Macaulay2 back in the main tree. Cleanup

6 files changed, 7 insertions, 478 deletions

diff --git a/sci-mathematics/Macaulay2/ChangeLog b/sci-mathematics/Macaulay2/ChangeLog
index a3aab0de1..107a4ca99 100644
--- a/sci-mathematics/Macaulay2/ChangeLog
+++ b/sci-mathematics/Macaulay2/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  12 Nov 2010; Thomas Kahle <tomka@gentoo.org>
+  -files/1.4_pre-paths-of-external-programs.patch,
+  -Macaulay2-1.3.1-r3.ebuild, -Macaulay2-1.4_pre.ebuild,
+  -Macaulay2-1.4.ebuild:
+  sci-mathematics/Macaulay2-1.4 added to main tree. Remove old. 
+
 *Macaulay2-1.4 (10 Nov 2010)
 
   10 Nov 2010; Thomas Kahle <tomka@gentoo.org>
diff --git a/sci-mathematics/Macaulay2/Macaulay2-1.3.1-r3.ebuild b/sci-mathematics/Macaulay2/Macaulay2-1.3.1-r3.ebuild
deleted file mode 100644
index 99d0b8fc1..000000000
--- a/sci-mathematics/Macaulay2/Macaulay2-1.3.1-r3.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit autotools elisp-common eutils flag-o-matic
-
-IUSE="emacs"
-
-DESCRIPTION="research tool for commutative algebra and algebraic geometry"
-SRC_URI="http://www.math.uiuc.edu/Macaulay2/Downloads/SourceCode/Macaulay2-${PV}-r10737.bz2 -> ${P}.tar.bz2"
-
-#	mirror://gentoo/${P}-src.tar.bz2
-
-HOMEPAGE="http://www.math.uiuc.edu/Macaulay2/"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="sys-libs/gdbm
-	>=dev-libs/ntl-5.5.2
-	>=dev-libs/boehm-gc-7.1
-	>=sci-mathematics/pari-2.3.4[gmp]
-	>=sys-libs/readline-6.0
-	dev-libs/libxml2
-	>=sci-libs/factory-3.1.0[-singular]
-	>=sci-libs/libfac-3.1.0[-singular]
-	sci-mathematics/frobby
-	sci-mathematics/4ti2
-	sci-mathematics/normaliz
-	sci-mathematics/gfan
-	>=dev-libs/mpfr-2.4.1
-	>=sci-libs/mpir-1.3.1[cxx]
-	sys-libs/gdbm
-	virtual/blas
-	virtual/lapack
-	dev-util/ctags
-	sys-libs/ncurses
-	sys-process/time
-	emacs? ( virtual/emacs )"
-RDEPEND="${DEPEND}"
-
-SITEFILE=70Macaulay2-gentoo.el
-
-S="${WORKDIR}/Macaulay2-${PV}-r10737"
-
-src_prepare() {
-	# Patching .m2 files to look for external programs in
-	# /usr/bin
-	epatch "${FILESDIR}/paths-of-dependencies.patch"
-
-	# Fixing make warnings about unavailable jobserver:
-	sed -i "s/\$(MAKE)/+ \$(MAKE)/g" "${S}"/distributions/Makefile.in
-
-	eautoreconf
-}
-
-src_configure (){
-
-	# Recommended in bug #268064 Possibly unecessary
-	# but should not hurt anybody.
