diff options
Diffstat (limited to 'sci-mathematics')
182 files changed, 648 insertions, 7831 deletions
diff --git a/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild b/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild deleted file mode 100644 index 46e370ce0..000000000 --- a/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild +++ /dev/null @@ -1,176 +0,0 @@ -# Copyright 1999-2014 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 git-r3 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=" - ${BASE_URI}/${FACTORY}.tar.gz - ${BASE_URI}/${FACTORY_GFTABLES}.tar.gz - ${BASE_URI}/gtest-1.7.0.tar.gz" -EGIT_REPO_URI="git://github.com/Macaulay2/M2.git" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="" -IUSE="debug emacs +optimization" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="${PYTHON_DEPS} - sys-process/time - virtual/pkgconfig - app-arch/unzip - app-text/dos2unix" -# Unzip and dos2unix just for normaliz - -RDEPEND="${PYTHON_DEPS} - sys-libs/gdbm - dev-libs/ntl - 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-7.2_alpha6[threads] - dev-libs/libatomic_ops - emacs? ( virtual/emacs )" - -SITEFILE=70Macaulay2-gentoo.el - -S="${WORKDIR}/${PN}-${PV}/" - -RESTRICT="mirror" - -src_unpack (){ - # unpack "Normaliz2.8.zip" - git-r3_src_unpack - # Undo one level of directory until git allows to checkout - # subdirectories - mv "${S}"/M2/* "${S}" || die - # Need to get rid of this now because install wants this location later - rm -r "${S}/M2" || die -} - -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() { - # Put updated Normaliz.m2 in place - # cp "${WORKDIR}/Normaliz2.8/Macaulay2/Normaliz.m2" \ - # "${S}/Macaulay2/packages" || die - # dos2unix "${S}/Macaulay2/packages/Normaliz.m2" || die - - # Patching .m2 files to look for external programs in - # /usr/bin - epatch "${FILESDIR}"/${PV}-paths-of-external-programs.patch - - # Shortcircuit lapack tests - epatch "${FILESDIR}"/${PV}-lapack.patch - - # Factory is a statically linked library which (in this flavor) are not used by any - # other program. We build it internally and don't install it. - cp "${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) \ - $(use_enable debug) \ - --enable-build-libraries="factory" \ - --with-unbuilt-programs="4ti2 gfan normaliz nauty cddplus lrslib" \ - || die "failed to configure Macaulay" -} - -src_compile() { - # Parallel build not supported yet - # emake -j1 - # For trunk builds we may wish to ignore example errors - emake IgnoreExampleErrors=true -j1 - - if use emacs; then - cd "${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 - # NumericalAlgebraicGeometry fails (during install too?) - 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 53f184fa9..000000000 --- a/sci-mathematics/Macaulay2/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -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/70Macaulay2-gentoo.el b/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el deleted file mode 100644 index ac86e2132..000000000 --- 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/9999-lapack.patch b/sci-mathematics/Macaulay2/files/9999-lapack.patch deleted file mode 100644 index e9a434eeb..000000000 --- a/sci-mathematics/Macaulay2/files/9999-lapack.patch +++ /dev/null @@ -1,50 +0,0 @@ ---- 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/9999-paths-of-external-programs.patch b/sci-mathematics/Macaulay2/files/9999-paths-of-external-programs.patch deleted file mode 100644 index 4c090deec..000000000 --- a/sci-mathematics/Macaulay2/files/9999-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/paths-of-dependencies.patch b/sci-mathematics/Macaulay2/files/paths-of-dependencies.patch deleted file mode 100644 index f8117a5fa..000000000 --- a/sci-mathematics/Macaulay2/files/paths-of-dependencies.patch +++ /dev/null @@ -1,48 +0,0 @@ -diff -rupN 1.3.1/Macaulay2/packages/FourTiTwo.m2 1.3.1-pathspatched/Macaulay2/packages/FourTiTwo.m2 ---- 1.3.1/Macaulay2/packages/FourTiTwo.m2 2009-11-12 18:40:50.000000000 +0100 -+++ 1.3.1-pathspatched/Macaulay2/packages/FourTiTwo.m2 2009-11-16 11:41:01.000000000 +0100 -@@ -47,7 +47,7 @@ export { - - 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 -rupN 1.3.1/Macaulay2/packages/gfanInterface.m2 1.3.1-pathspatched/Macaulay2/packages/gfanInterface.m2 ---- 1.3.1/Macaulay2/packages/gfanInterface.m2 2009-11-12 18:40:50.000000000 +0100 -+++ 1.3.1-pathspatched/Macaulay2/packages/gfanInterface.m2 2009-11-16 11:41:17.000000000 +0100 -@@ -26,7 +26,7 @@ export { - } - - gfan'path = gfanInterface#Options#Configuration#"path" --if gfan'path == "" then gfan'path = prefixDirectory | currentLayout#"programs" -+if gfan'path == "" then gfan'path = "/usr/bin/" - - fig2dev'path = gfanInterface#Options#Configuration#"fig2devpath" - -diff -rupN 1.3.1/Macaulay2/packages/Normaliz.m2 1.3.1-pathspatched/Macaulay2/packages/Normaliz.m2 ---- 1.3.1/Macaulay2/packages/Normaliz.m2 2009-11-12 18:40:50.000000000 +0100 -+++ 1.3.1-pathspatched/Macaulay2/packages/Normaliz.m2 2009-11-16 11:42:01.000000000 +0100 -@@ -30,7 +30,7 @@ export{setNmzExecPath, getNmzExecPath, - - - -- initialising some values --nmzExecPath=prefixDirectory|currentLayout#"programs"; -+nmzExecPath="/usr/bin/"; - nmzDataPath=""; - nmzFilename=""; - nmzUserCalled=true; -- wether the user calls a method -diff -rupN 1.3.1/Macaulay2/packages/StatePolytope.m2 1.3.1-pathspatched/Macaulay2/packages/StatePolytope.m2 ---- 1.3.1/Macaulay2/packages/StatePolytope.m2 2009-11-12 18:40:50.000000000 +0100 -+++ 1.3.1-pathspatched/Macaulay2/packages/StatePolytope.m2 2009-11-16 11:41:13.000000000 +0100 -@@ -31,7 +31,7 @@ export { - - - 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/metadata.xml b/sci-mathematics/Macaulay2/metadata.xml deleted file mode 100644 index 05e3f791a..000000000 --- a/sci-mathematics/Macaulay2/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>tom111@gmx.de</email> - <name>Thomas Kahle</name> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <use> - <flag name="optimization">Disable to build with -O0 for debugging.</flag> - </use> - <longdescription lang="en"> -Macaulay2 is a research tool for algraic geometry and commutative -algebra. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/Oid/Manifest b/sci-mathematics/Oid/Manifest index 109bdc2b8..dbc9c4bab 100644 --- a/sci-mathematics/Oid/Manifest +++ b/sci-mathematics/Oid/Manifest @@ -1,2 +1,2 @@ -DIST Oid4-0.tar.gz 244760 BLAKE2B 6acf06087bffac9bca6ed14bdd2319201e14d126b3299049ee713ebe87c00dfdc783559df06f2e8c1e56af469cdce296a42cb1927bae0b878a4c8187b67b7b9d SHA512 82d4039c3d8d499f7ad4e2df3626782c6c92629f141c12dd78b3b9d9175cfd3aeb0a4ed3a211e3aa7a6b0fec3b0b9112deb6c28c866013e1cf62cb165e786ef5 +DIST Oid-4.0.tar.gz 244760 BLAKE2B 6acf06087bffac9bca6ed14bdd2319201e14d126b3299049ee713ebe87c00dfdc783559df06f2e8c1e56af469cdce296a42cb1927bae0b878a4c8187b67b7b9d SHA512 82d4039c3d8d499f7ad4e2df3626782c6c92629f141c12dd78b3b9d9175cfd3aeb0a4ed3a211e3aa7a6b0fec3b0b9112deb6c28c866013e1cf62cb165e786ef5 DIST OidUserManual4-0.pdf 191264 BLAKE2B bddb1aa328195adb02d9ce25670a2c5c6feea5104168d7a4f65e2d69c0c106ac193dc63bc661c1efebc4feedbaf1db10cdf1fc41eb4d16dd26d2698e3f0e0776 SHA512 bccefaf64a9765bb3bf3927091f2d467e773c12b4694dcf7fd42d761545ad324a3bc4398ae5d3fdffef466e3731fcbc322016af9148cd81705df52d4da756043 diff --git a/sci-mathematics/Oid/Oid-4.0.ebuild b/sci-mathematics/Oid/Oid-4.0.ebuild index bbc267637..ce967fd46 100644 --- a/sci-mathematics/Oid/Oid-4.0.ebuild +++ b/sci-mathematics/Oid/Oid-4.0.ebuild @@ -1,35 +1,38 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils java-pkg-2 versionator +inherit java-pkg-2 -MY_PV=$(replace_version_separator 1 '-') +MY_PV="${PV//./-}" MY_P="${PN}${MY_PV}" DESCRIPTION="An interactive, extensible software system for experimenting with matroids" -HOMEPAGE="http://sites.google.com/site/wwwmatroids/" +HOMEPAGE="https://sites.google.com/site/wwwmatroids/" SRC_URI=" - http://sites.google.com/site/wwwmatroids/${MY_P}.tar.gz - doc? ( http://sites.google.com/site/wwwmatroids/${PN}UserManual${MY_PV}.pdf )" + https://sites.google.com/site/wwwmatroids/${MY_P}.tar.gz -> ${P}.tar.gz + https://sites.google.com/site/wwwmatroids/${PN}UserManual${MY_PV}.pdf +" KEYWORDS="~amd64 ~x86" SLOT="0" LICENSE="GPL-2" -IUSE="doc" DEPEND=">=virtual/jdk-1.4:*" RDEPEND=">=virtual/jre-1.4:*" # The source uses 'enum' as an identifier, therefore: JAVA_PKG_WANT_SOURCE="1.4" +S="${WORKDIR}" src_prepare () { mkdir classes || die -# change path names + # change path names sed -i -e 's:NAME = ":NAME = "/usr/share/Oid/:' MatroidToolkit.java || die + + default } src_compile () { @@ -42,8 +45,7 @@ src_install () { java-pkg_dojar Oid.jar java-pkg_dolauncher - - use doc && dodoc "${DISTDIR}"/OidUserManual4-0.pdf + dodoc "${DISTDIR}"/OidUserManual4-0.pdf insinto /usr/share/Oid doins matroid*.txt diff --git a/sci-mathematics/Oid/metadata.xml b/sci-mathematics/Oid/metadata.xml index a457ecd20..7206a3f8f 100644 --- a/sci-mathematics/Oid/metadata.xml +++ b/sci-mathematics/Oid/metadata.xml @@ -9,7 +9,4 @@ <email>sci-mathematics@gentoo.org</email> <name>Gentoo Mathematics Project</name> </maintainer> - <longdescription lang="en"> -Oid is a tool to experiment with matroids -</longdescription> </pkgmetadata> diff --git a/sci-mathematics/acl2/Manifest b/sci-mathematics/acl2/Manifest deleted file mode 100644 index 1444f00a9..000000000 --- a/sci-mathematics/acl2/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST acl2-7.1.tar.gz 63345284 SHA256 1a8503095a4e1deb6a6b0f3bc51823ba65cad38466def8d6845f193d73338f9d SHA512 5875b88615930fc841cd1d7ed30ada7c04b241a391eeee22184b4e3630e57cc6304a51e445e33ca1284576c2b4110c269f9eb59c47bd2eb47659134450151e27 WHIRLPOOL 632012e3d8998c67f70cd19b8fa7c7ff8000dbdba2d87dfdd56d5b4b39ebb390503d243e051c308c8a5aea0097bb48fa4e5c510b24478886a4a8bfca2c8d0645 diff --git a/sci-mathematics/acl2/acl2-7.1.ebuild b/sci-mathematics/acl2/acl2-7.1.ebuild deleted file mode 100644 index 774c5a6d3..000000000 --- a/sci-mathematics/acl2/acl2-7.1.ebuild +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils - -DESCRIPTION="Industrial strength theorem prover" -HOMEPAGE="http://www.cs.utexas.edu/users/moore/acl2/" -MY_PN=${PN}-devel -SRC_URI="https://github.com/${MY_PN}/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" -IUSE="books" - -DEPEND=" - dev-lisp/sbcl:= - books? ( dev-lang/perl )" -RDEPEND="${DEPEND}" -S="${WORKDIR}/${MY_PN}-${PV}" - -src_compile() { - emake LISP="sbcl --noinform --noprint \ - --no-sysinit --no-userinit --disable-debugger" - - if use books; then - echo - einfo "Building certificates ..." - einfo "(this may take hours to finish)" - emake certify-books - fi -} - -src_install() { - SAVED_NAME=saved_acl2 - sed -e "s:${S}:/usr/share/acl2:g" -i ${SAVED_NAME} || die - if use books; then - sed -e "/5/a export ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \ - -i ${SAVED_NAME} || die - fi - dobin ${SAVED_NAME} - - insinto /usr/share/acl2 - doins TAGS ${SAVED_NAME}.core - if use books; then - doins -r books - fi -} diff --git a/sci-mathematics/acl2/metadata.xml b/sci-mathematics/acl2/metadata.xml deleted file mode 100644 index b77817aa3..000000000 --- a/sci-mathematics/acl2/metadata.xml +++ /dev/null @@ -1,27 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>dongxuli2011@gmail.com</email> - <name>Dongxu Li</name> - <description>Industrial strength theorem prover</description> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription> -ACL2 is both a programming language in which you can model computer systems and -a tool to help you prove properties of those models. ACL2 is part of the -Boyer-Moore family of provers, for which its authors have received the 2005 ACM -Software System Award. -</longdescription> - <use> - <flag name="books"> -build community books, the canonical collection of open-source libraries -</flag> - </use> - <upstream> - <remote-id type="github">acl2-devel/acl2-devel</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/alt-ergo/Manifest b/sci-mathematics/alt-ergo/Manifest deleted file mode 100644 index ad6a8ca8d..000000000 --- a/sci-mathematics/alt-ergo/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST alt-ergo-0.95.2.tar.gz 233778 SHA256 5a6cd4349c144653be19a1ba4c254bbf626bdfd97c54d1c13ba63e396006eeac SHA512 e4bb73719d67e44bac058ea53082879534c93d47fd931ec927e7f1e59330a60915ae73c662153207e6229ae914a5c0b8b16c04763f1ae3e251668a336a11d382 WHIRLPOOL aa5f8f0bf46eb93d4e8e4be4e6a30facd7b97d35fd110e4081a61826edb1def7dc5724db08c05f714c3bc1a70add9aaa961e9757492aa47f9c97ad48069f5ae9 diff --git a/sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild b/sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild deleted file mode 100644 index 3532fdc0c..000000000 --- a/sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils - -DESCRIPTION="Alt-Ergo is an automatic theorem prover" -HOMEPAGE="http://alt-ergo.ocamlpro.com" -SRC_URI="http://dev.gentoo.org/~jauhien/distfiles/${P}.tar.gz" - -LICENSE="CeCILL-C" -SLOT="0" -KEYWORDS="~amd64" -IUSE="+ocamlopt gtk" - -DEPEND=" - >=dev-lang/ocaml-3.12.1[ocamlopt?] - >=dev-ml/ocamlgraph-1.8.2[gtk?,ocamlopt?] - dev-ml/zarith - gtk? ( - >=x11-libs/gtksourceview-2.8:2.0 - >=dev-ml/lablgtk-2.14[sourceview,ocamlopt?] - )" -RDEPEND="${DEPEND}" - -src_prepare(){ - sed \ - -e 's: /usr/share/: $(DESTDIR)/usr/share/:g' \ - -e 's:cp -f altgr-ergo.opt:mkdir -p $(DESTDIR)/usr/share/gtksourceview-2.0/language-specs/\n\tcp -f altgr-ergo.opt:g' \ - -i "${S}"/Makefile.in || die -} -src_compile(){ - default - use gtk && emake gui -} - -src_install(){ - default - use gtk && emake install-gui DESTDIR="${D}" - dodoc README.md CHANGES -} diff --git a/sci-mathematics/alt-ergo/metadata.xml b/sci-mathematics/alt-ergo/metadata.xml deleted file mode 100644 index a28eb2ec7..000000000 --- a/sci-mathematics/alt-ergo/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> - <longdescription> -Alt-Ergo is an open source automatic theorem prover dedicated to program verification. -It is an SMT solver based on CC(X): a congruence closure algorithm parameterized by an -equational theory X. Alt-Ergo is based on a home-made SAT-solver and implements an -instantiation mechanism for quantified formulas. Its architecture is summarized by the -the following picture. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/apron/Manifest b/sci-mathematics/apron/Manifest deleted file mode 100644 index 280448adb..000000000 --- a/sci-mathematics/apron/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST apron-0.9.10.tgz 1694989 BLAKE2B 434366f9ead2bc233ff24d0ac65c76d35ccf66b11b97e8a1fcad561629d0c9bb6a817dae800dc41f323f5b484790adfb2e6dd8db333ade5ff6b18f484b276357 SHA512 9b84bf6b5d34ee34558e8224ecd09d48ff2013b7a301a8749512aaea8b8c99da394bb0550055b9bc37692187ca8956bf25e74535c1d41ac1907e161163bc6e8a diff --git a/sci-mathematics/apron/apron-0.9.10-r1.ebuild b/sci-mathematics/apron/apron-0.9.10-r1.ebuild deleted file mode 100644 index c2fd73233..000000000 --- a/sci-mathematics/apron/apron-0.9.10-r1.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Static analysis of the numerical variables by Abstract Interpretation" -HOMEPAGE="http://apron.cri.ensmp.fr/library/" -SRC_URI="http://apron.cri.ensmp.fr/library/${P}.tgz" - -LICENSE="LGPL-2 GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc ocaml" - -RDEPEND=" - ocaml? ( - >=dev-lang/ocaml-3.09 - dev-ml/camlidl - dev-ml/mlgmpidl - ) - dev-libs/gmp:0= - dev-libs/mpfr:0=" -DEPEND="${RDEPEND} - doc? ( - app-text/texlive - app-text/ghostscript-gpl - )" - -src_prepare() { - mv Makefile.config.model Makefile.config || die - - #fix compile process - sed -i Makefile.config \ - -e "s/FLAGS = \\\/FLAGS += \\\/g" \ - -e "s/-O3 -DNDEBUG/-DNDEBUG/g" \ - -e "s/APRON_PREFIX =.