gentoo resync : 15.01.2020

6 files changed, 0 insertions, 291 deletions

diff --git a/sci-mathematics/Macaulay2/Macaulay2-1.8.2.1-r1.ebuild b/sci-mathematics/Macaulay2/Macaulay2-1.8.2.1-r1.ebuild
deleted file mode 100644
index acd1d0deb899..000000000000
--- a/sci-mathematics/Macaulay2/Macaulay2-1.8.2.1-r1.ebuild
+++ /dev/null
@@ -1,136 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools elisp-common eutils flag-o-matic multilib 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="https://dev.gentoo.org/~tomka/files/"
-SRC_URI="
-	${BASE_URI2}/${P}-fat.tar.bz2
-"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~arm ~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/" \
-		--libdir='${exec_prefix}'/$(get_libdir)/ \
-		--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
deleted file mode 100644
index 4356ae237912..000000000000
--- a/sci-mathematics/Macaulay2/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX 1.6-paths-of-external-programs.patch 3767 BLAKE2B 01c974baf0dbf8246eb3c8aa747f0fc5dc02853fa28fdef417deffb56f8a1af9919ba50f9fcaa42ed575c90761519b6239e9544f8600b1f086d8215ca466a9ae SHA512 556944da47742a3c4539e084bb6dab7c2375733eb4cbe4d14e1dea852bba3ac61e5f6ad5f805958a52d371a918c8672f7f0308c7c0454a502ca61bb59fea6bf5
-AUX 70Macaulay2-gentoo.el 597 BLAKE2B 58de58a469874a24be539fc104d829304d58237b1780dff5b61e6e5a497b150a0e4b342e797ab33de7d22ca58b93cbfd50f41057749fb6f3f84083eec4bb2d24 SHA512 2d6b6d3c85ca93bf4d4100f2172013074dec83f8ce067af219b026ca2b495ff1aa7fb3da027b64ef8e55ad431ce5d42bffdad1ab474bb3e95240ac4235f2f986
-AUX Macaulay2-1.8.2.1-lapack.patch 1836 BLAKE2B 6464d859336d16fffcb8bc1aaed9442a258429e9e325118cc1d55944fe851c0a531da3fca3f57849341066167b3c1a768051b78c25763ca958b90de27061fb34 SHA512 d3d13a67daeda87753c7c4daf888d2982109cb13bc0b88be46c2dd4993715077cf0ce5e155876bf5aaf51c886ce348df550184ade4af71e7143c2c2eb16c3b7f
-DIST Macaulay2-1.8.2.1-fat.tar.bz2 26102483 BLAKE2B 3841505051b544cc2bc2c302032120b0019e8cd7bf5573c958e0309bf40fbb89f5a57da81759f5880d2fb2c1bc586c3af4b5488500cad43699e7562da0f4f821 SHA512 64f7ea9b01cdb308023a55d8ab8bd6733540f25161dacf27052c071e143418c68c639d5115cf32540c11594b70eae14473f4ef6ce5bd12b6df0722da7c13dd2c
-EBUILD Macaulay2-1.8.2.1-r1.ebuild 3279 BLAKE2B 5653e6a759199ccf422d4142ff55fbc6caa33c7e2500070573f2c11298a12be361b1e11a3d1167ff8ecc1ba1cefc811fa6c4ac61dd3030156c788a8c6f1724af SHA512 ff3476345a0786ac0754de306c273650499f9f7a6264b199ffebd339988e07b33abf4583ee2b96a73c0f3c3c3f731957af760d84f883c32cad61ccd6783a9960
-MISC metadata.xml 527 BLAKE2B 8aac8a049fbb72e0ee7ee5cd71204857d86f00aa97c892f84b771628f1511e5124de7769006efb98e29e4644e9bcdf5a35c17eda63ca3d7c58a04e23cba19ab1 SHA512 7ca19042c8405096453426ec3582c3d342ff9a37ec520372f11ffd4e00a78ef018cc49d3f851e6dff2a000314f0eb6de0a4640d37edcb19ff2ad65196aaa03a1
diff --git a/sci-mathematics/Macaulay2/files/1.6-paths-of-external-programs.patch b/sci-mathematics/Macaulay2/files/1.6-paths-of-external-programs.patch
deleted file mode 100644
index 4c090deec9d8..000000000000
--- a/sci-mathematics/Macaulay2/files/1.6-paths-of-external-programs.patch
+++ /dev/null
@@ -1,73 +0,0 @@
-diff -U 3 -dHrN M2source/Macaulay2/packages/FourTiTwo.m2 M2source.patch/Macaulay2/packages/FourTiTwo.m2
---- M2source/Macaulay2/packages/FourTiTwo.m2	2011-09-22 14:36:51.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/FourTiTwo.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -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/Macaulay2/packages/gfanInterface.m2 M2source.patch/Macaulay2/packages/gfanInterface.m2
---- M2source/Macaulay2/packages/gfanInterface.m2	2011-05-14 12:00:59.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/gfanInterface.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -25,7 +25,7 @@
-      }
- 
- 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/Macaulay2/packages/NautyGraphs.m2 M2source.patch/Macaulay2/packages/NautyGraphs.m2
---- M2source/Macaulay2/packages/NautyGraphs.m2	2011-08-26 11:05:30.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/NautyGraphs.m2	2011-09-24 21:25:53.000000000 +0100
-@@ -32,7 +32,7 @@
- -- Check the ~/.Macaulay2/init-NautyGraphs.m2 file for the absolute path.