-	if ! use emacs; then
-		tags="ctags"
-	fi
-
-	CPPFLAGS="-I/usr/include/frobby" \
-		./configure --prefix="${D}/usr" \
-		--disable-encap \
-		--disable-strip \
-		--with-unbuilt-programs="4ti2 gfan normaliz" \
-		|| die "failed to configure Macaulay"
-}
-
-src_compile() {
-	# Parallel build not supported yet
-	emake -j1 || die "failed to build Macaulay"
-
-	if use emacs; then
-		cd "${S}/Macaulay2/emacs"
-		elisp-compile *.el || die "elisp-compile failed"
-	fi
-}
-
-src_test() {
-	emake check || die "tests failed"
-}
-
-src_install () {
-	# Parallel install not supported yet
-	emake -j1 install || die "install failed"
-
-	# Remove emacs files and install them in the
-	# correct place if use emacs
-
-	rm -rf "${D}"/usr/share/emacs/site-lisp
-	if use emacs; then
-		cd "${S}/Macaulay2/emacs"
-		elisp-install ${PN} *.elc *.el || die "elisp-install failed"
-		elisp-site-file-install "${FILESDIR}/${SITEFILE}"
-	fi
-}
-
-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/Macaulay2-1.4.ebuild b/sci-mathematics/Macaulay2/Macaulay2-1.4.ebuild
deleted file mode 100644
index 2e014ffb5..000000000
--- a/sci-mathematics/Macaulay2/Macaulay2-1.4.ebuild
+++ /dev/null
@@ -1,138 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit autotools elisp-common eutils
-
-IUSE="emacs optimization"
-MY_REV="12617"
-
-FACTORYVER="3-1-1"
-
-DESCRIPTION="research tool for commutative algebra and algebraic geometry"
-SRC_BASE="http://www.math.uiuc.edu/${PN}/Downloads/"
-SRC_URI="${SRC_BASE}/OtherSourceCode/1.4/factory-${FACTORYVER}.tar.gz
-		 ${SRC_BASE}/OtherSourceCode/1.4/libfac-${FACTORYVER}.tar.gz
-		 http://www.math.uiuc.edu/${PN}/Extra/gc-7.2alpha5-2010-09-03.tar.gz
-		 ${SRC_BASE}/SourceCode/${P}-r${MY_REV}-src.tar.bz2"
-
-HOMEPAGE="http://www.math.uiuc.edu/Macaulay2/"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="sys-libs/gdbm
-	>=dev-libs/ntl-5.5.2
-	>=sci-mathematics/pari-2.3.4[gmp]
-	>=sys-libs/readline-6.1
-	dev-libs/libxml2
-	sci-mathematics/frobby
-	sci-mathematics/4ti2
-	sci-mathematics/nauty
-	>=sci-mathematics/normaliz-2.5
-	sci-mathematics/gfan
-	>=dev-libs/mpfr-3.0.0
-	>=sci-libs/mpir-2.1.1[cxx]
-	sci-libs/cddlib
-	sci-libs/cdd+
-	sci-libs/lrslib[gmp]
-	virtual/blas
-	virtual/lapack
-	dev-util/ctags
-	sys-libs/ncurses
-	sys-process/time
-	emacs? ( virtual/emacs )"
-RDEPEND="${DEPEND}"
-
-SITEFILE=70Macaulay2-gentoo.el
-
-S="${WORKDIR}/${P}-r${MY_REV}"
-
-pkg_setup () {
-		tc-export CC CPP CXX
-}
-
-src_prepare() {
-	# Patching .m2 files to look for external programs in
-	# /usr/bin
-	epatch "${FILESDIR}"/${PV}-paths-of-external-programs.patch
-
-	# Fixing make warnings about unavailable jobserver:
-	sed -i "s/\$(MAKE)/+ \$(MAKE)/g" "${S}"/distributions/Makefile.in
-
-	# Factory, and libfac are statically linked libraries which (in this flavor)
-	# are not used by any other program. We build them internally and don't install them
-	mkdir "${S}/BUILD/tarfiles" || die "Creation of directory failed"
-	cp "${DISTDIR}/factory-3-1-1.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-	cp "${DISTDIR}/libfac-3-1-1.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-	# Macaulay 2 in this version insists on a snapshot of boehm-gc that is not available elsewhere
-	# We will let it build its internal version for now.
-	cp "${DISTDIR}/gc-7.2alpha5-2010-09-03.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-
-	eautoreconf
-}
-
-src_configure (){
-
-	# Recommended in bug #268064 Possibly unecessary
-	# but should not hurt anybody.