*/APRON_PREFIX = \$(DESTDIR)\/usr/g" \ - -e "s/MLGMPIDL_PREFIX =.*/MLGMPIDL_PREFIX = \$(DESTDIR)\/usr/g" \ - || die - - #fix doc building process - sed -i Makefile -e "s/; make html/; make/g" - sed -i apronxx/Makefile \ - -e "s:cd doc/latex && make:cd doc/latex; rubber refman.tex; dvipdf refman.dvi:g" - sed -i apronxx/doc/Doxyfile \ - -e "s/OUTPUT_DIRECTORY = \/.*/OUTPUT_DIRECTORY = .\//g" \ - -e "s/STRIP_FROM_PATH = \/.*/STRIP_FROM_PATH = .\//g" - - if [[ "$(gcc-major-version)" == "4" ]]; then - sed -i -e "s/# HAS_LONG_DOUBLE = 1/HAS_LONG_DOUBLE = 1/g" Makefile.config - fi - if use !ocaml; then - sed -i -e "s/HAS_OCAML = 1/#HAS_OCAML = 0/g" Makefile.config - fi -} - -src_compile() { - emake -j1 -} - -src_install(){ - default - - if use doc; then - dodoc apron/apron.pdf - if use ocaml; then - dodoc mlapronidl/mlapronidl.pdf - fi - fi -} diff --git a/sci-mathematics/apron/metadata.xml b/sci-mathematics/apron/metadata.xml deleted file mode 100644 index d31da6be0..000000000 --- a/sci-mathematics/apron/metadata.xml +++ /dev/null @@ -1,18 +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> - <longdescription> -The APRON library is dedicated to the static analysis of the numerical -variables of a program by Abstract Interpretation. The aim of such an -analysis is to infer invariants about these variables. The APRON library -is intended to be a common interface to various underlying -libraries/abstract domains and to provide additional services that can -be implemented independently from the underlying library/abstract -domain, as shown by the poster on the right (presented at the SAS 2007 -conference. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/aribas/Manifest b/sci-mathematics/aribas/Manifest deleted file mode 100644 index 3425d4c91..000000000 --- a/sci-mathematics/aribas/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST aribas-1.63.tar.gz 291939 BLAKE2B 6bd58fce7b64a8808b566446930f62647afcddcea7e72a6c6d62b57d669a270c37a1392300853d228a2b39cde14b1d9825fc769085ea4e72f031f873af3c9573 SHA512 740d03c96c9b12ba4ce62edc63952419bd07fed26f9de6f36fdeda1cac52e01ddd9c8d817b746a2ab3668549f6457ecfced2184fceb8a4307f204a185a765059 diff --git a/sci-mathematics/aribas/aribas-1.63.ebuild b/sci-mathematics/aribas/aribas-1.63.ebuild deleted file mode 100644 index 0759b3158..000000000 --- a/sci-mathematics/aribas/aribas-1.63.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit elisp-common versionator - -DESCRIPTION="Interpreter for big integer and multi-precision floating point arithmetic" -HOMEPAGE="http://www.mathematik.uni-muenchen.de/~forster/sw/${PN}.html" -SRC_URI="ftp://ftp.mathematik.uni-muenchen.de/pub/forster/${PN}/UNIX_LINUX/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~x86" -IUSE="doc emacs examples" - -RDEPEND="emacs? ( virtual/emacs )" -DEPEND="${RDEPEND}" - -SITEFILE=64${PN}-gentoo.el -CH_PV=$(delete_all_version_separators) - -src_prepare() { - # Linux x86 assembly piece - if use x86; then - mv LINUX/arito386.S . || die - mv LINUX/Makefile.linux Makefile || die - fi - - # removing strip - sed -e '/^ strip \$(PROGRAM)$/d' -i Makefile || die "sed failed" -} - -src_compile() { - cd src || die - if use x86; then - emake CFLAGS="-DLiNUX -DPROTO ${CFLAGS}" - else - emake CC=gcc CFLAGS="-DUNiX -DPROTO ${CFLAGS}" - fi - - if use emacs; then - cd EL || doe - elisp-compile *.el - fi -} - -src_install() { - dobin src/${PN} - doman doc/*.1 - dodoc CHANGES${CH_PV}.txt - - if use doc; then - dodoc doc/${PN}.doc doc/${PN}.tut - fi - - if use examples; then - insinto /usr/share/${P} - doins -r examples - fi - - if use emacs; then - cd src/EL || die - elisp-install ${PN} *.el *.elc - elisp-site-file-install "${FILESDIR}"/${SITEFILE} - newdoc EL/README README.emacs - fi -} - -pkg_postinst() { - use emacs && elisp-site-regen -} - -pkg_postrm() { - use emacs && elisp-site-regen -} diff --git a/sci-mathematics/aribas/files/64aribas-gentoo.el b/sci-mathematics/aribas/files/64aribas-gentoo.el deleted file mode 100644 index 3598e39ca..000000000 --- a/sci-mathematics/aribas/files/64aribas-gentoo.el +++ /dev/null @@ -1,3 +0,0 @@ -;; aribas mode -(add-to-list 'load-path "@SITELISP@") -(autoload 'run-aribas "aribas" "Run ARIBAS." t) diff --git a/sci-mathematics/aribas/metadata.xml b/sci-mathematics/aribas/metadata.xml deleted file mode 100644 index 146901339..000000000 --- a/sci-mathematics/aribas/metadata.xml +++ /dev/null @@ -1,13 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>grozin@gentoo.org</email> - <name>Andrey Grozin</name> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription>Interpreter for big integer and multi-precision floating point arithmetic</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/axiom/Manifest b/sci-mathematics/axiom/Manifest deleted file mode 100644 index 5f29166eb..000000000 --- a/sci-mathematics/axiom/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST axiom-aug2014-src.tgz 166822164 BLAKE2B 44d7c89278405a8e5dfa1e0cee9f32a095c62cb95708a6d8edead54eb7d0c1481d7c52bf2c1d6d91cf5bbe62feb66e5bf0ebb94425120df553957bcaf1eaf697 SHA512 88a27967a6e0b4d5ab1beffeb8a3d0968c432f71258e8d21d77191e8ad79e77ba3c316850af976a52b28d4d05f1001fba39a966c6f008a89bf493569fb183be0 diff --git a/sci-mathematics/axiom/axiom-201408.ebuild b/sci-mathematics/axiom/axiom-201408.ebuild deleted file mode 100644 index 99483d63b..000000000 --- a/sci-mathematics/axiom/axiom-201408.ebuild +++ /dev/null @@ -1,67 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic multilib - -DESCRIPTION="Axiom is a general purpose Computer Algebra system" -HOMEPAGE="http://axiom.axiom-developer.org/" -SRC_URI="http://axiom.axiom-developer.org/axiom-website/downloads/axiom-aug2014-src.tgz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="" -IUSE="" - -# NOTE: Do not strip since this seems to remove some crucial -# runtime paths as well, thereby, breaking axiom -RESTRICT="strip" - -# Seems to need a working version of pstricks package these days Bummer: <gmp-5 is needed for the -# interal gcl, otherwise axiom will try to build an internal copy of gmp-4 which fails. -RDEPEND=" - dev-libs/gmp:0= - x11-libs/libXaw" -DEPEND="${RDEPEND} - app-text/dvipdfm - dev-texlive/texlive-pstricks - sys-apps/debianutils - sys-process/procps - virtual/latex-base" - -S="${WORKDIR}"/${PN} - -src_prepare() { - append-flags -fno-strict-aliasing -} - -src_compile() { - sed -e "s:X11R6/lib:$(get_libdir):g" -i Makefile.pamphlet \ - || die "Failed to fix libXpm lib paths" - - # This will fix the internal gmp. This package will stay unkeyworded until this is resolved - # upstream. - unset ABI - - # Let the fun begin... - AXIOM="${S}"/mnt/linux emake -j1 -} - -src_install() { - emake DESTDIR="${ED}"/opt/axiom COMMAND="${ED}"/opt/axiom/mnt/linux/bin/axiom install - - mv "${ED}"/opt/axiom/mnt/linux/* "${ED}"/opt/axiom \ - || die "Failed to mv axiom into its final destination path." - rm -fr "${ED}"/opt/axiom/mnt \ - || die "Failed to remove old directory." - - dosym ../../axiom/bin/axiom /usr/bin/axiom - - sed \ - -e "2d;3i AXIOM=/opt/axiom" \ - -i "${D}"/opt/axiom/bin/axiom \ - || die "Failed to patch axiom runscript!" - - dodoc changelog readme faq -} diff --git a/sci-mathematics/axiom/metadata.xml b/sci-mathematics/axiom/metadata.xml deleted file mode 100644 index 514f7304d..000000000 --- a/sci-mathematics/axiom/metadata.xml +++ /dev/null @@ -1,8 +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> -</pkgmetadata> diff --git a/sci-mathematics/burrtools/Manifest b/sci-mathematics/burrtools/Manifest deleted file mode 100644 index ca9d6fa8c..000000000 --- a/sci-mathematics/burrtools/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST burrtools-0.5.2-A4.pdf 1268505 BLAKE2B ca62f01883959e28d3e98523b4f122c819f2134e39d1d5f0db4a868b969cc3f81cb1937949bf8d15b705dcfdd0cd9ba9d98e5ca1786e6e37adff1dae56d80bd1 SHA512 560bfb05a2fe84eb4502a9f9503edd2e8af2a0c67f5e05819d3ae8df6e599d8f39c917577d49ff4103b1c330ca8a61eba430c206a1b895be06b154386dadfccd -DIST burrtools-0.5.2.tar.gz 1920561 BLAKE2B d796ffa916df237e7bbe12fc8a421f20ab15d8e40401d9cb8c7eb8b0e737d19a0986ba4b7fdff9c77b599e5369c5ce79f17ba07213d49f1806558812ade244c3 SHA512 7b73b619c6d042fd7e879ef675e8abd6977c9df276b410cb466e555810a83906e51d7b085679096e828929b62851be5ca304292f1e500b963053d81d968860e8 diff --git a/sci-mathematics/burrtools/burrtools-0.5.2-r1.ebuild b/sci-mathematics/burrtools/burrtools-0.5.2-r1.ebuild deleted file mode 100644 index 3f5280649..000000000 --- a/sci-mathematics/burrtools/burrtools-0.5.2-r1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -DESCRIPTION="Program to solve assembly and interlocking puzzles" -HOMEPAGE="http://burrtools.sourceforge.net/" -SRC_URI=" - mirror://sourceforge/${PN}/${P}.tar.gz - doc? ( mirror://sourceforge/${PN}/${P}-A4.pdf )" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~x86" -IUSE="doc examples" - -DEPEND=" - x11-libs/fltk:1 - media-libs/libpng:0=" -RDEPEND="${DEPEND} - app-text/htmldoc" - -src_compile() { - default - cd doc || die - cp ../doc_src/*.png . || die - echo "User Guide for BurrTools ${PV}" > doc/userGuide.t2t - cat ../doc_src/userGuide.t2t >> userGuide.t2t - mkdir html || die - ../doc_src/txt2tags.py -t html -o - userGuide.t2t > userGuide.html - htmldoc --format htmlsep --toclevels 2 --outdir html userGuide.html || die - cd .. || die -} - -src_install() { - default - use doc && dodoc "${DISTDIR}"/${P}-A4.pdf - if use examples; then - insinto /usr/share/${PN} - doins -r examples - fi -} diff --git a/sci-mathematics/burrtools/metadata.xml b/sci-mathematics/burrtools/metadata.xml deleted file mode 100644 index a7fbeb904..000000000 --- a/sci-mathematics/burrtools/metadata.xml +++ /dev/null @@ -1,17 +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> - <longdescription lang="en"> -This (set of) program(s) will help you solve a certain kind of puzzle. -Namely puzzles that are made out of square or dice shaped units, spheres or -prisms with an equilateral triangle as base and where the pieces are also -aligned along those grids in the solutions. -</longdescription> - <upstream> - <remote-id type="sourceforge">burrtools</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/cadabra/Manifest b/sci-mathematics/cadabra/Manifest deleted file mode 100644 index 045c33e9d..000000000 --- a/sci-mathematics/cadabra/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST cadabra-1.39.tar.gz 1377279 SHA256 a1fda2f9c43b3b56c3cfcd0e6fce2a692b3f4fb2941fd7e2a0033c39fe013507 SHA512 e4c81bfbd1102449114d135d596526340451ce284c5ce796ffd3367c4040d434266564760628b367f40fe61bc59d7e6f067f8150601a7fa4f88101da60fbab06 WHIRLPOOL 4b36c377a42ad4d22d56712b9f9ae4a1c58265e86eb2a728e1926ea74e07f984b42475cee6eb1ff2d47f994c3904e99bb80d2c61b6fb5b4098af4b0719f3c5b7 diff --git a/sci-mathematics/cadabra/cadabra-1.39.ebuild b/sci-mathematics/cadabra/cadabra-1.39.ebuild deleted file mode 100644 index 095ab87dd..000000000 --- a/sci-mathematics/cadabra/cadabra-1.39.ebuild +++ /dev/null @@ -1,88 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils texlive-common - -DESCRIPTION="Field-theory motivated computer algebra system" -HOMEPAGE="http://cadabra.phi-sci.com" -SRC_URI="http://cadabra.phi-sci.com/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc examples X test" - -CDEPEND=" - sci-libs/modglue - sci-mathematics/lie - dev-libs/gmp[cxx] - dev-libs/libpcre - X? ( - x11-libs/gtk+:2 - dev-cpp/gtkmm:2.4 - dev-cpp/pangomm:1.4 - app-text/dvipng )" -DEPEND="${CDEPEND} - doc? ( - app-doc/doxygen - dev-texlive/texlive-latexextra - app-text/texlive-core - ) - test? ( sys-process/time )" -RDEPEND="${CDEPEND} - virtual/latex-base - dev-texlive/texlive-latexrecommended" - -src_prepare(){ - # fixing the flag mess - epatch "${FILESDIR}/${P}-FLAGS.patch" -} - -src_configure(){ - econf $(use_enable X gui) \ - --disable-runtime-dependency-check -} - -src_compile() { - default - - if use doc; then - cd "${S}/doc" || die - default - cd doxygen/latex || die - emake pdf - fi -} - -src_install() { - # cadabra strip binaries unless you are on OS X. - # So faking it to avoid outright stripping. - emake DESTDIR="${D}" DEVDESTDIR="${D}" MACTEST=1 install - - dodoc AUTHORS ChangeLog INSTALL - - if use doc; then - cd "${S}/doc/doxygen" || die - dohtml html/* - dodoc latex/*.pdf - fi - - if use examples; then - dodoc -r "${S}/examples/" - fi - - rm -rf "${D}/usr/share/TeXmacs" || die -} - -pkg_postinst() { - etexmf-update - elog "This version of the cadabra ebuild is still under development." - elog "Help us improve the ebuild in:" - elog "http://bugs.gentoo.org/show_bug.cgi?id= 194393" -} - -pkg_postrm() { - etexmf-update -} diff --git a/sci-mathematics/cadabra/files/cadabra-1.33-FLAGS.patch b/sci-mathematics/cadabra/files/cadabra-1.33-FLAGS.patch deleted file mode 100644 index 2d78e9327..000000000 --- a/sci-mathematics/cadabra/files/cadabra-1.33-FLAGS.patch +++ /dev/null @@ -1,171 +0,0 @@ ---- Makefile.in.orig 2013-09-05 21:45:20.026339263 +1200 -+++ Makefile.in 2013-09-05 21:48:20.859739672 +1200 -@@ -24,7 +24,7 @@ - ( cd src && $(MAKE) static ); - - profile: -- ( export CFLAGS=-pg && export LDFLAGS=-pg && cd src && $(MAKE) ); -+ ( export CFLAGS="$(CFLAGS) -pg" && CXXFLAGS="$(CXXFLAGS) -pg" && cd src && $(MAKE) ); - - doc: - ( cd doc && $(MAKE) ); ---- src/Makefile.in.orig 2013-09-05 21:45:35.546373837 +1200 -+++ src/Makefile.in 2013-09-05 21:53:51.146459582 +1200 -@@ -22,12 +22,13 @@ - - SRCS = `find . -name "*.cc"` - MCFLAGS = @CFLAGS@ -I. -I@top_srcdir@/src `pkg-config modglue --cflags` -+MCXXFLAGS = @CXXFLAGS@ -I. -I@top_srcdir@/src `pkg-config modglue --cflags` - TIMESTAMP = -D"RELEASE=\"${RELEASE}\"" -D"DATETIME=\"`date | sed -e 's/ / /'`\"" -DHOSTNAME=\"`hostname`\" - - - - %.o: %.cc -- @CXX@ ${MCFLAGS} ${TIMESTAMP} -c -o $@ $< -+ @CXX@ ${MCXXFLAGS} ${TIMESTAMP} -c -o $@ $< - - modules/xperm.o: modules/xperm.c - @CC@ @NESTED@ ${MCFLAGS} ${TIMESTAMP} -c -o $@ $< -@@ -42,10 +43,10 @@ - - ifeq ($(strip $(MACTEST)),) - cadabra: $(OBJS) $(MOBJS) -- @CXX@ -o cadabra ${LDFLAGS} -Wl,--as-needed $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp -+ @CXX@ -o cadabra ${MCXXFLAGS} ${LDFLAGS} -Wl,--as-needed $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp - else - cadabra: $(OBJS) $(MOBJS) -- @CXX@ -o cadabra ${LDFLAGS} -Wl,-dead_strip_dylibs $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp -+ @CXX@ -o cadabra ${MCXXFLAGS} ${LDFLAGS} -Wl,-dead_strip_dylibs $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp - endif - - #`pkg-config glib-2.0 --libs` -@@ -53,15 +54,15 @@ - - cadabra_static: $(OBJS) $(MOBJS) - rm -f main.o -- @CXX@ -Wall -g ${MCFLAGS} ${TIMESTAMP} -DSTATICBUILD -c -o main.o main.cc -+ @CXX@ -Wall -g ${MCXXFLAGS} ${TIMESTAMP} -DSTATICBUILD -c -o main.o main.cc - ifeq ($(strip $(MACTEST)),) -- @CXX@ -o cadabra -static $+ ${LDFLAGS} `pkg-config modglue --libs` -lmodglue \ -+ @CXX@ -o cadabra -static ${MCXXFLAGS} $+ ${LDFLAGS} `pkg-config modglue --libs` -lmodglue \ - -lgmpxx -lgmp -lpcrecpp -lpcre \ - `pkg-config sigc++-2.0 --libs` -lsigc-2.0 -lutil - - else - export MACOSX_DEPLOYMENT_TARGET=10.3 -- @CXX@ -o cadabra $+ ${LDFLAGS} `pkg-config modglue --libs` \ -+ @CXX@ -o cadabra ${MCXXFLAGS} $+ ${LDFLAGS} `pkg-config modglue --libs` \ - -lgmp -lgmpxx -lpcre++ -lpcre -lexpect - endif - -@@ -77,32 +78,32 @@ - # @CXX@ -c -o defaults.o defaults.cc - - test_tree: test_tree.o -- @CXX@ -o test_tree test_tree.o -+ @CXX@ ${MCXXFLAGS} -o test_tree test_tree.o - - test_lie: test_lie.o modules/lie.o - ifeq ($(strip $(MACTEST)),) -- @CXX@ -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue` -+ @CXX@ ${MCXXFLAGS} -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue` - else -- @CXX@ -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue` -+ @CXX@ ${MCXXFLAGS} -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue` - endif - - tree_regression_tests: tree_regression_tests.o -- @CXX@ -o tree_regression_tests tree_regression_tests.o -+ @CXX@ ${MCXXFLAGS} -o tree_regression_tests tree_regression_tests.o - - test_xperm: test_xperm.o modules/xperm.o -- @CXX@ -o test_xperm test_xperm.o modules/xperm.o -+ @CXX@ ${MCXXFLAGS} -o test_xperm test_xperm.o modules/xperm.o - - tree_example: tree_example.o tree.hh -- @CXX@ -o tree_example tree_example.o -+ @CXX@ ${MCXXFLAGS} -o tree_example tree_example.o - - test_combinatorics: test_combinatorics.o combinatorics.o -- @CXX@ -o test_combinatorics test_combinatorics.o combinatorics.o -+ @CXX@ ${MCXXFLAGS} -o test_combinatorics test_combinatorics.o combinatorics.o - - test_young: test_young.o youngtab.o combinatorics.o -- @CXX@ -o test_young test_young.o youngtab.o combinatorics.o ${LDFLAGS} -lgmpxx -lgmp -+ @CXX@ ${MCXXFLAGS} -o test_young test_young.o youngtab.o combinatorics.o ${LDFLAGS} -lgmpxx -lgmp - - test_preprocessor: test_preprocessor.o preprocessor.o -- @CXX@ -o test_preprocessor test_preprocessor.o preprocessor.o ${LDFLAGS} -lgmpxx -lgmp -+ @CXX@ ${MCXXFLAGS} -o test_preprocessor test_preprocessor.o preprocessor.o ${LDFLAGS} -lgmpxx -lgmp - - mpi_pass_tree: mpi_pass_tree.o - @CXX@ -o mpi_pass_tree mpi_pass_tree.o -L/usr/lib/mpich/lib -lmpich++ -lpmpich -lmpich -@@ -133,13 +134,13 @@ - # Then the actual compilation. - - lex.yy.o: lex.yy.c parser2.tab.h -- @CXX@ -c -o lex.yy.o lex.yy.c -+ @CXX@ ${MCXXFLAGS} -c -o lex.yy.o lex.yy.c - - parser2.tab.o: parser2.tab.c -- @CXX@ -c -o parser2.tab.o parser2.tab.c -+ @CXX@ ${MCXXFLAGS} -c -o parser2.tab.o parser2.tab.c - - parser2: parser2.tab.o lex.yy.o storage.o props.o -- @CXX@ -o parser2 $+ -ll -ly -lgmpxx -lgmp -lpcrecpp -+ @CXX@ ${MCXXFLAGS} -o parser2 $+ -ll -ly -lgmpxx -lgmp -lpcrecpp - - - -@@ -170,7 +171,7 @@ - .depend: - rm -f .depend - for i in ${SRCS}; \ -- do @CXX@ ${MCFLAGS} -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CFLAGS} $$i >> .depend; \ -+ do @CXX@ ${MCXXFLAGS} -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CXXFLAGS} $$i >> .depend; \ - done - - include .depend ---- gui/Makefile.in.orig 2013-09-05 21:45:50.989408184 +1200 -+++ gui/Makefile.in 2013-09-05 21:57:17.495902104 +1200 -@@ -8,26 +8,26 @@ - static: xcadabra_static - - OBJS = help.o widgets.o window.o main.o ../src/stopwatch.o --CFLAGS = -O2 -I. -I@top_srcdir@/include `pkg-config modglue --cflags` `pkg-config --cflags gtkmm-2.4` \ -+MCXXFLAGS = -O2 $(CXXFLAGS) -I. -I@top_srcdir@/include `pkg-config modglue --cflags` `pkg-config --cflags gtkmm-2.4` \ - `pkg-config --cflags pango` - SRCS = `find . -name "*.cc"` - TIMESTAMP = -D"RELEASE=\"${RELEASE}\"" -D"DATETIME=\"`date | sed -e 's/ / /'`\"" -DHOSTNAME=\"`hostname`\" - - %.o: %.cc -- @CXX@ -Wall @CFLAGS@ -D"DESTDIR=\"@prefix@\"" ${TIMESTAMP} ${CFLAGS} -c -o $@ $< -+ @CXX@ -Wall $(MCXXFLAGS) -D"DESTDIR=\"@prefix@\"" ${TIMESTAMP} -c -o $@ $< - - main.o: $(OBJS) Makefile - - xcadabra: $(OBJS) -- @CXX@ -o xcadabra $+ `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp -+ @CXX@ $(MCXXFLAGS) -o xcadabra $+ $(LDFLAGS) `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp - - xcadabra_static: $(OBJS) -- @CXX@ -o xcadabra -static $+ -L@prefix@/lib `pkg-config modglue --libs` \ -+ @CXX@ $(MCXXFLAGS) -o xcadabra -static $+ $(LDFLAGS) -L@prefix@/lib `pkg-config modglue --libs` \ - `pkg-config --libs gtkmm-2.4` `pkg-config libxml++-2.6` \ - -lpthread -lexpat - - test_texit: texit.o test_texit.o -- @CXX@ -o test_texit `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` $+ -+ @CXX@ $(MCXXFLAGS) -o test_texit `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` $+ - - install: - ifeq ($(strip $(MACTEST)),) -@@ -50,7 +50,7 @@ - .depend: - rm -f .depend - for i in ${SRCS}; \ -- do g++ -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CFLAGS} $$i >> .depend; \ -+ do g++ -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${MCXXFLAGS} $$i >> .depend; \ - done - - include .depend diff --git a/sci-mathematics/cadabra/files/cadabra-1.39-FLAGS.patch b/sci-mathematics/cadabra/files/cadabra-1.39-FLAGS.patch deleted file mode 100644 index 2f18edb2a..000000000 --- a/sci-mathematics/cadabra/files/cadabra-1.39-FLAGS.patch +++ /dev/null @@ -1,171 +0,0 @@ ---- Makefile.in -+++ Makefile.in -@@ -24,7 +24,7 @@ - ( cd src && $(MAKE) static ); - - profile: -- ( export CFLAGS=-pg && export LDFLAGS=-pg && cd src && $(MAKE) ); -+ ( export CFLAGS="$(CFLAGS) -pg" && CXXFLAGS="$(CXXFLAGS) -pg" && cd src && $(MAKE) ); - - doc: - ( cd doc && $(MAKE) ); ---- gui/Makefile.in -+++ gui/Makefile.in -@@ -8,26 +8,26 @@ - static: xcadabra_static - - OBJS = help.o widgets.o window.o main.o ../src/stopwatch.o --CFLAGS = -O2 -I. -I@top_srcdir@/include `pkg-config modglue --cflags` `pkg-config --cflags gtkmm-2.4` \ -+MCXXFLAGS = -O2 $(CXXFLAGS) -I. -I@top_srcdir@/include `pkg-config modglue --cflags` `pkg-config --cflags gtkmm-2.4` \ - `pkg-config --cflags pango` - SRCS = `find . -name "*.cc"` - TIMESTAMP = -D"RELEASE=\"${RELEASE}\"" -D"DATETIME=\"`date | sed -e 's/ / /'`\"" -DHOSTNAME=\"`hostname`\" - - %.o: %.cc -- @CXX@ -Wall @CFLAGS@ -D"DESTDIR=\"@prefix@\"" ${TIMESTAMP} ${CFLAGS} -c -o $@ $< -+ @CXX@ -Wall $(MCXXFLAGS) -D"DESTDIR=\"@prefix@\"" ${TIMESTAMP} -c -o $@ $< - - main.o: $(OBJS) Makefile - - xcadabra: $(OBJS) -- @CXX@ -o xcadabra $+ `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp -+ @CXX@ $(MCXXFLAGS) -o xcadabra $+ $(LDFLAGS) `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp - - xcadabra_static: $(OBJS) -- @CXX@ -o xcadabra -static $+ -L@prefix@/lib `pkg-config modglue --libs` \ -+ @CXX@ $(MCXXFLAGS) -o xcadabra -static $+ $(LDFLAGS) -L@prefix@/lib `pkg-config modglue --libs` \ - `pkg-config --libs gtkmm-2.4` `pkg-config libxml++-2.6` \ - -lpthread -lexpat - - test_texit: texit.o test_texit.o -- @CXX@ -o test_texit `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` $+ -+ @CXX@ $(MCXXFLAGS) -o test_texit `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` $+ - - install: - ifeq ($(strip $(MACTEST)),) -@@ -50,7 +50,7 @@ - .depend: - rm -f .depend - for i in ${SRCS}; \ -- do g++ -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CFLAGS} $$i >> .depend; \ -+ do g++ -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${MCXXFLAGS} $$i >> .depend; \ - done - - include .depend -diff -u -r cadabra-1.39.orig/src/Makefile.in cadabra-1.39/src/Makefile.in ---- src/Makefile.in -+++ src/Makefile.in -@@ -22,12 +22,13 @@ - - SRCS = `find . -name "*.cc"` - MCFLAGS = @CFLAGS@ -I. -I@top_srcdir@/src `pkg-config modglue --cflags` -+MCXXFLAGS = @CXXFLAGS@ -I. -I@top_srcdir@/src `pkg-config modglue --cflags` - TIMESTAMP = -D"RELEASE=\"${RELEASE}\"" -D"DATETIME=\"`date | sed -e 's/ / /'`\"" -DHOSTNAME=\"`hostname`\" - - - - %.o: %.cc -- @CXX@ ${MCFLAGS} ${TIMESTAMP} -c -o $@ $< -+ @CXX@ ${MCXXFLAGS} ${TIMESTAMP} -c -o $@ $< - - # modules/xperm.o: modules/xperm.c - # @CC@ @NESTED@ ${MCFLAGS} ${TIMESTAMP} -c -o $@ $< -@@ -42,10 +43,10 @@ - - ifeq ($(strip $(MACTEST)),) - cadabra: $(OBJS) $(MOBJS) -- @CXX@ -o cadabra ${LDFLAGS} -Wl,--as-needed $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp -+ @CXX@ -o cadabra ${MCXXFLAGS} ${LDFLAGS} -Wl,--as-needed $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp - else - cadabra: $(OBJS) $(MOBJS) -- @CXX@ -o cadabra ${LDFLAGS} -Wl,-dead_strip_dylibs $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp -+ @CXX@ -o cadabra ${MCXXFLAGS} ${LDFLAGS} -Wl,-dead_strip_dylibs $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp - endif - - #`pkg-config glib-2.0 --libs` -@@ -53,15 +54,15 @@ - - cadabra_static: $(OBJS) $(MOBJS) - rm -f main.o -- @CXX@ -Wall -g ${MCFLAGS} ${TIMESTAMP} -DSTATICBUILD -c -o main.o main.cc -+ @CXX@ -Wall -g ${MCXXFLAGS} ${TIMESTAMP} -DSTATICBUILD -c -o main.o main.cc - ifeq ($(strip $(MACTEST)),) -- @CXX@ -o cadabra -static $+ ${LDFLAGS} `pkg-config modglue --libs` -lmodglue \ -+ @CXX@ -o cadabra -static ${MCXXFLAGS} $+ ${LDFLAGS} `pkg-config modglue --libs` -lmodglue \ - -lgmpxx -lgmp -lpcrecpp -lpcre \ - `pkg-config sigc++-2.0 --libs` -lsigc-2.0 -lutil - - else - export MACOSX_DEPLOYMENT_TARGET=10.3 -- @CXX@ -o cadabra $+ ${LDFLAGS} `pkg-config modglue --libs` \ -+ @CXX@ -o cadabra ${MCXXFLAGS} $+ ${LDFLAGS} `pkg-config modglue --libs` \ - -lgmp -lgmpxx -lpcre++ -lpcre -lexpect - endif - -@@ -77,32 +78,32 @@ - # @CXX@ -c -o defaults.o defaults.cc - - test_tree: test_tree.o -- @CXX@ -o test_tree test_tree.o -+ @CXX@ ${MCXXFLAGS} -o test_tree test_tree.o - - test_lie: test_lie.o modules/lie.o - ifeq ($(strip $(MACTEST)),) -- @CXX@ -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue` -+ @CXX@ ${MCXXFLAGS} -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue` - else -- @CXX@ -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue` -+ @CXX@ ${MCXXFLAGS} -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue` - endif - - tree_regression_tests: tree_regression_tests.o -- @CXX@ -o tree_regression_tests tree_regression_tests.o -+ @CXX@ ${MCXXFLAGS} -o tree_regression_tests tree_regression_tests.o - - #test_xperm: test_xperm.o modules/xperm_new.o - # @CXX@ -o test_xperm test_xperm.o modules/xperm_new.o - - tree_example: tree_example.o tree.hh -- @CXX@ -o tree_example tree_example.o -+ @CXX@ ${MCXXFLAGS} -o tree_example tree_example.o - - test_combinatorics: test_combinatorics.o combinatorics.o -- @CXX@ -o test_combinatorics test_combinatorics.o combinatorics.o -+ @CXX@ ${MCXXFLAGS} -o test_combinatorics test_combinatorics.o combinatorics.o - - test_young: test_young.o youngtab.o combinatorics.o -- @CXX@ -o test_young test_young.o youngtab.o combinatorics.o ${LDFLAGS} -lgmpxx -lgmp -+ @CXX@ ${MCXXFLAGS} -o test_young test_young.o youngtab.o combinatorics.o ${LDFLAGS} -lgmpxx -lgmp - - test_preprocessor: test_preprocessor.o preprocessor.o -- @CXX@ -o test_preprocessor test_preprocessor.o preprocessor.o ${LDFLAGS} -lgmpxx -lgmp -+ @CXX@ ${MCXXFLAGS} -o test_preprocessor test_preprocessor.o preprocessor.o ${LDFLAGS} -lgmpxx -lgmp - - mpi_pass_tree: mpi_pass_tree.o - @CXX@ -o mpi_pass_tree mpi_pass_tree.o -L/usr/lib/mpich/lib -lmpich++ -lpmpich -lmpich -@@ -133,13 +134,13 @@ - # Then the actual compilation. - - lex.yy.o: lex.yy.c parser2.tab.h -- @CXX@ -c -o lex.yy.o lex.yy.c -+ @CXX@ ${MCXXFLAGS} -c -o lex.yy.o lex.yy.c - - parser2.tab.o: parser2.tab.c -- @CXX@ -c -o parser2.tab.o parser2.tab.c -+ @CXX@ ${MCXXFLAGS} -c -o parser2.tab.o parser2.tab.c - - parser2: parser2.tab.o lex.yy.o storage.o props.o -- @CXX@ -o parser2 $+ -ll -ly -lgmpxx -lgmp -lpcrecpp -+ @CXX@ ${MCXXFLAGS} -o parser2 $+ -ll -ly -lgmpxx -lgmp -lpcrecpp - - - -@@ -170,7 +171,7 @@ - .depend: - rm -f .depend - for i in ${SRCS}; \ -- do @CXX@ ${MCFLAGS} -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CFLAGS} $$i >> .depend; \ -+ do @CXX@ ${MCXXFLAGS} -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CXXFLAGS} $$i >> .depend; \ - done - - include .depend diff --git a/sci-mathematics/cadabra/metadata.xml b/sci-mathematics/cadabra/metadata.xml deleted file mode 100644 index 0cc2fca48..000000000 --- a/sci-mathematics/cadabra/metadata.xml +++ /dev/null @@ -1,9 +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> - <longdescription>Cadabra is a computer algebra system (CAS) designed specifically for the solution of problems encountered in field theory. It has extensive functionality for tensor computer algebra, tensor polynomial simplification including multi-term symmetries, fermions and anti-commuting variables, Clifford algebras and Fierz transformations, implicit coordinate dependence, multiple index types and many more.</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/cipi/cipi-1.0-r1.ebuild b/sci-mathematics/cipi/cipi-1.0-r1.ebuild new file mode 100644 index 000000000..6cd189e33 --- /dev/null +++ b/sci-mathematics/cipi/cipi-1.0-r1.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake flag-o-matic + +DESCRIPTION="Computing information projections iteratively" +HOMEPAGE="https://github.com/tom111/cipi" +SRC_URI="https://github.com/tom111/cipi/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +IUSE="doc" + +DEPEND=" + dev-libs/boost:= + doc? ( virtual/latex-base )" +RDEPEND="${DEPEND}" + +DOCS="AUTHORS README" + +CMAKE_IN_SOURCE_BUILD="yes" + +PATCHES=( + "${FILESDIR}/${P}-boost.patch" +) + +src_prepare() { + cmake_src_prepare + append-ldflags -Wl,--copy-dt-needed-entries +} + +src_configure() { + mycmakeargs=( + -DENABLE_DOC=$(usex doc ON OFF) + ) + + cmake_src_configure +} + +pkg_postinst() { + elog + elog "The sample PARAM file has been installed to /usr/share/${PN}-${PV}" + elog + if use doc; then + elog "A pdf manual has been installed to /usr/share/${PN}-${PV}" + fi +} diff --git a/sci-mathematics/cipi/cipi-1.0.ebuild b/sci-mathematics/cipi/cipi-1.0.ebuild index 03c1afef3..33d744c7c 100644 --- a/sci-mathematics/cipi/cipi-1.0.ebuild +++ b/sci-mathematics/cipi/cipi-1.0.ebuild @@ -1,17 +1,18 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit cmake-utils +inherit cmake flag-o-matic DESCRIPTION="Computing information projections iteratively" -HOMEPAGE="http://github.com/tom111/cipi" -SRC_URI="https://github.com/tom111/cipi/archive/1.0.tar.gz -> ${P}.tar.gz" +HOMEPAGE="https://github.com/tom111/cipi" +SRC_URI="https://github.com/tom111/cipi/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" + IUSE="doc" DEPEND=" @@ -23,12 +24,17 @@ DOCS="AUTHORS README" CMAKE_IN_SOURCE_BUILD="yes" +src_prepare() { + cmake_src_prepare + append-ldflags -Wl,--copy-dt-needed-entries +} + src_configure() { mycmakeargs=( - $(cmake-utils_use_enable doc) + $(use_enable doc) ) - cmake-utils_src_configure + cmake_src_configure } pkg_postinst() { diff --git a/sci-mathematics/cipi/files/cipi-1.0-boost.patch b/sci-mathematics/cipi/files/cipi-1.0-boost.patch new file mode 100644 index 000000000..66aa9fd3f --- /dev/null +++ b/sci-mathematics/cipi/files/cipi-1.0-boost.patch @@ -0,0 +1,11 @@ +--- a/src/CMakeLists.txt 2024-02-16 21:36:58.808186061 +0100 ++++ b/src/CMakeLists.txt 2024-02-16 21:36:55.288131610 +0100 +@@ -8,7 +8,7 @@ + Message("Boost found" ${Boost_LIBRARY_DIR}) + INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIR}) + #MESSAGE("Boost was found" ${Boost_INCLUDE_DIR}) +- TARGET_LINK_LIBRARIES (cipi boost_thread-mt) ++ TARGET_LINK_LIBRARIES (cipi boost_thread) + ENDIF (Boost_FOUND) + + INSTALL(PROGRAMS cipi DESTINATION bin) diff --git a/sci-mathematics/dolfin/Manifest b/sci-mathematics/dolfin/Manifest deleted file mode 100644 index 67b7f0be8..000000000 --- a/sci-mathematics/dolfin/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST dolfin-0.9.9.tar.gz 10229504 BLAKE2B dc59633d82b8e1b98a1b270c0e24332bd2f80e5bbf017b54268c951fd843172101813dc66c5c6eb5c5276adf4c4e5820d9a547fe02d8d7ac0b6794f050e23545 SHA512 1b9e3dfe7dca47a535328c9dab29128262075ac28b7ec18878704d244a27ec417c7d9c00b518dbaa782c2daccaa3affe4b8f9f60df19e1e9b4ca2c70fc2a2483 -DIST dolfin-2016.2.0.tar.gz 9702541 BLAKE2B 0e6b73419bbaf5b24e63d5b5347e9e8ee280b86868f02aadae06ee638053554b55277fecfe124982b99debc0402744cddb5aa81283d8413c5d5cde9c39cd12bc SHA512 1886513b433845c1026c37a7ac574d8bb7d08e896e5e54a0cca7f2ba3dde02b5c3551c005a408de151a915ca890ba8e65ebfd53abaef980132cc636c47f8f5fa -DIST dolfin-2017.1.0.tar.gz 13264977 BLAKE2B 1fa0c0921196749e19582201cbf7ed19c38b59436fad01afc766dc2dc77387385d2765e844b62741481292652b4154035f811f454bda4e85e93bcd0b7fd1bab4 SHA512 60b6c2128b5249eb94551e23b3c1e2eb014af7336ddea629c8d496be0d3782bcdc03b494b6a12ba3fc948e8dcca8bffce412da1a7c7038464e5a747ec5430f94 diff --git a/sci-mathematics/dolfin/dolfin-0.9.9.ebuild b/sci-mathematics/dolfin/dolfin-0.9.9.ebuild deleted file mode 100644 index 4677e51b2..000000000 --- a/sci-mathematics/dolfin/dolfin-0.9.9.