diff options
Diffstat (limited to 'sci-mathematics/Macaulay2')
| -rw-r--r-- | sci-mathematics/Macaulay2/Macaulay2-1.7_pre.ebuild | 154 | ||||
| -rw-r--r-- | sci-mathematics/Macaulay2/Manifest | 4 | ||||
| -rw-r--r-- | sci-mathematics/Macaulay2/files/1.6-lapack.patch | 50 | ||||
| -rw-r--r-- | sci-mathematics/Macaulay2/files/1.6-paths-of-external-programs.patch | 73 | ||||
| -rw-r--r-- | sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el | 11 | ||||
| -rw-r--r-- | sci-mathematics/Macaulay2/metadata.xml | 16 |
6 files changed, 308 insertions, 0 deletions
diff --git a/sci-mathematics/Macaulay2/Macaulay2-1.7_pre.ebuild b/sci-mathematics/Macaulay2/Macaulay2-1.7_pre.ebuild new file mode 100644 index 000000000000..b7bd82d811d8 --- /dev/null +++ b/sci-mathematics/Macaulay2/Macaulay2-1.7_pre.ebuild @@ -0,0 +1,154 @@ +# 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 + +FACTORY="factory-4.0.0+m4" +FACTORY_GFTABLES="factory.4.0.1-gftables" + +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/trunk" +SRC_URI=" + http://dev.gentoo.org/~tomka/files/${P}.tar.bz2 + ${BASE_URI}/${FACTORY}.tar.gz + ${BASE_URI}/${FACTORY_GFTABLES}.tar.gz + ${BASE_URI}/gtest-1.7.0.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="amd64 x86" +IUSE="debug emacs +optimization" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS} + sys-process/time + virtual/pkgconfig" + +RDEPEND="${PYTHON_DEPS} + sys-libs/gdbm + <dev-libs/ntl-7 + 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/mpir[cxx] + dev-libs/mpfr + 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="${WORKDIR}/M2/" + +pkg_setup () { + tc-export CC CPP CXX PKG_CONFIG + append-cppflags "-I/usr/include/frobby" + # gtest needs python:2 + python-single-r1_pkg_setup +} + +src_prepare() { + # Patching .m2 files to look for external programs in + # /usr/bin + epatch "${FILESDIR}"/1.6-paths-of-external-programs.patch + + # Shortcircuit lapack tests + epatch "${FILESDIR}"/1.6-lapack.patch + + # Factory is a statically linked library which (in this flavor) are not used by any + # other program. We build it internally and don't install it. + cp "${DISTDIR}/${FACTORY}.tar.gz" "${S}/BUILD/tarfiles/" \ + || die "copy failed" + cp "${DISTDIR}/${FACTORY_GFTABLES}.tar.gz" "${S}/BUILD/tarfiles/" \ + || die "copy failed" + # Macaulay2 developers want that gtest is built internally because + # the documentation says it may fail if build with options not the + # same as the tested program. + cp "${DISTDIR}/gtest-1.7.0.tar.gz" "${S}/BUILD/tarfiles/" \ + || die "copy failed" + + eautoreconf +} + +src_configure (){ + # Recommended in bug #268064 Possibly unecessary + # but should not hurt anybody. + if ! use emacs; then + tags="ctags" + fi + + # configure instead of econf to enable install with --prefix + ./configure LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" \ + --prefix="${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=550 -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 new file mode 100644 index 000000000000..1cab32948f73 --- /dev/null +++ b/sci-mathematics/Macaulay2/Manifest @@ -0,0 +1,4 @@ +DIST Macaulay2-1.7_pre.tar.bz2 4639477 SHA256 b14918187724f8911bc50edf87c9692209ff0c2191feb257084adc87609eb1cd SHA512 e70376d1e54b6e239ebb3bf676507a2115fdf5c4fbe05f320553029a84114b74d78f54e4d1bdc7643131f3c45c301e83c21ff99e4d4b675372e971368398d6f5 WHIRLPOOL 396311aadb8a7845deaee5aeca49c431430abc46201e935ef72c4579c9cbe6cd4da85f3e09ff0fe647031f8050fb7c62f63ecce251bf34648c1848cd00eef68e +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/1.6-lapack.patch b/sci-mathematics/Macaulay2/files/1.6-lapack.patch new file mode 100644 index 000000000000..e9a434eeb28e --- /dev/null +++ b/sci-mathematics/Macaulay2/files/1.6-lapack.patch @@ -0,0 +1,50 @@ +--- configure.ac 2012-10-24 09:29:55.240498786 -0700 ++++ configure.ac.2 2012-10-30 15:07:27.172846300 -0700 +@@ -1285,46 +1285,7 @@ + done + test $BUILD_factory = yes && BUILTLIBS="$SINGULARLIBS $BUILTLIBS" + +-# 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 vecLib framework is available]) +- SAVELIBS=$LIBS LIBS="-framework vecLib $LIBS" +- AC_LANG(C) +- AC_LINK_IFELSE( +- [AC_LANG_PROGRAM(,[sgemv_();dgetrf_();])], +- [ +- AC_MSG_RESULT(yes) +- ], +- [ +- AC_MSG_RESULT(no) +- LIBS=$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 -lblas $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" + + if test $BUILD_memtailor = yes + then BUILTLIBS="-lmemtailor $BUILTLIBS" 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 new file mode 100644 index 000000000000..4c090deec9d8 --- /dev/null +++ b/sci-mathematics/Macaulay2/files/1.6-paths-of-external-programs.patch @@ -0,0 +1,73 @@ +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 new file mode 100644 index 000000000000..ac86e2132ed5 --- /dev/null +++ b/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el @@ -0,0 +1,11 @@ +;; 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/metadata.xml b/sci-mathematics/Macaulay2/metadata.xml new file mode 100644 index 000000000000..3513de74db1a --- /dev/null +++ b/sci-mathematics/Macaulay2/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>tomka@gentoo.org</email> + <name>Thomas Kahle</name> + </maintainer> + <herd>sci-mathematics</herd> + <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> |