-	if ! use emacs; then
-		tags="ctags"
-	fi
-
-	CPPFLAGS="-I/usr/include/frobby" \
-		./configure --prefix="${D}/usr" \
-		--disable-encap \
-		--disable-strip \
-		$(use_enable optimization optimize) \
-		--enable-build-libraries="factory libfac" \
-		--with-unbuilt-programs="4ti2 gfan normaliz nauty cddplus lrslib" \
-		|| die "failed to configure Macaulay"
-}
-
-src_compile() {
-	# Parallel build not supported yet
-	emake -j1 || die "failed to build Macaulay"
-
-	if use emacs; then
-		cd "${S}/Macaulay2/emacs"
-		elisp-compile *.el || die "elisp-compile failed"
-	fi
-}
-
-src_test() {
-	emake check || die "tests failed"
-}
-
-src_install () {
-	# Parallel install not supported yet
-	emake -j1 install || die "install failed"
-
-	# Remove emacs files and install them in the
-	# correct place if use emacs
-
-	rm -rf "${D}"/usr/share/emacs/site-lisp
-	if use emacs; then
-		cd "${S}/Macaulay2/emacs"
-		elisp-install ${PN} *.elc *.el || die "elisp-install failed"
-		elisp-site-file-install "${FILESDIR}/${SITEFILE}"
-	fi
-}
-
-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/Macaulay2-1.4_pre.ebuild b/sci-mathematics/Macaulay2/Macaulay2-1.4_pre.ebuild
deleted file mode 100644
index 79cab13a0..000000000
--- a/sci-mathematics/Macaulay2/Macaulay2-1.4_pre.ebuild
+++ /dev/null
@@ -1,146 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit autotools elisp-common eutils subversion
-
-IUSE="emacs optimization"
-
-ESVN_REPO_URI="svn://svn.macaulay2.com/Macaulay2/release-branches/1.4"
-
-FACTORYVER="3-1-1"
-
-DESCRIPTION="research tool for commutative algebra and algebraic geometry"
-SRC_BASE="http://www.math.uiuc.edu/${PN}/Downloads/"
-SRC_URI="${SRC_BASE}/OtherSourceCode/1.4/factory-${FACTORYVER}.tar.gz
-		 ${SRC_BASE}/OtherSourceCode/1.4/libfac-${FACTORYVER}.tar.gz
-		 http://www.math.uiuc.edu/Macaulay2/Extra/gc-7.2alpha5-2010-09-03.tar.gz"
-
-HOMEPAGE="http://www.math.uiuc.edu/Macaulay2/"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS=""
-
-DEPEND="sys-libs/gdbm
-	>=dev-libs/ntl-5.5.2
-	>=sci-mathematics/pari-2.3.4[gmp]
-	>=sys-libs/readline-6.1
-	dev-libs/libxml2
-	sci-mathematics/frobby
-	sci-mathematics/4ti2
-	sci-mathematics/nauty
-	>=sci-mathematics/normaliz-2.5
-	sci-mathematics/gfan
-	>=dev-libs/mpfr-3.0.0
-	>=sci-libs/mpir-2.1.1[cxx]
-	sci-libs/cddlib
-	sci-libs/cdd+
-	sci-libs/lrslib[gmp]
-	virtual/blas
-	virtual/lapack
-	dev-util/ctags
-	sys-libs/ncurses
-	sys-process/time
-	emacs? ( virtual/emacs )"
-RDEPEND="${DEPEND}"
-
-SITEFILE=70Macaulay2-gentoo.el
-
-S="${WORKDIR}/${PN}-${PV}"
-
-RESTRICT="mirror"
-
-pkg_setup () {
-		tc-export CC CPP CXX
-}
-
-src_prepare() {
-	# Patching .m2 files to look for external programs in
-	# /usr/bin
-	epatch "${FILESDIR}"/${PV}-paths-of-external-programs.patch
-
-	# This is now a configure option:
-# 	if ! use optimization ; then
-# 		epatch "${FILESDIR}"/respect-CFLAGS.patch
-# 	fi
-
-	# Fixing make warnings about unavailable jobserver:
-	sed -i "s/\$(MAKE)/+ \$(MAKE)/g" "${S}"/distributions/Makefile.in
-
-	# Factory, and libfac are statically linked libraries which (in this flavor)
-	# are not used by any other program. We build them internally and don't install them
-	# Permission was granted to tomka by bicatali on IRC.