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils eutils python-single-r1 - -DESCRIPTION="C++/Python interface of FEniCS" -HOMEPAGE="https://launchpad.net/dolfin/" -SRC_URI="https://launchpad.net/${PN}/0.x/${PV}/+download/${P}.tar.gz" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="~amd64" -IUSE="cgal cholmod gmp mpi parmetis python scotch umfpack zlib" -# scotch and parmetis require mpi; wait for EAPI 4 - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -DEPEND=" - dev-libs/boost - dev-libs/libxml2:2 - sci-libs/armadillo - sci-mathematics/ufc - python? ( - ${PYTHON_DEPS} - dev-python/ufl[${PYTHON_USEDEP}] - dev-python/ffc[${PYTHON_USEDEP}] - dev-python/fiat[${PYTHON_USEDEP}] - dev-python/instant[${PYTHON_USEDEP}] - dev-python/viper[${PYTHON_USEDEP}] - )" -RDEPEND="${DEPEND}" - -pkg_setup() { - use python && python-single-r1_pkg_setup -} - -src_prepare() { - epatch "${FILESDIR}"/"${P}"-find-armadillo.patch -} - -pkg_setup() { - mycmakeargs="${mycmakeargs} - $(cmake-utils_use cgal DOLFIN_ENABLE_CGAL) - $(cmake-utils_use cholmod DOLFIN_ENABLE_CHOLMOD) - $(cmake-utils_use gmp DOLFIN_ENABLE_GMP) - $(cmake-utils_use mpi DOLFIN_ENABLE_MPI) - $(cmake-utils_use parmetis DOLFIN_ENABLE_PARMETIS) - $(cmake-utils_use python DOLFIN_ENABLE_PYTHON) - $(cmake-utils_use scotch DOLFIN_ENABLE_SCOTCH) - $(cmake-utils_use umfpack DOLFIN_ENABLE_UMFPACK) - $(cmake-utils_use zlib DOLFIN_ENABLE_ZLIB)" -} diff --git a/sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild b/sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild deleted file mode 100644 index 4d5d8f716..000000000 --- a/sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils eutils python-single-r1 - -DESCRIPTION="C++/Python interface of FEniCS" -HOMEPAGE="https://bitbucket.org/fenics-project/dolfin" -SRC_URI="https://bitbucket.org/fenics-project/${PN}/downloads/${P}.tar.gz" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="~amd64" -IUSE="hdf5 mpi parmetis petsc scotch trilinos umfpack zlib vtk" - -REQUIRED_USE="${PYTHON_REQUIRED_USE} - trilinos? ( mpi )" - -# Yes, swig is an RDEPEND -DEPEND=" - ${PYTHON_DEPS} - dev-cpp/eigen:3 - dev-lang/swig:0= - dev-libs/boost:= - dev-libs/libxml2:2 - ~dev-python/dijitso-${PV}[${PYTHON_USEDEP}] - ~dev-python/ffc-${PV}[${PYTHON_USEDEP}] - ~dev-python/fiat-${PV}[${PYTHON_USEDEP}] - ~dev-python/instant-${PV}[${PYTHON_USEDEP}] - dev-python/sympy - ~dev-python/ufl-${PV}[${PYTHON_USEDEP}] - virtual/blas - virtual/lapack - hdf5? ( sci-libs/hdf5[mpi=] ) - mpi? ( virtual/mpi ) - parmetis? ( sci-libs/parmetis[mpi(+)] ) - petsc? ( sci-mathematics/petsc[mpi=] ) - sci-libs/armadillo - scotch? ( sci-libs/scotch ) - trilinos? ( sci-libs/trilinos ) - umfpack? ( - sci-libs/amd - sci-libs/cholmod - sci-libs/umfpack - ) - vtk? ( sci-libs/vtk ) - zlib? ( sys-libs/zlib )" -RDEPEND="${DEPEND}" - -PATCHES=( - "${FILESDIR}"/${P}-trilinos-superlu.patch -) - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_configure() { - # *sigh* - addpredict /proc/mtrr - addpredict /sys/devices/system/cpu/ - - mycmakeargs=( - -DDOLFIN_ENABLE_CHOLMOD="$(usex umfpack)" - -DDOLFIN_ENABLE_HDF5="$(usex hdf5)" - -DDOLFIN_ENABLE_MPI="$(usex mpi)" - -DDOLFIN_ENABLE_PARMETIS="$(usex parmetis)" - -DDOLFIN_ENABLE_PETSC="$(usex petsc)" - -DDOLFIN_ENABLE_PYTHON="yes" - -DDOLFIN_ENABLE_SCOTCH="$(usex scotch)" - -DDOLFIN_ENABLE_TRILINOS="$(usex trilinos)" - -DDOLFIN_ENABLE_UMFPACK="$(usex umfpack)" - -DDOLFIN_ENABLE_VTK="$(usex vtk)" - -DDOLFIN_ENABLE_ZLIB="$(usex zlib)" - ) - cmake-utils_src_configure -} diff --git a/sci-mathematics/dolfin/dolfin-2017.1.0.ebuild b/sci-mathematics/dolfin/dolfin-2017.1.0.ebuild deleted file mode 100644 index 64e736315..000000000 --- a/sci-mathematics/dolfin/dolfin-2017.1.0.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python3_4 python3_5 python3_6 ) - -inherit cmake-utils eutils python-single-r1 - -DESCRIPTION="C++/Python interface of FEniCS" -HOMEPAGE="https://bitbucket.org/fenics-project/dolfin" -SRC_URI="https://bitbucket.org/fenics-project/${PN}/downloads/${P}.tar.gz" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="~amd64" -IUSE="hdf5 mpi parmetis petsc scotch trilinos umfpack zlib vtk" - -REQUIRED_USE="${PYTHON_REQUIRED_USE} - trilinos? ( mpi )" - -# Yes, swig is an RDEPEND -DEPEND=" - ${PYTHON_DEPS} - dev-cpp/eigen:3 - dev-lang/swig:0= - dev-libs/boost:= - dev-libs/libxml2:2 - ~dev-python/dijitso-${PV}[${PYTHON_USEDEP}] - ~dev-python/ffc-${PV}[${PYTHON_USEDEP}] - ~dev-python/fiat-${PV}[${PYTHON_USEDEP}] - ~dev-python/instant-${PV}[${PYTHON_USEDEP}] - dev-python/sympy - ~dev-python/ufl-${PV}[${PYTHON_USEDEP}] - virtual/blas - virtual/lapack - hdf5? ( sci-libs/hdf5[mpi=] ) - mpi? ( virtual/mpi ) - parmetis? ( sci-libs/parmetis[mpi(+)] ) - petsc? ( sci-mathematics/petsc[mpi=] ) - sci-libs/armadillo - scotch? ( sci-libs/scotch ) - trilinos? ( sci-libs/trilinos ) - umfpack? ( - sci-libs/amd - sci-libs/cholmod - sci-libs/umfpack - ) - vtk? ( sci-libs/vtk ) - zlib? ( sys-libs/zlib )" -RDEPEND="${DEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-2016.2.0-trilinos-superlu.patch -) - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_configure() { - # *sigh* - addpredict /proc/mtrr - addpredict /sys/devices/system/cpu/ - - mycmakeargs=( - -DDOLFIN_ENABLE_CHOLMOD="$(usex umfpack)" - -DDOLFIN_ENABLE_HDF5="$(usex hdf5)" - -DDOLFIN_ENABLE_MPI="$(usex mpi)" - -DDOLFIN_ENABLE_PARMETIS="$(usex parmetis)" - -DDOLFIN_ENABLE_PETSC="$(usex petsc)" - -DDOLFIN_ENABLE_PYTHON="yes" - -DDOLFIN_ENABLE_SCOTCH="$(usex scotch)" - -DDOLFIN_ENABLE_TRILINOS="$(usex trilinos)" - -DDOLFIN_ENABLE_UMFPACK="$(usex umfpack)" - -DDOLFIN_ENABLE_VTK="$(usex vtk)" - -DDOLFIN_ENABLE_ZLIB="$(usex zlib)" - ) - cmake-utils_src_configure -} diff --git a/sci-mathematics/dolfin/files/dolfin-0.9.9-find-armadillo.patch b/sci-mathematics/dolfin/files/dolfin-0.9.9-find-armadillo.patch deleted file mode 100644 index 677a78aab..000000000 --- a/sci-mathematics/dolfin/files/dolfin-0.9.9-find-armadillo.patch +++ /dev/null @@ -1,25 +0,0 @@ -diff -Naur a/cmake/modules/FindArmadillo.cmake b/cmake/modules/FindArmadillo.cmake ---- a/cmake/modules/FindArmadillo.cmake 2010-09-02 02:49:57.000000000 +0200 -+++ b/cmake/modules/FindArmadillo.cmake 2010-12-15 14:21:34.810300165 +0100 -@@ -95,8 +95,8 @@ - #include <armadillo> - int main() - { -- arma::mat A = arma::rand(4, 4); -- arma::vec b = arma::rand(4); -+ arma::mat A = arma::randu(4, 4); -+ arma::vec b = arma::randu(4); - arma::vec x = arma::solve(A, b); - return 0; - } -@@ -112,8 +112,8 @@ - #include <armadillo> - int main() - { -- arma::mat A = arma::rand(4, 4); -- arma::vec b = arma::rand(4); -+ arma::mat A = arma::randu(4, 4); -+ arma::vec b = arma::randu(4); - arma::vec x = arma::solve(A, b); - return 0; - } diff --git a/sci-mathematics/dolfin/files/dolfin-2016.2.0-trilinos-superlu.patch b/sci-mathematics/dolfin/files/dolfin-2016.2.0-trilinos-superlu.patch deleted file mode 100644 index 7282766fe..000000000 --- a/sci-mathematics/dolfin/files/dolfin-2016.2.0-trilinos-superlu.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff --git a/dolfin/CMakeLists.txt b/dolfin/CMakeLists.txt -index 26bc21a..0caf7ca 100644 ---- a/dolfin/CMakeLists.txt -+++ b/dolfin/CMakeLists.txt -@@ -2,6 +2,7 @@ set(DOLFIN_H dolfin.h) - install(FILES ${DOLFIN_H} DESTINATION ${DOLFIN_INCLUDE_DIR} - COMPONENT Development) - -+ - # Configure and install dolfin/common/version.h file - string(REPLACE "+" "" DOLFIN_VERSION_MICRO_STRIPPED ${DOLFIN_VERSION_MICRO}) - configure_file(${DOLFIN_SOURCE_DIR}/dolfin/common/version.h.in -@@ -12,6 +13,8 @@ install(FILES ${CMAKE_BINARY_DIR}/dolfin/common/version.h - ) - include_directories(${CMAKE_BINARY_DIR}) - -+include_directories(/usr/include/superlu) -+ - #------------------------------------------------------------------------------ - # DOLFIN source directories - diff --git a/sci-mathematics/dolfin/metadata.xml b/sci-mathematics/dolfin/metadata.xml deleted file mode 100644 index 26a0480f0..000000000 --- a/sci-mathematics/dolfin/metadata.xml +++ /dev/null @@ -1,26 +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> - <longdescription lang="en"> -DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations. -</longdescription> - <use> - <flag name="cgal">Adds support for geometric algorithms with <pkg>sci-mathematics/cgal</pkg></flag> - <flag name="cholmod">Adds support for sparse Cholesky factorization with <pkg>sci-libs/cholmod</pkg></flag> - <flag name="hdf5">Adds support for <pkg>sci-libs/hdf5</pkg></flag> - <flag name="parmetis">Adds support for parallel graph partitioning with <pkg>sci-libs/parmetis</pkg></flag> - <flag name="petsc">Adds support for numerical linear algebra toolkit <pkg>sci-mathematics/petsc</pkg></flag> - <flag name="scotch">Adds support for graph partitioning with <pkg>sci-libs/scotch</pkg></flag> - <flag name="trilinos">Adds support for numerical linear algebra toolkit <pkg>sci-libs/trilinos</pkg></flag> - <flag name="umfpack">Adds support for sparse solving with <pkg>sci-libs/umfpack</pkg></flag> - <flag name="vtk">Adds support for the visualization toolkit <pkg>sci-libs/vtk</pkg></flag> - </use> - <upstream> - <remote-id type="bitbucket">fenics-project/dolfin</remote-id> - <remote-id type="launchpad">dolfin</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/dsfmt/Manifest b/sci-mathematics/dsfmt/Manifest deleted file mode 100644 index cd9c966ec..000000000 --- a/sci-mathematics/dsfmt/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST dSFMT-src-2.2.tar.gz 291253 BLAKE2B 0b9762094450fb8d21a8786531df0a91a9750bddec9882e4d68607def42caaf5cf37a6f9ec41f84794e971bb60e708568f6b152610bafa72d757cb43d4512abb SHA512 e59d54166dc2df9f6e6abd68658c3624082feabe445215256fead47a8944c41578d11c2b4ba57eac174587a45e445b2aabd867db24fd9e951842513cf914f60b diff --git a/sci-mathematics/dsfmt/dsfmt-2.2.ebuild b/sci-mathematics/dsfmt/dsfmt-2.2.ebuild deleted file mode 100644 index 173384bac..000000000 --- a/sci-mathematics/dsfmt/dsfmt-2.2.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -MYP=dSFMT-src-${PV} - -DESCRIPTION="Double precision SIMD-oriented Fast Mersenne Twister library" -HOMEPAGE="http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT" -SRC_URI="${HOMEPAGE}/${MYP}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -S="${WORKDIR}/${MYP}" - -src_test() { - emake std-check -} - -src_install() { - doheader dSFMT.c d*.h - dodoc README*txt CHANGE* -} diff --git a/sci-mathematics/dsfmt/metadata.xml b/sci-mathematics/dsfmt/metadata.xml deleted file mode 100644 index d2482ce5f..000000000 --- a/sci-mathematics/dsfmt/metadata.xml +++ /dev/null @@ -1,17 +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> - <longdescription lang="en"> -The purpose of Double precision SIMD-oriented Fast Mersenne Twister (dSFMT) -is to speed up the generation by avoiding the expensive conversion -of integer to double (floating point). dSFMT directly generates -double precision floating point pseudorandom numbers which have the -IEEE Standard for Binary Floating-Point Arithmetic (ANSI/IEEE Std -754-1985) format. dSFMT is only available on the CPUs which use IEEE -754 format double precision floating point numbers. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/flocq/Manifest b/sci-mathematics/flocq/Manifest deleted file mode 100644 index 25a417be1..000000000 --- a/sci-mathematics/flocq/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST flocq-2.3.0.tar.gz 155465 BLAKE2B 8cf3c10799643b24b17b50c118bf344d95fba1ecb6faa0d12e559f15f449eb1c6b75f2b1707e6e770abbffeb26d73e094941828a785224f426c4cf6e6fc13a2d SHA512 964b87f3df3ab76549dace5d8c16c7e7890dc70b64f54db3555023dcd6b32648b19030ad25ecb5b6e99bca5139f289a2ecfd3a1fe8bc1e1dfe7429f3d4f1ebc3 diff --git a/sci-mathematics/flocq/flocq-2.3.0.ebuild b/sci-mathematics/flocq/flocq-2.3.0.ebuild deleted file mode 100644 index d875e9186..000000000 --- a/sci-mathematics/flocq/flocq-2.3.0.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -DESCRIPTION="A floating-point formalization for the Coq system" -HOMEPAGE="http://flocq.gforge.inria.fr/" -SRC_URI="https://gforge.inria.fr/frs/download.php/33502/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="sci-mathematics/coq" -RDEPEND="${DEPEND}" - -src_prepare() { - sed -i Remakefile.in \ - -e "s:mkdir -p @libdir@:mkdir -p \${DESTDIR}@libdir@:g" \ - -e "s:cp \$f @libdir@:cp \$f \${DESTDIR}@libdir@:g" -} - -src_configure() { - econf --libdir="`coqc -where`/user-contrib/Flocq" -} - -src_compile() { - ./remake || die "emake failed" -} - -src_install() { - DESTDIR="${D}" ./remake install || die - dodoc NEWS README AUTHORS ChangeLog -} diff --git a/sci-mathematics/flocq/metadata.xml b/sci-mathematics/flocq/metadata.xml deleted file mode 100644 index de5ba354b..000000000 --- a/sci-mathematics/flocq/metadata.xml +++ /dev/null @@ -1,14 +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> - <longdescription> -Flocq (Floats for Coq) is a floating-point formalization for the Coq -system. It provides a comprehensive library of theorems on a multi-radix -multi-precision arithmetic. It also supports efficient numerical -computations inside Coq. