sci-mathematics/Macaulay2: bump to 1.8.2.1

Package-Manager: portage-2.2.26

3 files changed, 187 insertions, 0 deletions

diff --git a/sci-mathematics/Macaulay2/Macaulay2-1.8.2.1.ebuild b/sci-mathematics/Macaulay2/Macaulay2-1.8.2.1.ebuild
new file mode 100644
index 000000000000..f77984467c87
--- /dev/null
+++ b/sci-mathematics/Macaulay2/Macaulay2-1.8.2.1.ebuild
@@ -0,0 +1,136 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools elisp-common eutils flag-o-matic python-single-r1 toolchain-funcs
+
+# To stop the download madness we now roll our own tarball (Feb 2016)
+DESCRIPTION="Research tool for commutative algebra and algebraic geometry"
+HOMEPAGE="http://www.math.uiuc.edu/Macaulay2/"
+BASE_URI="http://www.math.uiuc.edu/Macaulay2/Downloads/OtherSourceCode/"
+BASE_URI2="http://dev.gentoo.org/~tomka/files/"
+SRC_URI="
+	${BASE_URI2}/${P}-fat.tar.bz2
+"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug emacs +optimization"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+	sys-process/time
+	virtual/pkgconfig"
+
+RDEPEND="${PYTHON_DEPS}
+	sys-libs/gdbm
+	sci-mathematics/pari[gmp]
+	>=sys-libs/readline-6.1
+	dev-libs/libxml2:2
+	sci-mathematics/flint[gc]
+	sci-mathematics/frobby
+	sci-mathematics/4ti2
+	sci-mathematics/nauty
+	>=sci-mathematics/normaliz-2.8
+	sci-mathematics/gfan
+	sci-libs/cdd+
+	sci-libs/cddlib
+	sci-libs/lrslib[gmp]
+	virtual/blas
+	virtual/lapack
+	dev-util/ctags
+	sys-libs/ncurses
+	>=dev-libs/boehm-gc-7.4[threads]
+	dev-libs/libatomic_ops
+	emacs? ( virtual/emacs )"
+
+SITEFILE=70Macaulay2-gentoo.el
+
+S="${WORKDIR}/M2/M2"
+
+pkg_setup () {
+	tc-export CC CPP CXX PKG_CONFIG
+	append-cppflags "-I/usr/include/frobby"
+	# gtest needs python:2
+	python-single-r1_pkg_setup
+}
+
+src_prepare() {
+	# Patching .m2 files to look for external programs in
+	# /usr/bin
+	epatch "${FILESDIR}"/1.6-paths-of-external-programs.patch
+
+	# Shortcircuit lapack tests
+	epatch "${FILESDIR}/${P}"-lapack.patch
+
+	eautoreconf
+}
+
+src_configure (){
+	# Recommended in bug #268064 Possibly unecessary
+	# but should not hurt anybody.
+	if ! use emacs; then
+		tags="ctags"
+	fi
+
+	# configure instead of econf to enable install with --prefix
+	./configure LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" \
+		--prefix="${D}/usr" \
+		--disable-encap \
+		--disable-strip \
+		--with-issue=Gentoo \
+		$(use_enable optimization optimize) \
+		$(use_enable debug) \
+		--enable-build-libraries="factory" \
+		--with-unbuilt-programs="4ti2 gfan normaliz nauty cddplus lrslib" \
+		|| die "failed to configure Macaulay"
+}
+
+src_compile() {
+	# Parallel build not supported yet
+	emake IgnoreExampleErrors=true -j1
+
+	if use emacs; then
+		cd "${S}/Macaulay2/emacs" || die
+		elisp-compile *.el
+	fi
+}
+
+src_test() {
+	# No parallel tests yet & Need to increase the time
+	# limit for long running tests in Schubert2 to pass
+	emake TLIMIT=750 -j1 check
+}
+
+src_install () {
+	# Parallel install not supported yet
+	emake IgnoreExampleErrors=true -j1 install
+
+	# Remove emacs files and install them in the
+	# correct place if use emacs
+	rm -rf "${ED}"/usr/share/emacs/site-lisp || die
+	if use emacs; then
+		cd "${S}/Macaulay2/emacs" || die
+		elisp-install ${PN} *.elc *.el
+		elisp-site-file-install "${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 1cab32948f73..0ee77b1659da 100644
--- a/sci-mathematics/Macaulay2/Manifest
+++ b/sci-mathematics/Macaulay2/Manifest
@@ -1,4 +1,5 @@
 DIST Macaulay2-1.7_pre.tar.bz2 4639477 SHA256 b14918187724f8911bc50edf87c9692209ff0c2191feb257084adc87609eb1cd SHA512 e70376d1e54b6e239ebb3bf676507a2115fdf5c4fbe05f320553029a84114b74d78f54e4d1bdc7643131f3c45c301e83c21ff99e4d4b675372e971368398d6f5 WHIRLPOOL 396311aadb8a7845deaee5aeca49c431430abc46201e935ef72c4579c9cbe6cd4da85f3e09ff0fe647031f8050fb7c62f63ecce251bf34648c1848cd00eef68e