-	# Macaulay 2 in this version insists on a snapshot of boehm-gc that is not available elsewhere
-	# We will let it build its internal version for now.
-	mkdir "${S}/BUILD/tarfiles" || die "Creation of directory failed"
-	cp "${DISTDIR}/factory-3-1-1.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-	cp "${DISTDIR}/libfac-3-1-1.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-	cp "${DISTDIR}/gc-7.2alpha5-2010-09-03.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-
-	eautoreconf
-}
-
-src_configure (){
-
-	# Recommended in bug #268064 Possibly unecessary
-	# but should not hurt anybody.
-	if ! use emacs; then
-		tags="ctags"
-	fi
-
-	CPPFLAGS="-I/usr/include/frobby" \
-		./configure --prefix="${D}/usr" \
-		--disable-encap \
-		--disable-strip \
-		$(use_enable optimization optimize) \
-		--enable-build-libraries="factory libfac" \
-		--with-unbuilt-programs="4ti2 gfan normaliz nauty cddplus lrslib" \
-		|| die "failed to configure Macaulay"
-}
-
-src_compile() {
-	# Parallel build not supported yet
-	emake -j1 || die "failed to build Macaulay"
-
-	if use emacs; then
-		cd "${S}/Macaulay2/emacs"
-		elisp-compile *.el || die "elisp-compile failed"
-	fi
-}
-
-src_test() {
-	emake check || die "tests failed"
-}
-
-src_install () {
-	# Parallel install not supported yet
-	emake -j1 install || die "install failed"
-
-	# Remove emacs files and install them in the
-	# correct place if use emacs
-
-	rm -rf "${D}"/usr/share/emacs/site-lisp
-	if use emacs; then
-		cd "${S}/Macaulay2/emacs"
-		elisp-install ${PN} *.elc *.el || die "elisp-install failed"
-		elisp-site-file-install "${FILESDIR}/${SITEFILE}"
-	fi
-}
-
-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
index 7eb626448..75fe514c2 100644
--- a/sci-mathematics/Macaulay2/Manifest
+++ b/sci-mathematics/Macaulay2/Manifest
@@ -1,32 +1,15 @@
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-DIST Macaulay2-1.4-r12617-src.tar.bz2 4003881 RMD160 cb7958d8a347e45e10d717a8654d04e05a17ff00 SHA1 b88115b748c43a4f306a7b9fe6b47f7554498ec8 SHA256 9ddaf6f7288629647150067f46ca634a9b3c88fedfe3a9e21231531867ad9d91
 DIST factory-3-1-0.tar.gz 565374 RMD160 059ed1697f282d309e89d1cc2e0ce8bd94a8b4b3 SHA1 c41ab3cdc6ea51332169645e35c35c3fd6c4d94b SHA256 cb1768ccaaa71557ace880be0e88100bcfd420d3094ffac59d229cd852edc0ff
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 DIST libfac-3-1-0.tar.gz 91544 RMD160 2500d402328ad532756c677015c1d01f8594e394 SHA1 d005ddd58a180b8a91fe5728b96bde515c5d9cc5 SHA256 fc3dda08f7ec039635f8d7f1629546f4ac7620a69cf9332ca39e29dd822aee7d
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diff --git a/sci-mathematics/Macaulay2/files/1.4_pre-paths-of-external-programs.patch b/sci-mathematics/Macaulay2/files/1.4_pre-paths-of-external-programs.patch
deleted file mode 100644
index 9b16e5a51..000000000
--- a/sci-mathematics/Macaulay2/files/1.4_pre-paths-of-external-programs.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff -U 3 -dHrN M2source.orig/Macaulay2/packages/FourTiTwo.m2 M2source.patches/Macaulay2/packages/FourTiTwo.m2
---- M2source.orig/Macaulay2/packages/FourTiTwo.m2	2010-09-19 02:32:45.000000000 +0200
-+++ M2source.patches/Macaulay2/packages/FourTiTwo.m2	2010-09-19 02:37:25.000000000 +0200
-@@ -47,7 +47,7 @@
- 
- path'4ti2 = (options FourTiTwo).Configuration#"path"
- -- NOTE: the absolute path should be put into the .init file for 4ti2 inside the .Macaulay2 directory.
