' \
- 		@srcdir@/setup.m2 @srcdir@/dumpdata.m2 '-edump()'
- else
- ARGS := -silent setup.m2
- endif
-diff -U 4 -H -d -r -N -- Macaulay2-0.9.2-org/Macaulay2/test/Makefile.in Macaulay2-0.9.2/Macaulay2/test/Makefile.in
---- Macaulay2-0.9.2-org/Macaulay2/test/Makefile.in	2001-08-15 22:46:13.000000000 +0200
-+++ Macaulay2-0.9.2/Macaulay2/test/Makefile.in	2004-04-27 21:11:44.443085688 +0200
-@@ -41,9 +41,9 @@
- endif
- 
- %.okay : %.m2
- 	@ echo testing $<
--	@ ulimit -t 600; time env M2HOME=.. ../libexec/Macaulay2 $(ARGS) $< '-eexit(0)'
-+	@ ulimit -t 600; env M2HOME=.. ../libexec/Macaulay2 $(ARGS) $< '-eexit(0)'
- 	@ touch $@
- 
- clean  :	
- 	rm -f *.okay
-diff -U 3 -dHrN -- Macaulay2-0.9.2-orig/Macaulay2/Makefile.in Macaulay2-0.9.2/Macaulay2/Makefile.in
---- Macaulay2-0.9.2-orig/Macaulay2/Makefile.in	2001-08-18 21:17:15.000000000 +0200
-+++ Macaulay2-0.9.2/Macaulay2/Makefile.in	2004-05-14 13:35:33.266819848 +0200
-@@ -8,11 +8,11 @@
- 
- include ../include/config.Makefile
- VPATH = @srcdir@
--install :: $(packagedir)/COPYING $(packagedir)/CHANGES $(packagedir)/README
--$(packagedir)/COPYING : COPYING $(packagedir) ; $(INSTALL_DATA) $< "$@"
--$(packagedir)/CHANGES : CHANGES $(packagedir) ; $(INSTALL_DATA) $< "$@"
--$(packagedir)/README  : README  $(packagedir) ; $(INSTALL_DATA) $< "$@"
--$(packagedir):; $(INSTALL) -d "$@"
-+install :: $(packagedocdir)/COPYING $(packagedocdir)/CHANGES $(packagedocdir)/README
-+$(packagedocdir)/COPYING : COPYING $(packagedocdir) ; $(INSTALL_DATA) $< "$@"
-+$(packagedocdir)/CHANGES : CHANGES $(packagedocdir) ; $(INSTALL_DATA) $< "$@"
-+$(packagedocdir)/README  : README  $(packagedocdir) ; $(INSTALL_DATA) $< "$@"
-+$(packagedocdir):; $(INSTALL) -d "$@"
- ################################# libexec
- libexec :; mkdir $@
- clean ::; rm -rf libexec
-@@ -76,15 +76,15 @@
- all ::;  $(MAKE) -C emacs all
- install distclean clean ::; $(MAKE) -C emacs $@
- ################################# libexec
--install :: $(packagedir)/libexec
--$(packagedir)/libexec:; $(INSTALL) -d "$@"
--install :: $(packagedir)/libexec/Macaulay2
--$(packagedir)/libexec/Macaulay2 : libexec/Macaulay2
--	$(INSTALL_PROGRAM) $^ $(packagedir)/libexec
-+install :: $(packageexecdir)/libexec
-+$(packageexecdir)/libexec:; $(INSTALL) -d "$@"
-+install :: $(packageexecdir)/libexec/Macaulay2
-+$(packageexecdir)/libexec/Macaulay2 : libexec/Macaulay2
-+	$(INSTALL_PROGRAM) $^ $(packageexecdir)/libexec
- ifeq "$(DUMPDATA)" "yes"
- ifeq "$(encap)" "no"
--install :: $(packagedir)/$(DUMPDATAFILE)
--$(packagedir)/$(DUMPDATAFILE) : $(DUMPDATAFILE); $(INSTALL) $< "$@"
-+install :: $(packageexecdir)/$(DUMPDATAFILE)
-+$(packageexecdir)/$(DUMPDATAFILE) : $(DUMPDATAFILE); $(INSTALL) $< "$@"
- endif
- endif
- #################################
-diff -U 3 -dHrN -- Macaulay2-0.9.2-orig/Macaulay2/html/Makefile.in Macaulay2-0.9.2/Macaulay2/html/Makefile.in