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/frama-c/Manifest b/sci-mathematics/frama-c/Manifest index 8380c7673..9681962f9 100644 --- a/sci-mathematics/frama-c/Manifest +++ b/sci-mathematics/frama-c/Manifest @@ -1 +1 @@ -DIST frama-c-Neon-20140301.tar.gz 3122492 BLAKE2B ba11361ac48e2416dd3fe05ceb2dd57a83a03b42c38d8670b16e6e9f9e1df12c7332820813d1986e9560a82f7535acad1b9946cb3c8fc593de2b3017d55e9609 SHA512 9cfe4c986004b4b991dbd2d7dc31777100bf85910c488d575c670d40d53b3e309667dfee75f22d121a6351f23753ed31decffbee08929ea129daf56f0c9a01e8 +DIST frama-c-22.0-Titanium.tar.gz 6008520 BLAKE2B 957f1fd383913718598c8d14bd0ff4b6251cc5350633888ca061fa0e44fae17273b379dcc1b70fe8a187975364aee1f255e0df232a4ee349ff29f9cb922a7b60 SHA512 7366127da4726ffec0022adc06fd867b6ea37fc23b6a5ddccbe7562fcaa635abc6894397d0101fcb0afc339c565299c6d637006305c8331aa62a8ce734740a0f diff --git a/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch b/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch deleted file mode 100644 index 798d17fd3..000000000 --- a/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch +++ /dev/null @@ -1,254 +0,0 @@ -From: Mehdi Dogguy <mehdi@debian.org> -Date: Sun, 27 Apr 2014 13:46:16 +0200 -Subject: Port to OCamlgraph 1.8.5 - ---- - src/impact/reason_graph.ml | 2 +- - src/kernel/stmts_graph.ml | 10 +++++----- - src/logic/property_status.ml | 8 ++++---- - src/misc/service_graph.ml | 4 ++-- - src/pdg_types/pdgTypes.ml | 6 +++--- - src/postdominators/print.ml | 2 +- - src/semantic_callgraph/register.ml | 4 ++-- - src/slicing/printSlice.ml | 10 +++++----- - src/syntactic_callgraph/register.ml | 4 ++-- - src/wp/cil2cfg.ml | 12 ++++++------ - 10 files changed, 31 insertions(+), 31 deletions(-) - -diff --git a/src/impact/reason_graph.ml b/src/impact/reason_graph.ml -index eabacb0..ce19b4a 100644 ---- a/src/impact/reason_graph.ml -+++ b/src/impact/reason_graph.ml -@@ -139,7 +139,7 @@ module Printer (X: AdditionalInfo) = struct - - let graph_attributes _ = [`Label "Impact graph"] - -- let default_vertex_attributes _g = [`Style [`Filled]; `Shape `Box] -+ let default_vertex_attributes _g = [`Style `Filled; `Shape `Box] - let default_edge_attributes _g = [] - - let vertex_attributes v = -diff --git a/src/kernel/stmts_graph.ml b/src/kernel/stmts_graph.ml -index a8fe121..16059c3 100644 ---- a/src/kernel/stmts_graph.ml -+++ b/src/kernel/stmts_graph.ml -@@ -157,12 +157,12 @@ module TP = struct - - let vertex_attributes s = - match s.skind with -- | Loop _ -> [`Color 0xFF0000; `Style [`Filled]] -- | If _ -> [`Color 0x00FF00; `Style [`Filled]; `Shape `Diamond] -- | Return _ -> [`Color 0x0000FF; `Style [`Filled]] -+ | Loop _ -> [`Color 0xFF0000; `Style `Filled] -+ | If _ -> [`Color 0x00FF00; `Style `Filled; `Shape `Diamond] -+ | Return _ -> [`Color 0x0000FF; `Style `Filled] - | Block _ -> [`Shape `Box; `Fontsize 8] -- | Goto _ -> [`Shape `Diamond; `Color 0x00FFFF ; `Style [`Filled]] -- | Instr (Skip _) -> [`Color 0x00FFFF ; `Style [`Filled]] -+ | Goto _ -> [`Shape `Diamond; `Color 0x00FFFF ; `Style `Filled] -+ | Instr (Skip _) -> [`Color 0x00FFFF ; `Style `Filled] - | _ -> [] - let default_vertex_attributes _ = [] - -diff --git a/src/logic/property_status.ml b/src/logic/property_status.ml -index f7c278d..47485f6 100644 ---- a/src/logic/property_status.ml -+++ b/src/logic/property_status.ml -@@ -1481,12 +1481,12 @@ module Consolidation_graph = struct - let s = get_status p in - let color = status_color p s in - let style = match s with -- | Never_tried -> [`Style [`Bold]; `Width 0.8 ] -- | _ -> [`Style [`Filled]] -+ | Never_tried -> [`Style `Bold; `Width 0.8 ] -+ | _ -> [`Style `Filled] - in - style @ [ label v; `Color color; `Shape `Box ] - | Emitter _ as v -> -- [ label v; `Shape `Diamond; `Color 0xb0c4de; `Style [`Filled] ] -+ [ label v; `Shape `Diamond; `Color 0xb0c4de; `Style `Filled ] - | Tuning_parameter _ as v -> - [ label v; (*`Style `Dotted;*) `Color 0xb0c4de; ] - (*| Correctness_parameter _ (*as v*) -> assert false (*[ label v; `Color 0xb0c4de ]*)*) -@@ -1495,7 +1495,7 @@ module Consolidation_graph = struct - | None -> [] - | Some s -> - let c = emitted_status_color s in -- [ `Color c; `Fontcolor c; `Style [`Bold] ] -+ [ `Color c; `Fontcolor c; `Style `Bold ] - - let default_vertex_attributes _ = [] - let default_edge_attributes _ = [] -diff --git a/src/misc/service_graph.ml b/src/misc/service_graph.ml -index 4f866c5..d158028 100644 ---- a/src/misc/service_graph.ml -+++ b/src/misc/service_graph.ml -@@ -289,7 +289,7 @@ Src root:%s in %s (is_root:%b) Dst:%s in %s (is_root:%b) [2d case]" - color e - else - match CallG.E.label e with -- | Inter_services -> [ `Style [`Invis] ] -+ | Inter_services -> [ `Style `Invis ] - | Inter_functions | Both -> color e - - let default_edge_attributes _ = [] -@@ -303,7 +303,7 @@ Src root:%s in %s (is_root:%b) Dst:%s in %s (is_root:%b) [2d case]" - sg_attributes = - [ `Label ("S " ^ cs); - `Color (Extlib.number_to_color id); -- `Style [`Bold] ] } -+ `Style `Bold ] } - - end - -diff --git a/src/pdg_types/pdgTypes.ml b/src/pdg_types/pdgTypes.ml -index 05754e4..74cdebf 100644 ---- a/src/pdg_types/pdgTypes.ml -+++ b/src/pdg_types/pdgTypes.ml -@@ -626,7 +626,7 @@ module Pdg = struct - - let graph_attributes _ = [`Rankdir `TopToBottom ] - -- let default_vertex_attributes _ = [`Style [`Filled]] -+ let default_vertex_attributes _ = [`Style `Filled] - let vertex_name v = string_of_int (Node.id v) - - let vertex_attributes v = -@@ -711,13 +711,13 @@ module Pdg = struct - if Dpd.is_ctrl d then (`Arrowtail `Odot)::attrib else attrib - in - let attrib = -- if Dpd.is_addr d then (`Style [`Dotted])::attrib else attrib -+ if Dpd.is_addr d then (`Style `Dotted)::attrib else attrib - in - attrib - - let get_subgraph v = - let mk_subgraph name attrib = -- let attrib = (`Style [`Filled]) :: attrib in -+ let attrib = (`Style `Filled) :: attrib in - Some { Graph.Graphviz.DotAttributes.sg_name= name; - sg_parent = None; - sg_attributes = attrib } -diff --git a/src/postdominators/print.ml b/src/postdominators/print.ml -index f2e3a25..15f4ff2 100644 ---- a/src/postdominators/print.ml -+++ b/src/postdominators/print.ml -@@ -63,7 +63,7 @@ module Printer = struct - - let graph_attributes (title, _) = [`Label title] - -- let default_vertex_attributes _g = [`Style [`Filled]] -+ let default_vertex_attributes _g = [`Style `Filled] - let default_edge_attributes _g = [] - - let vertex_attributes (s, has_postdom) = -diff --git a/src/semantic_callgraph/register.ml b/src/semantic_callgraph/register.ml -index 1c79dcc..071f061 100644 ---- a/src/semantic_callgraph/register.ml -+++ b/src/semantic_callgraph/register.ml -@@ -102,8 +102,8 @@ module Service = - let name = Kernel_function.get_name - let attributes v = - [ `Style -- [if Kernel_function.is_definition v then `Bold -- else `Dotted] ] -+ (if Kernel_function.is_definition v then `Bold -+ else `Dotted) ] - let entry_point () = - try Some (fst (Globals.entry_point ())) - with Globals.No_such_entry_point _ -> None -diff --git a/src/slicing/printSlice.ml b/src/slicing/printSlice.ml -index c5363f9..211e0bb 100644 ---- a/src/slicing/printSlice.ml -+++ b/src/slicing/printSlice.ml -@@ -227,7 +227,7 @@ module PrintProject = struct - - let graph_attributes (name, _) = [`Label name] - -- let default_vertex_attributes _ = [`Style [`Filled]] -+ let default_vertex_attributes _ = [`Style `Filled] - - let vertex_name v = match v with - | Src fi -> SlicingMacros.fi_name fi -@@ -280,16 +280,16 @@ module PrintProject = struct - - let edge_attributes (e, call) = - let attrib = match e with -- | (Src _, Src _) -> [`Style [`Invis]] -- | (OptSliceCallers _, _) -> [`Style [`Invis]] -- | (_, OptSliceCallers _) -> [`Style [`Invis]] -+ | (Src _, Src _) -> [`Style `Invis] -+ | (OptSliceCallers _, _) -> [`Style `Invis] -+ | (_, OptSliceCallers _) -> [`Style `Invis] - | _ -> [] - in match call with None -> attrib - | Some call -> (`Label (string_of_int call.sid)):: attrib - - let get_subgraph v = - let mk_subgraph name attrib = -- let attrib = (*(`Label name) ::*) (`Style [`Filled]) :: attrib in -+ let attrib = (*(`Label name) ::*) (`Style `Filled) :: attrib in - Some { Graph.Graphviz.DotAttributes.sg_name= name; - sg_parent = None; - sg_attributes = attrib } -diff --git a/src/syntactic_callgraph/register.ml b/src/syntactic_callgraph/register.ml -index d4669c4..d41980e 100644 ---- a/src/syntactic_callgraph/register.ml -+++ b/src/syntactic_callgraph/register.ml -@@ -37,8 +37,8 @@ module Service = - let name v = nodeName v.cnInfo - let attributes v = - [ match v.cnInfo with -- | NIVar (_,b) when not !b -> `Style [`Dotted] -- | _ -> `Style [`Bold] ] -+ | NIVar (_,b) when not !b -> `Style `Dotted -+ | _ -> `Style `Bold ] - let equal v1 v2 = id v1 = id v2 - let compare v1 v2 = - let i1 = id v1 in -diff --git a/src/wp/cil2cfg.ml b/src/wp/cil2cfg.ml -index 6d8cf09..ba5f410 100644 ---- a/src/wp/cil2cfg.ml -+++ b/src/wp/cil2cfg.ml -@@ -1278,9 +1278,9 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct - | Vstart | Vend | Vexit -> [`Color 0x0000FF; `Shape `Doublecircle] - | VfctIn | VfctOut -> [`Color 0x0000FF; `Shape `Box] - | VblkIn _ | VblkOut _ -> [`Shape `Box] -- | Vloop _ | Vloop2 _ -> [`Color 0xFF0000; `Style [`Filled]] -+ | Vloop _ | Vloop2 _ -> [`Color 0xFF0000; `Style `Filled] - | Vtest _ | Vswitch _ -> -- [`Color 0x00FF00; `Style [`Filled]; `Shape `Diamond] -+ [`Color 0x00FF00; `Style `Filled; `Shape `Diamond] - | Vcall _ | Vstmt _ -> [] - in (`Label (String.escaped label))::attr - -@@ -1290,15 +1290,15 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct - let attr = [] in - let attr = (`Label (String.escaped (PE.edge_txt e)))::attr in - let attr = -- if is_back_edge e then (`Constraint false)::(`Style [`Bold])::attr -+ if is_back_edge e then (`Constraint false)::(`Style `Bold)::attr - else attr - in - let attr = match (edge_type e) with - | Ethen | EbackThen -> (`Color 0x00FF00)::attr - | Eelse | EbackElse -> (`Color 0xFF0000)::attr -- | Ecase [] -> (`Color 0x0000FF)::(`Style [`Dashed])::attr -+ | Ecase [] -> (`Color 0x0000FF)::(`Style `Dashed)::attr - | Ecase _ -> (`Color 0x0000FF)::attr -- | Enext -> (`Style [`Dotted])::attr -+ | Enext -> (`Style `Dotted)::attr - | Eback -> attr (* see is_back_edge above *) - | Enone -> attr - in -@@ -1308,7 +1308,7 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct - - let get_subgraph v = - let mk_subgraph name attrib = -- let attrib = (`Style [`Filled]) :: attrib in -+ let attrib = (`Style `Filled) :: attrib in - Some { Graph.Graphviz.DotAttributes.sg_name= name; - sg_parent = None; - sg_attributes = attrib } --- diff --git a/sci-mathematics/frama-c/frama-c-20140301.ebuild b/sci-mathematics/frama-c/frama-c-22.0.ebuild index 0d7376d21..aaf815f4f 100644 --- a/sci-mathematics/frama-c/frama-c-20140301.ebuild +++ b/sci-mathematics/frama-c/frama-c-22.0.ebuild @@ -1,69 +1,61 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit autotools eutils +inherit autotools + +NAME="Titanium" DESCRIPTION="Framework for analysis of source codes written in C" -HOMEPAGE="http://frama-c.com" -NAME="Neon" -SRC_URI="http://frama-c.com/download/${PN/-c/-c-$NAME}-${PV/_/-}.tar.gz" +HOMEPAGE="https://frama-c.com" +SRC_URI="https://frama-c.com/download/${P}-${NAME}.tar.gz" LICENSE="LGPL-2" SLOT="0" KEYWORDS="~amd64" + IUSE="doc gtk +ocamlopt" RESTRICT="strip" DEPEND=" >=dev-lang/ocaml-3.12.1[ocamlopt?] - >=dev-ml/ocamlgraph-1.8.5[gtk?,ocamlopt?] + >=dev-ml/ocamlgraph-1.8.5[ocamlopt?] dev-ml/zarith + dev-ml/yojson sci-mathematics/coq sci-mathematics/ltl2ba sci-mathematics/alt-ergo gtk? ( >=x11-libs/gtksourceview-2.8:2.0 >=gnome-base/libgnomecanvas-2.26 - >=dev-ml/lablgtk-2.14[sourceview,gnomecanvas,ocamlopt?] + >=dev-ml/lablgtk-2.14[sourceview,gnomecanvas(-),ocamlopt?] )" RDEPEND="${DEPEND}" -S="${WORKDIR}/${PN/-c/-c-$NAME}-${PV/_/-}" +S="${WORKDIR}/${P}-${NAME}" src_prepare(){ touch config_file || die rm -f ocamlgraph.tar.gz || die - epatch "${FILESDIR}/ocamlgraph185_compat.patch" + default eautoreconf } src_configure(){ - if use gtk; then - myconf="--enable-gui" - else - myconf="--disable-gui" - fi - econf ${myconf} + econf "$(use_enable gtk gui )" } src_compile(){ # dependencies can not be processed in parallel, # this is the intended behavior. - emake -j1 depend + emake depend emake all top DESTDIR="/" - if use doc; then - emake -j1 doc doc-tgz - tar -xzf frama-c-api.tar.gz -C doc/ - fi + use doc && emake doc } src_install(){ default - - if use doc; then - dohtml -A svg -r doc/frama-c-api/* - fi + use doc && dodoc -r doc/doxygen/html/* } diff --git a/sci-mathematics/freefem++/Manifest b/sci-mathematics/freefem++/Manifest index 1ab28a71b..cde77c554 100644 --- a/sci-mathematics/freefem++/Manifest +++ b/sci-mathematics/freefem++/Manifest @@ -1 +1 @@ -DIST freefem++-3.8.tar.gz 21848854 BLAKE2B 6d4c725d553be936a899a341ae74ee6672ee94fcf799a27f984eca839cef2d88be56172e24dc3de9216b68c5f1c791bcf98b5fbea5ac034c72481625e64340c3 SHA512 357dbbe1d5598da43ce2d6071bc939daac4c2b2f700879e8f9b47e68a15c95be030b69da48d49a097b02814d6596250cc5c2e50417bef23c2db2da6222909519 +DIST freefem++-4.10.tar.gz 12607380 BLAKE2B 2adcbcb48555c218bdec087b52b955fef7d2b8c0b17045be64d8acf9cde0910dd9c1a1856c046582e3d3e3024848db284cf8262f2e7c9a2e46024768f0dbad7a SHA512 768e8657884e92cd32f08ea82b3f384ed1522d1a693c6de95281fe1bf49e61d084d7d4d5c6c31f70a05ed95ba7cc0af75979242225466d06c2173176e862995e diff --git a/sci-mathematics/freefem++/files/freefem++-acoptim.patch b/sci-mathematics/freefem++/files/freefem++-acoptim.patch deleted file mode 100644 index 087b077cb..000000000 --- a/sci-mathematics/freefem++/files/freefem++-acoptim.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- freefem++-2.20-1/acoptim.m4 2006-01-27 16:51:16.000000000 +0100 -+++ freefem++-2.20-1.new/acoptim.m4 2007-11-14 18:50:37.000000000 +0100 -@@ -16,14 +16,6 @@ - AC_ARG_ENABLE(debug,[ --enable-debug Turn on debug versions of FreeFem++]) - AC_ARG_ENABLE(optim,[ --enable-optim Turn on compiler optimization]) - --# Autoconf always chooses -O2. -O2 in gcc makes some functions --# disappear. This is not ideal for debugging. And when we optimize, we --# do not use -O2 anyway. -- --CFLAGS="`echo $CFLAGS | sed 's/-O2//g'`" --FFLAGS="`echo $FFLAGS | sed 's/-O2//g'`" --CXXFLAGS="`echo $CXXFLAGS | sed 's/-O2//g'`" -- - if test "$enable_debug" = yes; - then - AC_MSG_RESULT(yes)
\ No newline at end of file diff --git a/sci-mathematics/freefem++/files/freefem++-no-doc-autobuild.patch b/sci-mathematics/freefem++/files/freefem++-no-doc-autobuild.patch deleted file mode 100644 index add003aea..000000000 --- a/sci-mathematics/freefem++/files/freefem++-no-doc-autobuild.patch +++ /dev/null @@ -1,30 +0,0 @@ -diff -urN freefem++-3.4.old/DOC/Makefile.am freefem++-3.4.new/DOC/Makefile.am ---- freefem++-3.4.old/DOC/Makefile.am 2009-07-15 17:19:57.000000000 +0200 -+++ freefem++-3.4.new/DOC/Makefile.am 2009-07-15 17:20:22.000000000 +0200 -@@ -1,4 +1,4 @@ --dist_pkgdata_DATA=$(DOCPDF) -+all: - documentation: $(DOCPDF) - docps: $(DOCPS) $(DOCPSGZ) - docpdf: $(DOCPDF) -@@ -117,4 +117,4 @@ - - - # do not delete the copy figure to long to created --.PRECIOUS: $(CPFIGS_PDF) $(CPFIGS_EPS) -\ No newline at end of file -+.PRECIOUS: $(CPFIGS_PDF) $(CPFIGS_EPS) -diff -urN freefem++-3.4.old/Makefile.am freefem++-3.4.new/Makefile.am ---- freefem++-3.4.old/Makefile.am 2009-07-15 17:19:57.000000000 +0200 -+++ freefem++-3.4.new/Makefile.am 2009-07-15 17:55:42.000000000 +0200 -@@ -147,10 +147,6 @@ - - # Native MacOS packaging - # ---------------------- --install-exec-local:: -- $(mkinstalldirs) -m 755 $(DESTDIR)$(pkgdatadir)/$(VERSION) -- tar cvf - $(FF_EXAMPLES_FILES)| (cd $(DESTDIR)$(pkgdatadir)/$(VERSION); tar xvf -) -- - ListFiles-natives: .FORCE - # echo COPYRIGHT HISTORY HISTORY_BEFORE_2005 README BUGS TODO INSTALL INSTALL-MacOSX INNOVATION >$@ - # echo mode-mi-edp.zip >> $@ diff --git a/sci-mathematics/freefem++/files/freefem++-path.patch b/sci-mathematics/freefem++/files/freefem++-path.patch deleted file mode 100644 index bc30a238d..000000000 --- a/sci-mathematics/freefem++/files/freefem++-path.patch +++ /dev/null @@ -1,105 +0,0 @@ -diff -up freefem++-3.8/configure.ac.r freefem++-3.8/configure.ac ---- freefem++-3.8/configure.ac.r 2010-02-04 14:48:19.000000000 +0100 -+++ freefem++-3.8/configure.ac 2010-02-25 22:53:52.000000000 +0100 -@@ -353,7 +355,7 @@ AC_DEFINE_UNQUOTED(VersionFreeFempp,$ff_ - # date is only useful for config-version.h - - test "$prefix" = NONE && prefix="$ac_default_prefix" --ff_prefix_dir="${prefix}/lib/ff++/$VERSION" -+ff_prefix_dir="${libdir}/freefem++" - AC_MSG_CHECKING(prefix dir freefem++ ) - AC_MSG_RESULT($ff_prefix_dir) - -@@ -1250,7 +1252,7 @@ then - AC_CHECK_LIB(umfpack,umf_i_malloc, - ff_umfpack_libs=" -lumfpack $ff_umfpack_libs" - ff_umfpack_ok=yes,,$ff_umfpack_libs) -- if test "$ff_umfpack_ok" != yes -o "$ff_umfpack_header" != yes ; then -+ if test "$ff_umfpack_ok" = yes -a "$ff_umfpack_header" != yes ; then - AC_MSG_WARN([ Sorry we find UMFPACK lib but not