--if path'4ti2 == "" then path'4ti2 = prefixDirectory | currentLayout#"programs"
-+if path'4ti2 == "" then path'4ti2 = "/usr/bin/"
- 
- getFilename = () -> (
-      filename := temporaryFileName();
-diff -U 3 -dHrN M2source.orig/Macaulay2/packages/gfanInterface.m2 M2source.patches/Macaulay2/packages/gfanInterface.m2
---- M2source.orig/Macaulay2/packages/gfanInterface.m2	2010-09-19 02:32:45.000000000 +0200
-+++ M2source.patches/Macaulay2/packages/gfanInterface.m2	2010-09-19 02:38:08.000000000 +0200
-@@ -26,7 +26,7 @@
-      }
- 
- gfan'path = gfanInterface#Options#Configuration#"path"
--if gfan'path == "" then gfan'path = prefixDirectory | currentLayout#"programs"
-+if gfan'path == "" then gfan'path = "/usr/bin/"
- if instance(gfan'path, String) then gfan'path = {gfan'path}
- if not instance(gfan'path,List) then error "expected configuration option gfan'path to be a list of strings or a string"
- gfan'path = join(
-diff -U 3 -dHrN M2source.orig/Macaulay2/packages/Nauty.m2 M2source.patches/Macaulay2/packages/Nauty.m2
---- M2source.orig/Macaulay2/packages/Nauty.m2	2010-09-19 02:33:04.000000000 +0200
-+++ M2source.patches/Macaulay2/packages/Nauty.m2	2010-09-19 02:40:46.000000000 +0200
-@@ -27,7 +27,8 @@
- -- Check the ~/.Macaulay2/init-Nauty.m2 file for the absolute path.
- -- If it's not there, then use the M2-Programs directory.
- nauty'path = (options Nauty).Configuration#"path";
--if nauty'path == "" then nauty'path = prefixDirectory | currentLayout#"programs";
-+if nauty'path == "" then nauty'path = "/usr/bin/";
-+
- 
- -------------------
- -- Exports
-diff -U 3 -dHrN M2source.orig/Macaulay2/packages/Normaliz.m2 M2source.patches/Macaulay2/packages/Normaliz.m2
---- M2source.orig/Macaulay2/packages/Normaliz.m2	2010-09-19 02:33:04.000000000 +0200
-+++ M2source.patches/Macaulay2/packages/Normaliz.m2	2010-09-19 02:39:12.000000000 +0200
-@@ -156,7 +156,7 @@
-         nmzExec="norm64";
-     );
- --    return nmzExec;
--    return prefixDirectory | currentLayout#"programs" | nmzExec;
-+    return "/usr/bin/" | nmzExec;
- );
- 
- 
-diff -U 3 -dHrN M2source.orig/Macaulay2/packages/StatePolytope.m2 M2source.patches/Macaulay2/packages/StatePolytope.m2
---- M2source.orig/Macaulay2/packages/StatePolytope.m2	2010-09-19 02:32:46.000000000 +0200
-+++ M2source.patches/Macaulay2/packages/StatePolytope.m2	2010-09-19 02:38:39.000000000 +0200
-@@ -31,7 +31,7 @@
- 
- 
- gfanCommand = (options StatePolytope)#Configuration#"gfan command"
--if gfanCommand === "gfan" then gfanCommand = prefixDirectory | currentLayout#"programs" | gfanCommand
-+if gfanCommand === "gfan" then gfanCommand = "/usr/bin/" | gfanCommand
- gfanCommand = "!" | gfanCommand
- 
- --The next two functions print out the ring and the ideal in the format required by gfan