- -- If it's not there, then use the M2-Programs directory.
- nauty'path = (options NautyGraphs).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/Macaulay2/packages/Nauty.m2 M2source.patch/Macaulay2/packages/Nauty.m2
---- M2source/Macaulay2/packages/Nauty.m2	2011-08-26 11:05:30.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/Nauty.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -48,7 +48,8 @@
- -- 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/Macaulay2/packages/Normaliz.m2 M2source.patch/Macaulay2/packages/Normaliz.m2
---- M2source/Macaulay2/packages/Normaliz.m2	2011-05-25 16:47:50.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/Normaliz.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -166,7 +166,7 @@
-         nmzExec="normaliz";
-     );
- --    return nmzExec;
--    return prefixDirectory | currentLayout#"programs" | nmzExec;
-+    return "/usr/bin/" | nmzExec;
- );
- 
- 
-diff -U 3 -dHrN M2source/Macaulay2/packages/StatePolytope.m2 M2source.patch/Macaulay2/packages/StatePolytope.m2
---- M2source/Macaulay2/packages/StatePolytope.m2	2010-09-10 16:47:20.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/StatePolytope.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -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
diff --git a/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el b/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el
deleted file mode 100644
index ac86e2132ed5..000000000000
--- a/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el
+++ /dev/null
@@ -1,11 +0,0 @@
-;; sci-mathematics/Macaulay2 init file
-
-(add-to-list 'load-path "/usr/share/emacs/site-lisp/Macaulay2")
-
-(defvar M2-exe "/usr/bin/M2" "*The default Macaulay2 executable name.")
-(autoload 'M2 "M2.el" "Run Macaulay 2 in a buffer." t)
-(autoload 'Macaulay2 "M2" "Run Macaulay 2 in a buffer, non-interactive." t)
-(autoload 'M2-mode "M2" "Macaulay 2 editing mode" t)
-(autoload 'm2-mode "M2" "Macaulay 2 editing mode, name in lower case" t)
-(autoload 'm2-comint-mode "M2" "Macaulay 2 command interpreter mode, name in lower case" t)
-(setq auto-mode-alist (append auto-mode-alist '(("\\.m2$" . M2-mode))))
\ No newline at end of file
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
deleted file mode 100644
index 25185e7c560e..000000000000
--- a/sci-mathematics/Macaulay2/files/Macaulay2-1.8.2.1-lapack.patch
+++ /dev/null
@@ -1,50 +0,0 @@
---- 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=
diff --git a/sci-mathematics/Macaulay2/metadata.xml b/sci-mathematics/Macaulay2/metadata.xml
deleted file mode 100644
index 76821a208f0c..000000000000
--- a/sci-mathematics/Macaulay2/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-mathematics@gentoo.org</email>
-    <name>Gentoo Mathematics Project</name>
-  </maintainer>
-  <use>
-    <flag name="optimization">Accept upstream's choices for -O option, i.e. -O3 almost everywhere.</flag>
-  </use>
-  <longdescription lang="en">
-  Macaulay2 is a research tool for algraic geometry and commutative
-  algebra. 
-</longdescription>
-</pkgmetadata>