---- Macaulay2-0.9.2-orig/Macaulay2/html/Makefile.in	2001-08-14 05:10:18.000000000 +0200
-+++ Macaulay2-0.9.2/Macaulay2/html/Makefile.in	2004-05-14 13:18:10.166395216 +0200
-@@ -54,7 +54,7 @@
- clean::; rm -f ./*.html
- clean::; rm -rf *.doc *.fn *.hl *.inv* *.cat *.src *.dct Macaulay2-index-cache
- distclean: clean; rm -f Makefile
--$(packagedir)/html:; $(INSTALL) -d "$@"
--install:: $(packagedir)/html
--	$(INSTALL_DATA) Makefile $(IMAGES) *.html @srcdir@/html.m2 $(packagedir)/html
-+$(packagehtmldir):; $(INSTALL) -d "$@"
-+install:: $(packagehtmldir)
-+	$(INSTALL_DATA) Makefile $(IMAGES) *.html @srcdir@/html.m2 $(packagehtmldir)
- 
-diff -U 3 -dHrN -- Macaulay2-0.9.2-orig/Macaulay2/tutorial/Makefile.in Macaulay2-0.9.2/Macaulay2/tutorial/Makefile.in
---- Macaulay2-0.9.2-orig/Macaulay2/tutorial/Makefile.in	2001-08-14 05:10:18.000000000 +0200
-+++ Macaulay2-0.9.2/Macaulay2/tutorial/Makefile.in	2004-05-14 13:48:15.494943560 +0200
-@@ -35,10 +35,10 @@
- 	../../bin/M2 -e'readExamples=true' tutbook.m2 '-e exit 0'
- 
- #################################
--install:: $(packagedir)/tutorial/final
-+install:: $(packagedocdir)/tutorial/final
- install:: $(TUTORIALS) $(OUTPUTS)
--	$(INSTALL_DATA) $^ "$(packagedir)/tutorial/final"
--$(packagedir)/tutorial/final :; $(INSTALL) -d "$@"
-+	$(INSTALL_DATA) $^ "$(packagedocdir)/tutorial/final"
-+$(packagedocdir)/tutorial/final :; $(INSTALL) -d "$@"
- #################################
- 
- clean :
-diff -U 3 -dHrN -- Macaulay2-0.9.2-orig/bin/M2-final.in Macaulay2-0.9.2/bin/M2-final.in
---- Macaulay2-0.9.2-orig/bin/M2-final.in	2001-08-15 15:52:20.000000000 +0200
-+++ Macaulay2-0.9.2/bin/M2-final.in	2004-05-14 12:45:00.298901056 +0200
-@@ -1,8 +1,8 @@
- #! /bin/sh
--M2HOME="`dirname $0`/../Macaulay2"
-+M2HOME="/usr/share/Macaulay2-0.9.2"
- export M2HOME
--EXE="$M2HOME/libexec/Macaulay2"
--DATA="$M2HOME/libexec/Macaulay2-`uname -m |sed s=/=-=g`-data"
-+EXE="/usr/libexec/Macaulay2"
-+DATA="/usr/libexec/Macaulay2-`uname -m |sed s=/=-=g`-data"
- SETUP="$M2HOME/m2/setup.m2"
- if [ -f "$DATA" ]
- then exec "$EXE" "-e loaddata \"$DATA\"" -- "-e runStartFunctions()" "$@"
-diff -U 3 -dHrN -- Macaulay2-0.9.2-orig/bin/M2-help.in Macaulay2-0.9.2/bin/M2-help.in
---- Macaulay2-0.9.2-orig/bin/M2-help.in	2002-01-09 17:21:35.000000000 +0100
-+++ Macaulay2-0.9.2/bin/M2-help.in	2004-05-14 12:45:48.760533768 +0200
-@@ -1,3 +1,3 @@
- #! /bin/sh
--M2HOME="`dirname $0`/../Macaulay2"
-+M2HOME="/usr/share/doc/Macaulay2-0.9.2"
- ${WWBROWSER:-netscape} "$M2HOME/html/index.html"
-diff -U 3 -dHrN -- Macaulay2-0.9.2-orig/bin/Makefile.in Macaulay2-0.9.2/bin/Makefile.in
---- Macaulay2-0.9.2-orig/bin/Makefile.in	2002-01-09 17:21:35.000000000 +0100
-+++ Macaulay2-0.9.2/bin/Makefile.in	2004-05-14 13:16:46.060181304 +0200
-@@ -10,8 +10,8 @@
- install :: $(bindir)/M2
- $(bindir)/M2 : M2-final.in