+DIST Macaulay2-1.8.2.1-fat.tar.bz2 26102483 SHA256 11e13fbb4aeeddae1547ed01e499e3f8961446cb9bec8b3162b29cadd2f280c1 SHA512 64f7ea9b01cdb308023a55d8ab8bd6733540f25161dacf27052c071e143418c68c639d5115cf32540c11594b70eae14473f4ef6ce5bd12b6df0722da7c13dd2c WHIRLPOOL 3f9c838d6624f95076957743bf402236708cb2af15b84d24c4446fb193f7608698cc63e43eb8eff8bf878963ce2a9fd85f37128f73d1dbd43d4c0bcda980753d
 DIST factory-4.0.0+m4.tar.gz 4711126 SHA256 9b2498cc7fc6765f1c586e8061ebe236cdce4b32a44721a235ad2644ec3124fb SHA512 1dacb9aae52e655bccbbc960397b02351050791594dd9c39771f0da7f8c6e8130a8827c2a675c3fbaaa214606e123ac9776e1c73d143649353cefc50cadeea3e WHIRLPOOL 47c4d6261fc6cc9c172035d8774f0cde9fa669fa164fc4a0f47e84ba789d69d14f5a16d042451564412fdedddec71335714ad751508495c22cea25b69f10b925
 DIST factory.4.0.1-gftables.tar.gz 2974152 SHA256 9cd158ceb1c2b1c47bdca2c0b004bba92cb0e0aaa0ea6a43ca784ebdce10eebd SHA512 060c58fe6e4565dd5e7649bfa070f14dec3c383a55ebab52a9f02b58a6405e2183e0c7e08964cddb87b81e872c0d8a52d7bd4575d07269547be544cf6a725a76 WHIRLPOOL a721a6824681118578c7289cea77a3f47e5c7654f30dc454eaac76b19cc89e416ae54b8d21a69f897d7087d4b67990634fc960f81df2ea53f428868d608dc9c2
 DIST gtest-1.7.0.tar.gz 1001582 SHA256 c0f860eee47c86e0aeb462fd0bdfd70e3975297e0b8b178e0e03a95e1f6c9bc4 SHA512 a9f5c047b39efb2d11b55ee9913662ca402ac6837b3ad2d278ecfbd1caf32ed4546f169e3e92503d57bf3b62ccf89cd062da1c7ea3638aae98e868d2766363c3 WHIRLPOOL 36edbdf8be7c3793a89918a3c43d74e75a6281a37c394f7d2f20506130a76aab04a3beddba01bf7f0e9b6901c7e834ca014c31c913c0ea846d3f6be9c93599d2
diff --git a/sci-mathematics/Macaulay2/files/Macaulay2-1.8.2.1-lapack.patch b/sci-mathematics/Macaulay2/files/Macaulay2-1.8.2.1-lapack.patch
new file mode 100644
index 000000000000..25185e7c560e
--- /dev/null
+++ b/sci-mathematics/Macaulay2/files/Macaulay2-1.8.2.1-lapack.patch
@@ -0,0 +1,50 @@
+--- configure.ac	2015-09-03 14:49:42.000000000 +0200
++++ configure.ac.new	2016-01-27 12:50:07.812215547 +0100
+@@ -1301,46 +1301,7 @@
+      BUILTLIBS="$SINGULARLIBS $BUILTLIBS"
+ fi
+ 
+-# we need to do the fortran library testing last, in case AC_SEARCH_LIBS adds
+-# one of them to $LIBS, making it impossible to check for the presence of C or
+-# C++ libraries.  (I'm not sure why putting -llapack on the gcc command line
+-# needlessly causes the library to be linked against.)
+-FORTRANUSED=no
+-if test "$LAPACK" = yes
+-then AC_MSG_CHECKING([whether the Accelerate framework is available])
+-     SAVELIBS=$LIBS LIBS="-framework Accelerate $LIBS"
+-     AC_LANG(C)
+-     AC_LINK_IFELSE(
+-	 [AC_LANG_PROGRAM(,[sgemv_();dgetrf_();])],
+-	 [
+-	     AC_MSG_RESULT(yes)
+-	     ],
+-	 [
+-	     AC_MSG_RESULT(no)
+-	     LIBS=$SAVELIBS
+-	     FORTRANUSED=yes
+-	     if test $BUILD_lapack = no
+-	     then AC_LANG(Fortran)
+-	     	  if test "$FC" = ""
+-		  then AC_MSG_ERROR(no fortran compiler found)
+-		  else AC_MSG_NOTICE(using fortran compiler $FC)
+-		  fi
+-		  AC_SEARCH_LIBS(sgemv,blas f77blas,,BUILD_lapack=yes)
+-		  AC_SEARCH_LIBS(dgetrf,lapack,,BUILD_lapack=yes)
+-	     fi
+-	 ])
+-fi
+-test $BUILD_lapack = yes && BUILTLIBS="-llapack -lrefblas $BUILTLIBS"
+-
+-if test $BUILD_lapack = yes
+-then # test whether the fortran compiler can handle lapack, which, starting with
+-     # version 3.2, requires fortran 90, not fortran 77
+-    AC_LANG(Fortran)
+-    AC_MSG_CHECKING([whether the fortran compiler is modern enough for lapack])
+-    AC_COMPILE_IFELSE([instrinsic maxloc],
+-	AC_MSG_ERROR(the fortran compiler ($FC) does not support the Fortran 90 language required for compiling lapack),
+-	AC_MSG_RESULT(yes))
+-fi
++BUILTLIBS="$(${PKG_CONFIG} --libs lapack) $BUILTLIBS"
+ 
+ test "$USE_FCLIBS" = no && FCLIBS=
+ test "$FORTRANUSED" = no && FCLIBS=