- 	$(INSTALL) -d $(bindir)
--	sed -e 's,^M2HOME=.*,M2HOME=$(prefix)/lib/Macaulay2-@PACKAGE_VERSION@,' $< >"$@".tmp
--	mv "$@".tmp "$@"
-+	#sed -e 's,^M2HOME=.*,M2HOME=$(prefix)/lib/Macaulay2-@PACKAGE_VERSION@,' $< >"$@".tmp
-+	mv M2-final.in "$@"
- 	chmod 0755 "$@"
- 
- all :: M2-help
-@@ -20,8 +20,8 @@
- install :: $(bindir)/M2-help
- $(bindir)/M2-help : M2-help
- 	$(INSTALL) -d $(bindir)
--	sed -e 's,^M2HOME=.*,M2HOME=$(prefix)/lib/Macaulay2-@PACKAGE_VERSION@,' $< >"$@".tmp
--	mv "$@".tmp "$@"
-+	#sed -e 's,^M2HOME=.*,M2HOME=$(prefix)/lib/Macaulay2-@PACKAGE_VERSION@,' $< >"$@".tmp
-+	mv M2-help.in "$@"
- 	chmod 0755 "$@"
- 
- clean :; rm -f M2
-diff -U 3 -dHrN -- Macaulay2-0.9.2-orig/include/config.Makefile.in Macaulay2-0.9.2/include/config.Makefile.in
---- Macaulay2-0.9.2-orig/include/config.Makefile.in	2002-01-09 17:21:35.000000000 +0100
-+++ Macaulay2-0.9.2/include/config.Makefile.in	2004-05-14 13:05:36.563960200 +0200
-@@ -57,7 +57,11 @@
- target = $(prefix)
- endif
- 
--packagedir = $(target)/lib/$(package)
-+packagedir = $(target)/share/$(package)
-+packageexecdir = $(target)
-+packagedocdir = $(target)/share/doc/$(package)
-+packagehtmldir = $(target)/share/doc/$(package)/html
-+
- bindir = $(target)/bin
- 
- RANLIB = @RANLIB@
---- Macaulay2-0.9.2/Macaulay2/e/EGB1.hpp	1999-09-09 23:47:12.000000000 +0200
-+++ Macaulay2-0.9.2/Macaulay2/e/EGB1.hpp.new	2004-12-13 11:48:17.208554431 +0100
-@@ -104,8 +104,6 @@
- };
- class EGB1 : public EGroebnerComputation
- {
--  class iterator;
--  friend class iterator;
- private:
-   // Ring information
-   const EInterface I;
-@@ -255,6 +253,9 @@
- 
-   virtual int new_calc(const EStopConditions &stop);
- 
-+  class iterator;
-+  friend class iterator;
-+
-   class iterator {
-     const EGB1 *comp;
-     int i;
---- Macaulay2-0.9.2/include/config.Makefile.in	2004-12-13 12:29:02.776249827 +0100
-+++ Macaulay2-0.9.2/include/config.Makefile.in.new	2004-12-13 12:47:35.221607868 +0100
-@@ -110,13 +110,6 @@
- ifeq "$(GCC)" "yes"
- CFLAGS   += -Wall -Wshadow -Wcast-qual
- CXXFLAGS += -Wall -Wshadow -Wcast-qual
--ifeq "$(OPTIMIZE)" "yes"
--CFLAGS   += -O3 -fexpensive-optimizations
--CXXFLAGS += -O3 -fexpensive-optimizations
--else
--CFLAGS   += -O0
--CXXFLAGS += -O0
--endif
- endif
- 
- ifeq "$(STRIP)" "no"
diff --git a/sci-mathematics/Macaulay2/metadata.xml b/sci-mathematics/Macaulay2/metadata.xml
deleted file mode 100644
index 773b7a2ab4a2..000000000000
--- a/sci-mathematics/Macaulay2/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci-mathematics</herd>
-<longdescription>
-Macaulay2 is a computer algebra system for doing polynomial computations, 
-particularly Grobner basis calculations. Macaulay2 is designed for solving 
-problems in algebraic geometry and has a quite simple syntax, 
-often described as "algebraic machine language"
-</longdescription>
-</pkgmetadata>