the include umfpack.h file]) - fi - fi -diff -up freefem++-3.8/examples++-3d/Makefile.am.r freefem++-3.8/examples++-3d/Makefile.am ---- freefem++-3.8/examples++-3d/Makefile.am.r 2009-11-10 20:28:06.000000000 +0100 -+++ freefem++-3.8/examples++-3d/Makefile.am 2010-02-25 22:41:45.000000000 +0100 -@@ -31,8 +31,8 @@ freefem++.pref: - echo loadpath += \"./\" >>freefem++.pref - - install-exec-local:: -- $(mkinstalldirs) -m 755 $(DESTDIR)$(ff_prefix_dir)/idp -- $(INSTALL) -m 555 $(LIST_IDP) $(DESTDIR)$(ff_prefix_dir)/idp -+ $(mkinstalldirs) -m 755 $(DESTDIR)$(datadir)/freefem++/idp -+ $(INSTALL) -m 555 $(LIST_IDP) $(DESTDIR)$(datadir)/freefem++/idp - - - -diff -up freefem++-3.8/examples++-load/load.link.in.r freefem++-3.8/examples++-load/load.link.in ---- freefem++-3.8/examples++-load/load.link.in.r 2009-12-04 15:53:45.000000000 +0100 -+++ freefem++-3.8/examples++-load/load.link.in 2010-02-25 22:41:45.000000000 +0100 -@@ -26,8 +26,8 @@ if [ -z "$INCFF" ] ; then - INCFF="-Iinclude" - elif [ -f "FFAPPLI_INC/ff++.hpp" ] ; then - INCFF="-IFFAPPLI_INC" -- elif [ -f '@ff_prefix_dir@/include/ff++.hpp' ] ; then -- INCFF='-I@ff_prefix_dir@/include' -+ elif [ -f '@includedir@/freefem++/ff++.hpp' ] ; then -+ INCFF='-I@includedir@/freefem++' - else - ff=`which freefem++.exe`; - ffinc=`dirname "$ff"`/examples++-load/include -diff -up freefem++-3.8/examples++-load/Makefile.am.r freefem++-3.8/examples++-load/Makefile.am ---- freefem++-3.8/examples++-load/Makefile.am.r 2010-01-28 20:38:21.000000000 +0100 -+++ freefem++-3.8/examples++-load/Makefile.am 2010-02-25 23:13:32.000000000 +0100 -@@ -95,7 +95,7 @@ all.edp: - regtests.edp: regtests.m4 ../regtests.m4 - m4 -DASSERT regtests.m4 > regtests.edp - --$(LIST_COMPILE):ff-c++ include Makefile -+$(LIST_COMPILE) $(LIST_COMPILE_PKG):ff-c++ include Makefile - - clean-local: - -rm *.o load.link WHERE_LIBRARY-download ff-get-dep ff-c++ ff-pkg-download \ -@@ -121,19 +121,19 @@ WHERE_LIBRARY-download:ff-pkg-download - freefem++.pref: - echo loadpath = \"./\" >freefem++.pref - install-exec-local:: load_compile -- $(mkinstalldirs) -m 755 $(DESTDIR)$(ff_prefix_dir)/lib -- $(mkinstalldirs) -m 755 $(DESTDIR)$(ff_prefix_dir)/include -- $(mkinstalldirs) -m 755 $(DESTDIR)$(ff_prefix_dir)/etc -- $(INSTALL_DATA) include/* $(DESTDIR)$(ff_prefix_dir)/include -- $(INSTALL) -m 555 $(LIST_COMPILE) $(DESTDIR)$(ff_prefix_dir)/lib -- echo loadpath += \"./\" >$(DESTDIR)$(ff_prefix_dir)/etc/freefem++.pref -- echo loadpath += \"$(ff_prefix_dir)/lib\" >>$(DESTDIR)$(ff_prefix_dir)/etc/freefem++.pref -- echo includepath += \"$(ff_prefix_dir)/idp\" >>$(DESTDIR)$(ff_prefix_dir)/etc/freefem++.pref -+ $(mkinstalldirs) -m 755 $(DESTDIR)$(libdir)/freefem++ -+ $(mkinstalldirs) -m 755 $(DESTDIR)$(includedir)/freefem++ -+ $(mkinstalldirs) -m 755 $(DESTDIR)$(sysconfdir) -+ $(INSTALL_DATA) include/* $(DESTDIR)$(includedir)/freefem++ -+ $(INSTALL) -m 555 $(LIST_COMPILE) $(DESTDIR)$(libdir)/freefem++ -+ echo loadpath += \"./\" >$(DESTDIR)$(sysconfdir)/freefem++.pref -+ echo loadpath += \"$(libdir)/freefem++\" >>$(DESTDIR)$(sysconfdir)/freefem++.pref -+ echo includepath += \"$(datadir)/freefem++/idp\" >>$(DESTDIR)$(sysconfdir)/freefem++.pref - $(INSTALL_SCRIPT) ff-c++ $(DESTDIR)${bindir} - $(INSTALL_SCRIPT) ff-pkg-download $(DESTDIR)${bindir} - $(INSTALL_SCRIPT) ff-get-dep $(DESTDIR)${bindir} - -for i in $(LIST_COMPILE_PKG); do \ -- if [ -f $$i ] ; then $(INSTALL) -m 555 $$i $(DESTDIR)$(ff_prefix_dir)/lib; fi; done -+ if [ -f $$i ] ; then $(INSTALL) -m 555 $$i $(DESTDIR)$(libdir)/freefem++; fi; done - - - -diff -up freefem++-3.8/src/lglib/Makefile.am.r freefem++-3.8/src/lglib/Makefile.am ---- freefem++-3.8/src/lglib/Makefile.am.r 2010-01-10 22:47:14.000000000 +0100 -+++ freefem++-3.8/src/lglib/Makefile.am 2010-02-25 22:41:45.000000000 +0100 -@@ -9,9 +9,9 @@ INCLUDES=-I../fflib -I../bamglib -I../Gr - BUILT_SOURCES=lg.tab.hpp lg.tab.cpp - - lg.tab.hpp lg.tab.cpp: lg.ypp -- -rm lg.tab.hpp lg.tab.cpp lg.tab.cpp.h -+ -rm -f lg.tab.hpp lg.tab.cpp lg.tab.cpp.h - bison -dtv -p lg $< -o lg.tab.cpp -- -mv lg.tab.cpp.h lg.tab.hpp # pour un pb entre des versions de bison -+ -mv -f lg.tab.cpp.h lg.tab.hpp # pour un pb entre des versions de bison - libfreefem++.dylib: lg.tab.o ../fflib/libff.a - g++ -bundle lg.tab.o ../fflib/libff.a $(UMFPACKLIB) $(ARPACKLIB) $(BLASLIB) $(LIBS) -o libfreefem++.dylib - EXTRA_DIST=lg.ypp diff --git a/sci-mathematics/freefem++/freefem++-3.8.ebuild b/sci-mathematics/freefem++/freefem++-4.10.ebuild index 545301816..5791c4bf6 100644 --- a/sci-mathematics/freefem++/freefem++-3.8.ebuild +++ b/sci-mathematics/freefem++/freefem++-4.10.ebuild @@ -1,20 +1,19 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=8 -inherit autotools eutils flag-o-matic mpi versionator toolchain-funcs - -MY_PV=$(replace_version_separator 2 '-') +inherit autotools toolchain-funcs DESCRIPTION="Solve PDEs using FEM on 2d and 3d domains" -HOMEPAGE="http://www.freefem.org/ff++/" -SRC_URI="http://www.freefem.org/ff++/ftp/old-v3/${PN}-${MY_PV}.tar.gz" +HOMEPAGE="https://freefem.org/" +SRC_URI="https://github.com/FreeFem/FreeFem-sources/archive/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/FreeFem-sources-${PV}" LICENSE="LGPL-2.1" SLOT="0" KEYWORDS="~amd64" -IUSE="doc examples mpi opengl X" +IUSE="examples mpi opengl X" RDEPEND=" sci-libs/fftw:3.0 @@ -22,7 +21,8 @@ RDEPEND=" virtual/lapack sci-libs/umfpack sci-libs/arpack - mpi? ( $(mpi_pkg_deplist) ) + sci-libs/hdf5[cxx] + mpi? ( virtual/mpi ) opengl? ( media-libs/freeglut virtual/opengl @@ -35,25 +35,11 @@ RDEPEND=" x11-libs/libXxf86vm )" -DEPEND="${RDEPEND} - virtual/pkgconfig - doc? ( - dev-texlive/texlive-latexrecommended - dev-texlive/texlive-latexextra - virtual/latex-base - media-gfx/imagemagick - )" - -S="${WORKDIR}/${PN}-${MY_PV}" +DEPEND="${RDEPEND}" +BDEPEND="virtual/pkgconfig" src_prepare() { - # acoptim.m4 forced -O2 removal - epatch "${FILESDIR}"/${PN}-acoptim.patch - # do not try to do a forced "manual" installation of - # examples and documentation - epatch "${FILESDIR}"/${PN}-no-doc-autobuild.patch - # Honor FHS - epatch "${FILESDIR}"/${PN}-path.patch + default eautoreconf } @@ -62,7 +48,7 @@ src_configure() { local myconf if use mpi; then - myconf="${myconf} --with-mpi=$(mpi_pkg_cxx)" + myconf="${myconf} --with-mpi=/usr/bin/mpi" else myconf="--without-mpi" fi @@ -74,18 +60,9 @@ src_configure() { --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \ --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" \ $(use_enable opengl) \ - $(use_with X x) \ ${myconf} } -src_compile() { - default - - if use doc; then - emake documentation - fi -} - src_test() { if use mpi; then # This may depend on the used MPI implementation. It is needed @@ -102,11 +79,6 @@ src_test() { src_install() { default - insinto /usr/share/doc/${PF} - if use doc; then - doins DOC/freefem++doc.pdf - fi - if use examples; then einfo "Installing examples..." diff --git a/sci-mathematics/freefem++/metadata.xml b/sci-mathematics/freefem++/metadata.xml index a605d78d7..5cee338ce 100644 --- a/sci-mathematics/freefem++/metadata.xml +++ b/sci-mathematics/freefem++/metadata.xml @@ -10,4 +10,7 @@ FreeFem++ is an implementation of a language dedicated to the finite element method. It enables you to solve Partial Differential Equations (PDE) easily. </longdescription> + <upstream> + <remote-id type="github">FreeFem/FreeFem-sources</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/gap/Manifest b/sci-mathematics/gap/Manifest deleted file mode 100644 index 9ee58f2a4..000000000 --- a/sci-mathematics/gap/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST gap4r4p12.tar.bz2 47715810 BLAKE2B a1b3dfa34b62cf62de34cc8513d12d692ccd8345c35afcc3c4175ed629bec7a737c41958d9c85ee6fe6105ac169e5e56b60b23cb396569049521292075082608 SHA512 2b97e8678a34ba4e90b47d90cefe426dbb68f9c0fbb984b6552a069481bfe370fdc0e0646b58d18ee414055980e25391d92bc3cab8de962a38ae9e66c7314034 -DIST xtom1r1p4.tar.bz2 4817504 BLAKE2B cc0bfb0afd5eaa78595a163a391c07c360df2dd3c4eb3d2d856dab623f3e53888bbc54b623093c08d1c9e9e09c760bb7c1b93dcc02c98ea4198bdb202a781741 SHA512 d24b2aa6d42e8080e235620a3ecc39dcf4b02d3a2713f1eada33adabcb4c3af3d9cbf9aace0f6e15f085692c2248b820091acce0199c66777458805fa44fcec1 diff --git a/sci-mathematics/gap/files/64gap-gentoo.el b/sci-mathematics/gap/files/64gap-gentoo.el deleted file mode 100644 index 24756c0b1..000000000 --- a/sci-mathematics/gap/files/64gap-gentoo.el +++ /dev/null @@ -1,10 +0,0 @@ -;; gap mode -(autoload 'gap-mode "gap-mode" "Gap editing mode" t) -(setq auto-mode-alist (append (list '("\\.g$" . gap-mode) - '("\\.gap$" . gap-mode)) - auto-mode-alist)) -(autoload 'gap "gap-process" "Run GAP in emacs buffer" t) - -(setq gap-executable "/usr/bin/gap") -(setq gap-start-options ()) -;; end gap mode diff --git a/sci-mathematics/gap/gap-4.4.12.ebuild b/sci-mathematics/gap/gap-4.4.12.ebuild deleted file mode 100644 index 5cd6089e6..000000000 --- a/sci-mathematics/gap/gap-4.4.12.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit elisp-common versionator - -XTOM_VERSION=1r1p4 - -PV1=$(get_version_component_range 1-2 ) -PV2=$(get_version_component_range 3 ) -PV1=$(replace_version_separator 1 'r' ${PV1} ) -PV2=${PV1}p${PV2} - -DESCRIPTION="System for computational discrete algebra" -HOMEPAGE="http://www.gap-system.org/" -SRC_URI=" - ftp://ftp.gap-system.org/pub/gap/gap44/tar.bz2/${PN}${PV2}.tar.bz2 - xtom? ( ftp://ftp.gap-system.org/pub/gap/gap44/tar.bz2/xtom${XTOM_VERSION}.tar.bz2 )" - -SLOT="0" -IUSE="emacs vim-syntax xtom" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - emacs? ( virtual/emacs ) - vim-syntax? ( || ( app-editors/vim app-editors/gvim ) )" -DEPEND="${RDEPEND}" - -S="${WORKDIR}"/${PN}${PV1} - -src_compile() { - emake CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" compile -} - -src_test() { - emake teststandard -} - -src_install() { - dodoc README description* - insinto /usr/share/${PN} - doins -r doc grp lib pkg prim small trans tst sysinfo.gap - source sysinfo.gap - exeinto /usr/libexec/${PN} - doexe bin/${GAParch}/gap - sed -e "s|@gapdir@|/usr/share/${PN}|" \ - -e "s|@target@-@CC@|/usr/libexec/${PN}|" \ - -e "s|@EXEEXT@||" \ - -e 's|$GAP_DIR/bin/||' \ - gap.shi > gap || doe - dobin gap - - if use emacs ; then - elisp-site-file-install etc/emacs/gap-mode.el - elisp-site-file-install etc/emacs/gap-process.el - elisp-site-file-install "${FILESDIR}"/64gap-gentoo.el - dodoc etc/emacs/gap-mode.doc - fi - - if use vim-syntax ; then - insinto /usr/share/vim/vimfiles/syntax - doins etc/gap.vim - insinto /usr/share/vim/vimfiles/indent - newins etc/gap_indent.vim gap.vim - insinto /usr/share/vim/vimfiles/plugin - newins etc/debug.vim debug_gap.vim - dodoc etc/README.vim-utils etc/debugvim.txt - fi -} - -pkg_postinst() { - use emacs && elisp-site-regen -} - -pkg_postrm() { - use emacs && elisp-site-regen -} diff --git a/sci-mathematics/gap/metadata.xml b/sci-mathematics/gap/metadata.xml deleted file mode 100644 index 2d5c1a14d..000000000 --- a/sci-mathematics/gap/metadata.xml +++ /dev/null @@ -1,25 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>A.G.Grozin@inp.nsk.su</email> - <name>Andrey Grozin</name> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription lang="en"> -Groups, Algorithms, Programming is a system for computational -discrete algebra, with particular emphasis on Computational Group -Theory. GAP provides a programming language, a library of thousands -of functions implementing algebraic algorithms written in the GAP -language as well as large data libraries of algebraic objects. GAP -is used in research and teaching for studying groups and their -representations, rings, vector spaces, algebras, combinatorial -structures, and more. -</longdescription> - <use> - <flag name="xtom">Automatically generated description for xtom</flag> - </use> -</pkgmetadata> diff --git a/sci-mathematics/gappa/Manifest b/sci-mathematics/gappa/Manifest deleted file mode 100644 index 416caf81e..000000000 --- a/sci-mathematics/gappa/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST gappa-1.1.1.tar.gz 399606 BLAKE2B 761439b96885434f42f57c253313b4cf8130bff6cc313a62480984d31bc3688c690da6ec688dcb97cb9f2d62533bccaa646d4df67222d8237cf06bdc314ba321 SHA512 95b01733554585729d73078522720f0c318f6e86eec02b869717e591bd1477a663c8f71d6c9362f8d5ec83d0a856be5771a27add426d8ac0eca429c4ded01a0e diff --git a/sci-mathematics/gappa/gappa-1.1.1.ebuild b/sci-mathematics/gappa/gappa-1.1.1.ebuild deleted file mode 100644 index 29de6ffa5..000000000 --- a/sci-mathematics/gappa/gappa-1.1.1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -DESCRIPTION="Verifying and proving properties on floating-point or fixed-point arithmetic" -HOMEPAGE="http://gappa.gforge.inria.fr/" -SRC_URI="http://gforge.inria.fr/frs/download.php/33486/${P}.tar.gz" - -LICENSE="|| ( CeCILL-2.0 GPL-2 )" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc" - -RDEPEND=" - dev-libs/gmp:0= - dev-libs/mpfr:0= - dev-libs/boost" -DEPEND="${RDEPEND} - doc? ( app-doc/doxygen )" - -src_prepare() { - sed -i Remakefile.in \ - -e "s:mkdir -p @bindir@:mkdir -p \${DESTDIR}@bindir@:g" \ - -e "s:cp src/gappa @bindir@:cp src/gappa \${DESTDIR}@bindir@:g" -} - -src_compile() { - ./remake -d ${MAKEOPTS} || die "emake failed" - if use doc; then - ./remake doc/html/index.html - fi -} - -src_install() { - DESTDIR="${D}" ./remake install - dodoc NEWS README AUTHORS ChangeLog - use doc && dohtml -A png -r doc/html/* -} diff --git a/sci-mathematics/gappa/metadata.xml b/sci-mathematics/gappa/metadata.xml deleted file mode 100644 index 448d16798..000000000 --- a/sci-mathematics/gappa/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> - <longdescription> -Gappa is a tool intended to help verifying and formally proving -properties on numerical programs dealing with floating-point or -fixed-point arithmetic. It has been used to write robust floating-point -filters for CGAL and it is used to certify elementary functions in -CRlibm. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/gappalib-coq/Manifest b/sci-mathematics/gappalib-coq/Manifest deleted file mode 100644 index d3808c01f..000000000 --- a/sci-mathematics/gappalib-coq/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST gappalib-coq-1.0.0.tar.gz 118901 BLAKE2B a72ae81f8003bd0e4fd58e57cd10612d5cea4657d4d1c59a17ef04075aed5de0ee836c632e904024553f912a8c52b221ed79d62377686fea5fe1c3b4982b98f5 SHA512 1aed7eafc24d82fbb3431e267ae0882560b34864f443fa95b450f465fe571cae558bc0ddf31db96477092518dd20a9870a9f8360ad8a0b3967d6f912c2bd0b67 diff --git a/sci-mathematics/gappalib-coq/gappalib-coq-1.0.0.ebuild b/sci-mathematics/gappalib-coq/gappalib-coq-1.0.0.ebuild deleted file mode 100644 index 6aef54089..000000000 --- a/sci-mathematics/gappalib-coq/gappalib-coq-1.0.0.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -DESCRIPTION="Allows the certificates Gappa generates to be imported by the Coq" -HOMEPAGE="http://gappa.gforge.inria.fr/" -SRC_URI="http://gforge.inria.fr/frs/download.php/32743/${P}.tar.gz" - -LICENSE="LGPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="sci-mathematics/gappa - sci-mathematics/coq - sci-mathematics/flocq" -RDEPEND="${DEPEND}" - -src_prepare() { - sed -i Remakefile.in \ - -e "s:mkdir -p @libdir@:mkdir -p \${DESTDIR}@libdir@:g" \ - -e "s:cp \$(OBJS) \$(MLTARGETS) @libdir@:cp \$(OBJS) \$(MLTARGETS) \${DESTDIR}@libdir@:g" -} - -src_compile() { - ./remake || die "emake failed" -} - -src_install() { - DESTDIR="${D}" ./remake install || die "emake install failed" - dodoc NEWS README AUTHORS ChangeLog -} diff --git a/sci-mathematics/gappalib-coq/metadata.xml b/sci-mathematics/gappalib-coq/metadata.xml deleted file mode 100644 index 182ed0520..000000000 --- a/sci-mathematics/gappalib-coq/metadata.xml +++ /dev/null @@ -1,13 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription> -While Gappa is intended to be used directly, it can also act as a -backend prover for the Why software verification plateform or as an -automatic tactic for the Coq proof assistant. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/giac/Manifest b/sci-mathematics/giac/Manifest deleted file mode 100644 index e523daca1..000000000 --- a/sci-mathematics/giac/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST giac-1.1.0.tar.bz2 43295079 SHA256 8d4f96a577d526caa201d8311f462828b92eead2938b00e563b208b4e255a340 SHA512 2b34c7913a6a24aa770094bc839c01f7f3d16689ed9673d56b72ce39d07004e20218e039c85fb15e9f39f5f9e6993e6cfff62e755997f1107cddf7e601658434 WHIRLPOOL ca761a1f2bd6ad88655a079a29f54344d101542ba7a0c09fe7d8e0077e36ab06235341210a7b2a0ef98d09d416756be2725b9cc7be676957eaa199a67d67e375 diff --git a/sci-mathematics/giac/giac-1.1.0.ebuild b/sci-mathematics/giac/giac-1.1.0.ebuild deleted file mode 100644 index 520a56151..000000000 --- a/sci-mathematics/giac/giac-1.1.0.ebuild +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -DESCRIPTION="A free C++ CAS (Computer Algebra System) library and its interfaces" -HOMEPAGE="http://www-fourier.ujf-grenoble.fr/~parisse/giac.html" -SRC_URI="http://www-fourier.ujf-grenoble.fr/~parisse/${PN}/${P}.tar.bz2" -LICENSE="GPL-2" - -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc examples fltk" - -AUTOTOOLS_IN_SOURCE_BUILD=true -inherit autotools-utils flag-o-matic pax-utils - -RDEPEND=">=dev-libs/gmp-3 - >=sys-libs/readline-4.2 - fltk? ( >=x11-libs/fltk-1.1.9 ) - dev-libs/mpfr - sci-libs/gsl - >=sci-mathematics/pari-2.3 - >=dev-libs/ntl-5.2" - -src_prepare(){ - sed -e "s:\$(prefix)/share:\$(DESTDIR)\$(prefix)/share:g" \ - -e "s:config.h \$(includedir)/giac:config.h \$(DESTDIR)\$(includedir)/giac:g" \ - -e "s:\$(DESTDIR)\$(DESTDIR):\$(DESTDIR):g" \ - -e "s:\$(DESTDIR)/\$(DESTDIR):\$(DESTDIR):g" \ - -i `find -name Makefile\*` || die - if use !fltk; then - sed -e "s: gl2ps\.[chlo]*::g" -i src/Makefile.* || die - fi -} - -src_configure(){ - if use fltk - then - append-cppflags -I$(fltk-config --includedir) - append-lfs-flags - append-libs $(fltk-config --ldflags | sed -e 's/\(-L\S*\)\s.*/\1/') || die - fi - local myeconfargs=( - $(use_enable fltk gui) - ) - autotools-utils_src_configure -} - -src_install() { - emake install DESTDIR="${D}" - dobin src/aide - rm "${D}"/usr/bin/*cas_help || die - dodoc AUTHORS ChangeLog INSTALL NEWS README TROUBLES - if use !fltk; then - rm "${D}"/usr/bin/x* || die - elif host-is-pax; then - pax-mark -m "${D}"/usr/bin/x* - fi - if use !doc; then - rm -R "${D}"/usr/share/doc "${D}"/usr/share/giac/doc/ || die - else - for LANG in el en es fr pt; do - if echo ${LINGUAS} | grep -v "$LANG" &> /dev/null; then - rm -R "${D}"/usr/share/giac/doc/"$LANG" - else - ln "${D}"/usr/share/giac/doc/aide_cas "${D}"/usr/share/giac/doc/"$LANG"/aide_cas || die - fi - done - fi - if use !examples; then - rm -R "${D}"/usr/share/giac/examples || die - fi -} diff --git a/sci-mathematics/giac/metadata.xml b/sci-mathematics/giac/metadata.xml deleted file mode 100644 index 60502e1d7..000000000 --- a/sci-mathematics/giac/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> - <longdescription> -Giac is a free computer algebra system that can be used to perform -computer algebra, function graphs, interactive geometry (2-d and 3-d), -spreadsheet and statistics, programmation. It may be used as a replacement -for high end graphic calculators for example on netbooks (for about -the same price as a calculator but with much more performances). -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/htk/Manifest b/sci-mathematics/htk/Manifest deleted file mode 100644 index c9f41b030..000000000 --- a/sci-mathematics/htk/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST HDecode-3.4.1.tar.gz 101930 SHA256 9517b25a91200e3e84ebed0d615f73715196dbfaf32ef854c2e964442175bee5 -DIST HTK-3.4.1.tar.gz 2101024 SHA256 42297b036ce3a47adeab26aaa42f51ac4b370ead7f53bab75fd27a52d38ae5ac diff --git a/sci-mathematics/htk/files/include_make_destdir.patch b/sci-mathematics/htk/files/include_make_destdir.patch deleted file mode 100644 index 55ea2c773..000000000 --- a/sci-mathematics/htk/files/include_make_destdir.patch +++ /dev/null @@ -1,73 +0,0 @@ -diff -Naur htk.old//HLMTools/Makefile.in htk//HLMTools/Makefile.in ---- htk.old//HLMTools/Makefile.in 2009-03-11 07:07:18.000000000 -0300 -+++ htk//HLMTools/Makefile.in 2011-09-02 18:46:15.452348315 -0300 -@@ -71,9 +71,9 @@ - -rm -f *.o $(PROGS) Makefile *.exe - - install: mkinstalldir $(PROGS) -- for program in $(PROGS) ; do $(INSTALL) -m 755 $${program}@BINARY_EXTENSION@ $(bindir) ; done -+ for program in $(PROGS) ; do $(INSTALL) -m 755 $${program}@BINARY_EXTENSION@ $(DESTDIR)$(bindir) ; done - - mkinstalldir: -- if [ ! -d $(bindir) -a X_@TRADHTK@ = X_yes ] ; then mkdir -p $(bindir) ; fi -+ if [ ! -d $(DESTDIR)$(bindir) -a X_@TRADHTK@ = X_yes ] ; then mkdir -p $(DESTDIR)$(bindir) ; fi - - .PHONY: all strip clean cleanup distclean install mkinstalldir -diff -Naur htk.old//HTKLVRec/Makefile.in htk//HTKLVRec/Makefile.in ---- htk.old//HTKLVRec/Makefile.in 2009-03-11 06:56:05.000000000 -0300 -+++ htk//HTKLVRec/Makefile.in 2011-09-02 18:44:40.072737063 -0300 -@@ -112,11 +112,11 @@ - -rm -f *.o HDecode HDecode.mod Makefile - - install: mkinstalldir -- $(INSTALL) -m 755 HDecode $(bindir) -- $(INSTALL) -m 755 HDecode.mod $(bindir) -+ $(INSTALL) -m 755 HDecode $(DESTDIR)$(bindir) -+ $(INSTALL) -m 755 HDecode.mod $(DESTDIR)$(bindir) - - mkinstalldir: -- -mkdir -p $(bindir) -+ -mkdir -p $(DESTDIR)$(bindir) - - .PHONY: std mod all strip clean cleanup distclean install mkinstalldir - -diff -Naur htk.old//HTKTools/Makefile.in htk//HTKTools/Makefile.in ---- htk.old//HTKTools/Makefile.in 2009-03-11 09:50:53.000000000 -0300 -+++ htk//HTKTools/Makefile.in 2011-09-02 18:45:41.423059972 -0300 -@@ -73,10 +73,10 @@ - -rm -f *.o $(PROGS) *.exe Makefile - - install: mkinstalldir $(PROGS) -- for program in $(PROGS) ; do $(INSTALL) -m 755 $${program} $(bindir) ; done -+ for program in $(PROGS) ; do $(INSTALL) -m 755 $${program} $(DESTDIR)$(bindir) ; done - - mkinstalldir: -- if [ ! -d $(bindir) ] ; then mkdir $(bindir) ; fi -+ if [ ! -d $(DESTDIR)$(bindir) ] ; then mkdir -p $(DESTDIR)$(bindir) ; fi - - - .PHONY: all strip clean cleanup distclean install mkinstalldir -diff -Naur htk.old//Makefile.in htk//Makefile.in ---- htk.old//Makefile.in 2009-03-11 07:08:06.000000000 -0300 -+++ htk//Makefile.in 2011-09-02 18:44:40.073737098 -0300 -@@ -119,16 +119,16 @@ - - # installation - install-htktools: htktools -- (cd $(HTKTOOLS) && $(MAKE) install) \ -+ (cd $(HTKTOOLS) && $(MAKE) DESTDIR=$(DESTDIR) install) \ - || case "$(MFLAGS)" in *k*) fail=yes;; *) exit 1;; esac; - install-hlmtools: hlmtools -- (cd $(HLMTOOLS) && $(MAKE) install) \ -+ (cd $(HLMTOOLS) && $(MAKE) DESTDIR=$(DESTDIR) install) \ - || case "$(MFLAGS)" in *k*) fail=yes;; *) exit 1;; esac; - install-hdecode: -- (cd $(LVREC) && $(MAKE) install) \ -+ (cd $(LVREC) && $(MAKE) DESTDIR=$(DESTDIR) install) \ - || case "$(MFLAGS)" in *k*) fail=yes;; *) exit 1;; esac; - install-book: book -- (cd $(HTKBOOK) && $(MAKE) install) \ -+ (cd $(HTKBOOK) && $(MAKE) DESTDIR=$(DESTDIR) install) \ - || case "$(MFLAGS)" in *k*) fail=yes;; *) exit 1;; esac; - - clean: diff --git a/sci-mathematics/htk/htk-3.4.1.ebuild b/sci-mathematics/htk/htk-3.4.1.ebuild deleted file mode 100644 index 08da48a4b..000000000 --- a/sci-mathematics/htk/htk-3.4.1.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils - -DESCRIPTION="Toolkit for building and manipulating hidden Markov models" -HOMEPAGE="http://htk.eng.cam.ac.uk/" -SRC_URI=" - http://htk.eng.cam.ac.uk/ftp/software/HTK-3.4.1.tar.gz -> HTK-3.4.1.tar.gz - hdecode? ( - http://htk.eng.cam.ac.uk/ftp/software/hdecode/HDecode-3.4.1.tar.gz -> HDecode-3.4.1.tar.gz - )" -HDECODE_HOME="http://htk.eng.cam.ac.uk/extensions/index.shtml" - -LICENSE="HTKCambridge hdecode? ( HDecodeCambridge )" -SLOT="0" -KEYWORDS="~amd64" -IUSE="-hlmtools -hslab -htkbook -hdecode" - -RESTRICT="fetch" - -S="${WORKDIR}/${PN}" - -pkg_nofetch() { - elog "Please download" - elog " - HTK-3.4.1.tar.gz" - elog "from ${HOMEPAGE}" - if use hdecode; then - elog " - HDecode-3.4.1.tar.gz" - elog "from ${HDECODE_HOME}" - fi - elog "and place them in ${DISTDIR}" -} - -src_prepare() { - epatch "${FILESDIR}/include_make_destdir.patch" -} - -src_configure() { - econf \ - $(use_enable hlmtools) \ - $(use_enable hslab) \ - $(use_enable htkbook) \ - $(use_enable hdecode) -} - -src_compile() { - if use hlmtools || use hdecode; then - emake -j1 - else - default - fi -} diff --git a/sci-mathematics/htk/metadata.xml b/sci-mathematics/htk/metadata.xml deleted file mode 100644 index c948fe4f4..000000000 --- a/sci-mathematics/htk/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>pedosb@gmail.com</email> - <name>Pedro Batista</name> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription>The Hidden Markov Model Toolkit (HTK) is a portable toolkit for building and manipulating hidden Markov models</longdescription> - <use> - <flag name="hlmtools">Install the tools for manipulation of language models</flag> - <flag name="hdecode">Install HDecode, a large vocabulary word recogniser</flag> - <flag name="htkbook">Build the HTK documentation (HTK Book)</flag> - <flag name="hslab">Install HSLab a label editor for speech label manipulation</flag> - </use> -</pkgmetadata> diff --git a/sci-mathematics/kash-bin/Manifest b/sci-mathematics/kash-bin/Manifest deleted file mode 100644 index 79cf5b878..000000000 --- a/sci-mathematics/kash-bin/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST KASH3-Linux-i686-2008-07-31.tar.bz2 17334852 BLAKE2B c2167825c7c3db866c4d7bfce4f6d7facc86203d094af9cadc54a0546408c307bf5b2b2b588303a2da4e6a318de4af4881935c12323abb0fa752f473532159d5 SHA512 7366692e8bca6dca0e706d9ecbd2466115fd0c5bf6d9614a26aedd309f50ec98fed5c6a34688f8733d6f9ec5bc917ed149b642ec5e1706bab8bc66a4b091557e -DIST KASH3-lib-archindep-2008-07-31.tar.bz2 3367591 BLAKE2B 55f7062ed117ade7e031a2aac52277d5fb312bd0b62a134d3a606aefb70c43f22213ca7e58baa203696af9c8145cacf15a3b2846203a9e2defed306ebdf38858 SHA512 f7a3318bf57b4dbd41f88e2405252828a3e4cc00f52b7e9363c5657e8213a2b158b4f8127eb30734c14b2b87c94daf932ca8dc6b832bd4f1b9ba9b3c4f5ee93b diff --git a/sci-mathematics/kash-bin/kash-bin-3.ebuild b/sci-mathematics/kash-bin/kash-bin-3.ebuild deleted file mode 100644 index 29ddbe0df..000000000 --- a/sci-mathematics/kash-bin/kash-bin-3.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -# inherit eutils - -DESCRIPTION="software package for algebraic number theory" -HOMEPAGE="http://page.math.tu-berlin.de/~kant/kash.html" -SRC_URI=" - ftp://ftp.math.tu-berlin.de/pub/algebra/Kant/Kash_3/KASH3-Linux-i686-2008-07-31.tar.bz2 - ftp://ftp.math.tu-berlin.de/pub/algebra/Kant/Kash_3/KASH3-lib-archindep-2008-07-31.tar.bz2" - -LICENSE="kash" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -MY_P="kash3" -S="${WORKDIR}/${MY_P}" - -# This is a binary package: -QA_PREBUILT="opt/${MY_P}/kash3" - -src_unpack() { - default - mkdir "${S}" && cd "${S}" || die - mv KASH3-Linux*/* "${S}" || die - mv KASH3-lib*/lib/* "${S}/lib/" || die -} - -# Binary package -# src_configure() { : } -# -# src_compile() { : } -# -src_install() { - cat > kash3.sh <<- EOF - #!"${EPREFIX}/bin/sh" - /opt/${MY_P}/kash3 -l "${EROOT}opt/${MY_P}/lib" - EOF - chmod 755 kash3.sh - dodir /opt/${MY_P} - cp -R "${S}/" "${ED}"opt/ || die - dosym ../${MY_P}/kash3.sh /opt/bin/kash3 -} diff --git a/sci-mathematics/kash-bin/metadata.xml b/sci-mathematics/kash-bin/metadata.xml deleted file mode 100644 index fc53f2207..000000000 --- a/sci-mathematics/kash-bin/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>tomka@gentoo.org</email> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription> -KANT is a computer algebra system for sophisticated computations in algebraic -number fields that has been developed under the project leadership of -Prof. Dr. M. E. Pohst at Technische Universität Berlin. - -The KANT functions are accessible through a user-friendly shell named KASH -(KAnt SHell) that is freely available. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/lattE-macchiato/Manifest b/sci-mathematics/lattE-macchiato/Manifest deleted file mode 100644 index 6bb5a9ff4..000000000 --- a/sci-mathematics/lattE-macchiato/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST latte-for-tea-too-1.2-mk-0.9.3.tar.gz 12782533 BLAKE2B 4d52a4add865077ff137c222a686792ac7c594e09711854d5befe96e305cb7b45f6b8ad26f18076c63322915699bfe07243bd3ab2b15faead5fb022a421cd751 SHA512 40bf1f4d830afcd092d38a329049096138d2ac840843493842a4d4636f51d8d8252eafe11609ed8f19a592baf1d7f4112a7c82d4c465ac3b89b326e268db5981 diff --git a/sci-mathematics/lattE-macchiato/files/buildpackages.patch b/sci-mathematics/lattE-macchiato/files/buildpackages.patch deleted file mode 100644 index f35a0fe75..000000000 --- a/sci-mathematics/lattE-macchiato/files/buildpackages.patch +++ /dev/null @@ -1,224 +0,0 @@ ---- ../latte-for-tea-too-1.2-mk-0.9.3/Makefile.am 2008-12-17 22:56:12.000000000 +0100 -+++ Makefile.am 2010-02-05 23:43:42.000000000 +0100 -@@ -6,29 +6,7 @@ - - ## Distribution variables. - --PACKAGES=gmp cddplus cddlib ntl latte --if ENABLE_LIDIA --PACKAGES+=lidia --endif --if ENABLE_4TI2 --PACKAGES+=glpk 4ti2 --endif -- --GMP_VERSION=4.2.4 --GMP_TARGZ=$(top_srcdir)/gmp-$(GMP_VERSION).tar.gz --GMP_DIR=gmp-$(GMP_VERSION) -- --CDDPLUS_VERSION=077a --CDDPLUS_TARGZ=$(top_srcdir)/cdd+-$(CDDPLUS_VERSION).tar.gz --CDDPLUS_DIR=cdd+-$(CDDPLUS_VERSION) -- --CDDLIB_VERSION=094f --CDDLIB_TARGZ=$(top_srcdir)/cddlib-$(CDDLIB_VERSION).tar.gz --CDDLIB_DIR=cddlib-$(CDDLIB_VERSION) -- --NTL_VERSION=5.4.2 --NTL_TARGZ=$(top_srcdir)/ntl-$(NTL_VERSION).tar.gz --NTL_DIR=ntl-$(NTL_VERSION) -+PACKAGES=latte lidia - - LIDIA_VERSION=2.2.1-pre1+svn-1069+lattepatches-0.1 - LIDIA_TARGZ=$(top_srcdir)/lidia-base-$(LIDIA_VERSION).tar.gz $(top_srcdir)/lidia-FF-$(LIDIA_VERSION).tar.gz $(top_srcdir)/lidia-LA-$(LIDIA_VERSION).tar.gz -@@ -39,16 +17,6 @@ - LATTE_TARGZ=$(top_srcdir)/latte-$(LATTE_VERSION).tar.gz - LATTE_DIR=latte-$(LATTE_VERSION) - --# GLPK is a prerequisite of 4ti2 --GLPK_VERSION=4.13 --GLPK_TARGZ=$(top_srcdir)/glpk-$(GLPK_VERSION).tar.gz --GLPK_DIR=glpk-$(GLPK_VERSION) -- --FORTYTWO_VERSION=1.3.2 --FORTYTWO_TARGZ=$(top_srcdir)/4ti2-$(FORTYTWO_VERSION).tar.gz --FORTYTWO_DIR=4ti2-$(FORTYTWO_VERSION) -- -- - INSTALL_DIR=$(CURDIR)/dest - - ## Exported variables. -@@ -87,140 +55,27 @@ - EXTRA_DIST+=$(GMP_TARGZ) $(CDDPLUS_TARGZ) $(CDDLIB_TARGZ) $(NTL_TARGZ) \ - $(LIDIA_TARGZ) $(LATTE_TARGZ) $(GLPK_TARGZ) $(FORTYTWO_TARGZ) - --# GMP. --# --# We do not give our CFLAGS and CXXFLAGS to GMP; it is easy to --# miscompile GMP if we force it to use our values of these variables. -- --build_gmp: $(GMP_DIR)/.built_gmp --configure_gmp: $(GMP_DIR)/config.status --#EXTRA_DIST += gmp-4.2.1-patch --$(GMP_DIR)/.unpacked_gmp: $(GMP_TARGZ) -- gunzip < $(GMP_TARGZ) | $(TAR) xf - \ -- && touch $@ --# (cd $(GMP_DIR) && patch -t -p1 ) < $(top_srcdir)/gmp-4.2.1-patch --$(GMP_DIR)/config.status: $(GMP_DIR)/.unpacked_gmp -- ( cd $(GMP_DIR) && unset CFLAGS CXXFLAGS; ./configure --prefix="$(INSTALL_DIR)" --enable-cxx --disable-shared $(GMP_CONFIGURE_OPTIONS) ) --$(GMP_DIR)/.built_gmp: $(GMP_DIR)/config.status -- ( cd $(GMP_DIR) && $(MAKE) && $(MAKE) install ) && touch $@ --clean_gmp: -- -( rm -f $(GMP_DIR)/.built_gmp && cd $(GMP_DIR) && $(MAKE) clean ) --distclean_gmp: -- -( rm -f $(GMP_DIR)/.built_gmp && cd $(GMP_DIR) && $(MAKE) distclean ) -- --# NTL. -- --NTL_CONFIG_FILE=$(NTL_DIR)/src/makefile --build_ntl: .built_ntl --configure_ntl: $(NTL_CONFIG_FILE) --.unpacked_ntl: $(NTL_TARGZ) -- gunzip < $(NTL_TARGZ) | $(TAR) xf - \ -- && touch $@ -- --## cd $(NTL_DIR) && patch -t -p1 ) < $(top_srcdir)/ntl-5.4-patch \ --## EXTRA_DIST += ntl-5.4-patch --$(NTL_CONFIG_FILE): .unpacked_ntl $(GMP_DIR)/.built_gmp -- ( cd $(NTL_DIR)/src && ./configure CC="$(CC)" CXX="$(CXX)" CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" PREFIX="$(INSTALL_DIR)" GMP_PREFIX="$(INSTALL_DIR)" NTL_GMP_LIP=on ) --.built_ntl: $(NTL_CONFIG_FILE) $(GMP_DIR)/.built_gmp -- ( cd $(NTL_DIR)/src && $(MAKE) setup1 && $(MAKE) setup2 && $(MAKE) setup3 && $(MAKE) setup4 && $(MAKE) ntl.a && $(MAKE) install ) && touch $@ --clean_ntl: -- -( rm -f .built_ntl && cd $(NTL_DIR)/src && $(MAKE) clean ) --distclean_ntl: -- -( rm -f .built_ntl && cd $(NTL_DIR)/src && $(MAKE) clean; rm -f $(NTL_CONFIG_FILE) ) -- - # LiDIA. - - build_lidia: $(LIDIA_DIR)/.built_lidia --configure_lidia: $(LIDIA_DIR)/config.status $(GMP_DIR)/.built_gmp -+configure_lidia: $(LIDIA_DIR)/config.status - #EXTRA_DIST += lidia-2.2.0.patch lidia-2.2.0-2.patch - $(LIDIA_DIR)/.unpacked_lidia: $(LIDIA_TARGZ) - for a in $(LIDIA_TARGZ); do \ - gunzip < $$a | $(TAR) xf - || exit 1; \ - done \ - && touch $@ --$(LIDIA_DIR)/config.status: $(LIDIA_DIR)/.unpacked_lidia $(GMP_DIR)/.built_gmp -- ( cd $(LIDIA_DIR) && ./configure --with-arithmetic=gmp --disable-nf --disable-ec --disable-eco --disable-gec --with-extra-includes="$(INSTALL_DIR)"/include --with-extra-libs="$(INSTALL_DIR)"/lib --prefix="$(INSTALL_DIR)" --disable-shared) -+$(LIDIA_DIR)/config.status: $(LIDIA_DIR)/.unpacked_lidia -+ ( cd $(LIDIA_DIR) && ./configure --with-arithmetic=gmp --disable-nf --disable-ec --disable-eco --disable-gec --with-extra-includes="$(INSTALL_DIR)"/include --with-extra-libs="$(INSTALL_DIR)"/lib --prefix="/usr" --disable-shared) - # LiDIA 2.2.0 installs its headers into lidia/ but expects them in LiDIA!?! - # So we make a symbolic link, just in case. --$(LIDIA_DIR)/.built_lidia: $(LIDIA_DIR)/config.status $(GMP_DIR)/.built_gmp -- ( cd $(LIDIA_DIR) && $(MAKE) && $(MAKE) install ) && ( cd "$(INSTALL_DIR)"/include && if [ ! -r LiDIA ] ; then ln -s lidia LiDIA; fi || true ) && touch $@ -+$(LIDIA_DIR)/.built_lidia: $(LIDIA_DIR)/config.status -+ ( cd $(LIDIA_DIR) && $(MAKE) ) && ( cd "$(INSTALL_DIR)"/include && if [ ! -r LiDIA ] ; then ln -s lidia LiDIA; fi || true ) && touch $@ - clean_lidia: - -( rm -f $(LIDIA_DIR)/.built_lidia && cd $(LIDIA_DIR) && $(MAKE) clean ) - distclean_lidia: - -( rm -f $(LIDIA_DIR)/.built_lidia && cd $(LIDIA_DIR) && $(MAKE) distclean ) - --# cddlib. --# --# cddlib 094b has a hard-coded location of GMP in /usr/local in its Makefile.am(!) --# We work around this by passing LDFLAGS to both configure and make. --build_cddlib: .built_cddlib --configure_cddlib: $(CDDLIB_DIR)/config.status $(GMP_DIR)/.built_gmp --.unpacked_cddlib: $(CDDLIB_TARGZ) -- for a in $(CDDLIB_TARGZ); do \ -- gunzip < $$a | $(TAR) xf - || exit 1; \ -- done && touch $@ --$(CDDLIB_DIR)/config.status: .unpacked_cddlib $(GMP_DIR)/.built_gmp -- ( cd $(CDDLIB_DIR) && ./configure CXX="$(CXX)" CFLAGS="$(CFLAGS) -I$(INSTALL_DIR)/include" CXXFLAGS="$(CXXFLAGS) -I$(INSTALL_DIR)/include" LDFLAGS="$(LDFLAGS) -L$(INSTALL_DIR)/lib" --prefix="$(INSTALL_DIR)" --disable-shared) --.built_cddlib: $(CDDLIB_DIR)/config.status $(GMP_DIR)/.built_gmp -- ( cd $(CDDLIB_DIR) && $(MAKE) LDFLAGS="$(LDFLAGS) -L$(INSTALL_DIR)/lib" && $(MAKE) install ) && touch $@ --clean_cddlib: -- -( rm -f .built_cddlib && cd $(CDDLIB_DIR) && $(MAKE) clean ) --distclean_cddlib: -- -( rm -f .built_cddlib && cd $(CDDLIB_DIR) && $(MAKE) distclean ) -- --# cdd+. -- --CDDPLUS_VARIABLES=CC="$(CXX)" LIBDIR="$(INSTALL_DIR)"/lib GMPLIBDIR="$(INSTALL_DIR)"/lib INCLUDEDIR="$(INSTALL_DIR)"/include GMPINCLUDEDIR="$(INSTALL_DIR)"/include OPTFLAGS="$(CXXFLAGS)" --build_cddplus: $(CDDPLUS_DIR)/.built_cddplus --configure_cddplus: .unpacked_cddplus $(GMP_DIR)/.built_gmp --EXTRA_DIST += cdd+-077a.patch --.unpacked_cddplus: $(CDDPLUS_TARGZ) -- for a in $(CDDPLUS_TARGZ); do \ -- gunzip < $$a | $(TAR) xf - || exit 1; \ -- done \ -- && (cd $(CDDPLUS_DIR) && $(PATCH) -p0) < $(top_srcdir)/cdd+-077a.patch \ -- && touch $@ --$(CDDPLUS_DIR)/.built_cddplus: .unpacked_cddplus $(GMP_DIR)/.built_gmp -- ( cd $(CDDPLUS_DIR) && $(MAKE) $(CDDPLUS_VARIABLES) cddr+ cddf+ && $(mkinstalldirs) "$(INSTALL_DIR)"/bin && $(INSTALL) cddr+ cddf+ "$(INSTALL_DIR)"/bin ) && touch $@ --clean_cddplus: -- -( rm -f $(CDDPLUS_DIR)/.built_cddplus && cd $(CDDPLUS_DIR) && $(MAKE) clean ) --distclean_cddplus: -- -( rm -f $(CDDPLUS_DIR)/.built_cddplus && cd $(CDDPLUS_DIR) && $(MAKE) clean ) -- --# GLPK. --build_glpk: $(GLPK_DIR)/.built_glpk --configure_glpk: $(GLPK_DIR)/config.status $(GMP_DIR)/.built_gmp --$(GLPK_DIR)/.unpacked_glpk: $(GLPK_TARGZ) -- gunzip < $(GLPK_TARGZ) | $(TAR) xf - \ -- && touch $@ --$(GLPK_DIR)/config.status: $(GLPK_DIR)/.unpacked_glpk $(GMP_DIR)/.built_gmp -- ( cd $(GLPK_DIR) && CC="$(CC)" CXX="$(CXX)" CPPFLAGS="$(CPPFLAGS) -I$(INSTALL_DIR)/include" CFLAGS="$(CFLAGS) -I$(INSTALL_DIR)/include" CXXFLAGS="$(CXXFLAGS) -I$(INSTALL_DIR)/include" LDFLAGS="$(LDFLAGS) -L$(INSTALL_DIR)/lib" ./configure --prefix="$(INSTALL_DIR)" --disable-shared $(GLPK_CONFIGURE_OPTIONS) ) --$(GLPK_DIR)/.built_glpk: $(GLPK_DIR)/config.status -- ( cd $(GLPK_DIR) && $(MAKE) && $(MAKE) install ) && touch $@ --clean_glpk: -- -( rm -f $(GLPK_DIR)/.built_glpk && cd $(GLPK_DIR) && $(MAKE) clean ) --distclean_glpk: -- -( rm -f $(GLPK_DIR)/.built_glpk && cd $(GLPK_DIR) && $(MAKE) distclean ) -- --# 4ti2. --build_4ti2: $(FORTYTWO_DIR)/.built_4ti2 --configure_4ti2: $(FORTYTWO_DIR)/config.status $(GLPK_DIR)/.built_glpk $(GMP_DIR)/.built_gmp --$(FORTYTWO_DIR)/.unpacked_4ti2: $(FORTYTWO_TARGZ) -- gunzip < $(FORTYTWO_TARGZ) | $(TAR) xf - \ -- && touch $@ --$(FORTYTWO_DIR)/config.status: $(FORTYTWO_DIR)/.unpacked_4ti2 $(GLPK_DIR)/.built_glpk $(GMP_DIR)/.built_gmp -- ( cd $(FORTYTWO_DIR) && CC="$(CC)" CXX="$(CXX)" CPPFLAGS="$(CPPFLAGS) -I$(INSTALL_DIR)/include" CFLAGS="$(CFLAGS) -I$(INSTALL_DIR)/include" CXXFLAGS="$(CXXFLAGS) -I$(INSTALL_DIR)/include" LDFLAGS="$(LDFLAGS) -L$(INSTALL_DIR)/lib" ./configure --prefix="$(INSTALL_DIR)" --with-gmp="$(INSTALL_DIR)" --with-glpk="$(INSTALL_DIR)" --disable-shared $(FORTYTWO_CONFIGURE_OPTIONS) ) --## We currently have header file clashes between zsolve and groebner on Mac OS, --## due to semi-case-insensitivity. Work around for now, by only installing --## the header files of groebner -- we only need those... --## (This is already fixed for the upcoming 4ti2 releases.) --$(FORTYTWO_DIR)/.built_4ti2: $(FORTYTWO_DIR)/config.status -- ( cd $(FORTYTWO_DIR) && $(MAKE) && $(MAKE) install-exec && (cd src/groebner && $(MAKE) install )) && touch $@ --clean_4ti2: -- -( rm -f $(FORTYTWO_DIR)/.built_4ti2 && cd $(FORTYTWO_DIR) && $(MAKE) clean ) --distclean_4ti2: -- -( rm -f $(FORTYTWO_DIR)/.built_4ti2 && cd $(FORTYTWO_DIR) && $(MAKE) distclean ) -- - # LattE. - - if ENABLE_LIDIA -@@ -236,19 +91,18 @@ - endif - - build_latte: .built_latte --configure_latte: $(LATTE_DIR)/config.status $(GMP_DIR)/.built_gmp .built_cddlib $(CDDPLUS_DIR)/.built_cddplus .built_ntl -+configure_latte: $(LATTE_DIR)/config.status - .unpacked_latte: $(LATTE_TARGZ) - for a in $(LATTE_TARGZ); do \ -- gunzip < $$a | $(TAR) xf - || exit 1; \ -+ (gunzip < $$a | $(TAR) xf - || exit 1;) && (sed "s/-lwrapgmp-gcc4//g" -i $(LATTE_DIR)/configure || exit 1;) \ - done && touch $@ --$(LATTE_DIR)/config.status: .unpacked_latte $(GMP_DIR)/.built_gmp .built_cddlib $(CDDPLUS_DIR)/.built_cddplus $(BUILT_LIDIA) .built_ntl $(BUILT_4TI2) -- ( cd $(LATTE_DIR) && ./configure --with-default="$(INSTALL_DIR)" --prefix="$(INSTALL_DIR)" ) --.built_latte: $(LATTE_DIR)/config.status $(GMP_DIR)/.built_gmp .built_cddlib $(CDDPLUS_DIR)/.built_cddplus $(BUILT_LIDIA) .built_ntl $(BUILT_4TI2) -- ( cd $(LATTE_DIR) && $(MAKE) && $(MAKE) install ) && touch $@ -+$(LATTE_DIR)/config.status: .unpacked_latte $(BUILT_LIDIA) -+ ( cd $(LATTE_DIR) && ./configure --prefix="/usr" --with-topcom="/" ) -+.built_latte: $(LATTE_DIR)/config.status $(BUILT_LIDIA) -+ ( cd $(LATTE_DIR) && $(MAKE) ) && touch $@ - clean_latte: - -( rm -f .built_latte && cd $(LATTE_DIR) && $(MAKE) clean ) - distclean_latte: - -( rm -f .built_latte && cd $(LATTE_DIR) && $(MAKE) distclean ) - --## Maintainer targets -- -+## Maintainer targets -\ No newline at end of file diff --git a/sci-mathematics/lattE-macchiato/lattE-macchiato-0.9.3.ebuild b/sci-mathematics/lattE-macchiato/lattE-macchiato-0.9.3.ebuild deleted file mode 100644 index 2b0505090..000000000 --- a/sci-mathematics/lattE-macchiato/lattE-macchiato-0.9.3.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit autotools eutils flag-o-matic - -DESCRIPTION="lattE-macchiato consists of tools for lattice point enumeration" -HOMEPAGE="http://www.math.ucdavis.edu/~mkoeppe/latte/" -SRC_URI="http://www.math.ucdavis.edu/~mkoeppe/latte/download/latte-for-tea-too-1.2-mk-0.9.3.tar.gz" -# mirror://gentoo/${P}-src.tar.bz2 - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=" - dev-libs/gmp:0=[cxx] - >=dev-libs/ntl-5.4.2 - sci-mathematics/4ti2 - >=sci-libs/cdd+-077a - >=sci-mathematics/glpk-4.13 - >=sci-libs/cddlib-094f" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/latte-for-tea-too-1.2-mk-0.9.3" - -# For now LattE builds an internal version of Lidia. -# This will not be split off for now because it is heavily patched -# and based on a version that was not even released. - -src_prepare() { - epatch "${FILESDIR}/buildpackages.patch" - - eautoreconf -} - -src_install() { - # install - cd "${S}"/lidia-2.2.1-pre1+svn-1069+lattepatches-0.1/ - default - cd "${S}"/latte-1.2-mk-0.9.3/ || die - default - # ... and get rid of minimize which is provided by 4ti2: - rm "${ED}"/usr/bin/minimize || die "Removing minimize failed" -} diff --git a/sci-mathematics/lattE-macchiato/metadata.xml b/sci-mathematics/lattE-macchiato/metadata.xml deleted file mode 100644 index f043b5060..000000000 --- a/sci-mathematics/lattE-macchiato/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>tom111@gmx.de</email> - <name>Thomas Kahle</name> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription lang="en"> -Macaulay2 is a research tool for algraic geometry and commutative -algebra. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/libsfmt/libsfmt-1.3.0.ebuild b/sci-mathematics/libsfmt/libsfmt-1.3.0.ebuild index e90437e41..c933eb0ac 100644 --- a/sci-mathematics/libsfmt/libsfmt-1.3.0.ebuild +++ b/sci-mathematics/libsfmt/libsfmt-1.3.0.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 DESCRIPTION="SIMD-oriented Fast Mersenne Twister" HOMEPAGE="http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/index.html" @@ -10,6 +10,7 @@ SRC_URI="http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/VERSIONS/ARCHIVES/ LICENSE="BSD" SLOT="0" KEYWORDS="~amd64 ~x86" + IUSE="cpu_flags_x86_sse2" src_configure() { diff --git a/sci-mathematics/lie/files/lie-2.2.2-make.patch b/sci-mathematics/lie/files/lie-2.2.2-debian.patch index cf6bd4537..4710cf60b 100644 --- a/sci-mathematics/lie/files/lie-2.2.2-make.patch +++ b/sci-mathematics/lie/files/lie-2.2.2-debian.patch @@ -1,55 +1,22 @@ -diff -u -r -P --new-file --exclude=CVS lie-2.2.2/debian/lie.1 lie-2.2.2-1/debian/lie.1 ---- lie-2.2.2/debian/lie.1 1970-01-01 01:00:00.000000000 +0100 -+++ lie-2.2.2-1/debian/lie.1 2007-02-13 14:32:47.000000000 +0000 -@@ -0,0 +1,27 @@ -+.TH LIE 1 "December 12, 2006" "" "" -+ -+.SH NAME -+LiE - A computer algebra package for Lie group computations -+.SH SYNOPSIS -+.BR "lie" -+.SH DESCRIPTION -+.B LiE -+LiE is a computer algebra system that is specialised in computations -+involving (reductive) Lie groups and their representations. -+ -+Full documentation about the program and the underlying mathematics -+can be found in /usr/share/doc/lie/manual.dvi. -+ -+Run-time help can be obtained by typing '?' for a list of help entries -+or '?help' for help information. -+ -+See the web page at -+.BR "http://young.sp2mi.univ-poitiers.fr/~marc/LiE/" -+for the CWEBx source code. -+.SH AUTHORS -+LiE was written by Arjeh M. Cohen <amc@win.tue.nl>, Marc van Leeuwen -+<maavl@mathlabo.univ-poitiers.fr> and Bert Lisser. -+.PP -+This manual page was written by Kasper Peeters -+<kasper.peeters@aei.mpg.de>, for the Debian project (but may be used -+by others). -diff -u -r -P --new-file --exclude=CVS lie-2.2.2/lie lie-2.2.2-1/lie ---- lie-2.2.2/lie 1970-01-01 01:00:00.000000000 +0100 -+++ lie-2.2.2-1/lie 2007-02-20 21:47:37.000000000 +0000 -@@ -0,0 +1,4 @@ -+#!/bin/sh -+PTH=`which ${0} | sed -e 's/bin\/lie//'` -+ -+exec ${PTH}/bin/Lie.exe initfile ${PTH}/share/lie -diff -u -r -P --new-file --exclude=CVS lie-2.2.2/lie_script lie-2.2.2-1/lie_script ---- lie-2.2.2/lie_script 1996-09-16 16:14:38.000000000 +0100 -+++ lie-2.2.2-1/lie_script 2006-12-17 13:42:23.000000000 +0000 -@@ -1,2 +1,3 @@ --LD=actual directory gets substituted here --exec $LD/Lie.exe initfile $LD -+#!/bin/sh -+#LD=actual directory gets substituted here -+exec /usr/bin/Lie.exe initfile /usr/share/lie -diff -u -r -P --new-file --exclude=CVS lie-2.2.2/Makefile lie-2.2.2-1/Makefile ---- lie-2.2.2/Makefile 2000-04-07 08:46:28.000000000 +0100 -+++ lie-2.2.2-1/Makefile 2007-02-20 20:41:22.000000000 +0000 -@@ -24,20 +24,36 @@ +diff --git a/Makefile b/Makefile +index c049e89..48b5c87 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,11 +1,11 @@ + srcdir :=$(shell pwd) + +-CFLAGS= -O ++CFLAGS?= -O + fixed-flags = -I$(srcdir) -I$(srcdir)/box + all-C-flags:= -ansi $(fixed-flags) $(CFLAGS) + non-ansi-flags := $(fixed-flags) $(CFLAGS) + +-CC = gcc # some compiler for ANSI/ISO C ++CC ?= gcc # some compiler for ANSI/ISO C + + # These settings should also be used in subdirectories: + export CC all-C-flags fixed-flags CFLAGS +@@ -24,20 +24,34 @@ GAP_objects=$(common_objects) gapprint.o gapgetl.o # Global organisation (phony targets) @@ -73,33 +40,42 @@ diff -u -r -P --new-file --exclude=CVS lie-2.2.2/Makefile lie-2.2.2-1/Makefile +# install manual/manual.dvi $(DESTDIR)/usr/share/doc/lie + install -d $(DESTDIR)/usr/share/man/man1 + install debian/lie.1 $(DESTDIR)/usr/share/man/man1 -+ gzip -f9 $(DESTDIR)/usr/share/man/man1/lie.1 ++# gzip -f9 $(DESTDIR)/usr/share/man/man1/lie.1 +# install debian/lie.1 $(DESTDIR)/usr/share/man/man1/Lie.exe.1 +# gzip -f9 $(DESTDIR)/usr/share/man/man1/Lie.exe.1 # To 'make all', we first descend into the subdirectories, and afterwards # return to finish here. - all: +-all: - $(MAKE) math_functions binding_functions -+ $(MAKE) math_functions binding_functions - $(MAKE) finish +- $(MAKE) finish ++all: math_functions binding_functions finish -finish: Lie.exe LEARN.ind INFO.ind # do not call 'make finish' directly +finish: lie Lie.exe LEARN.ind INFO.ind # do not call 'make finish' directly math_functions: $(MAKE) -C box all -@@ -88,7 +104,7 @@ +@@ -82,13 +96,13 @@ gapgetl.o: getl.c + # been set to the most recent one of object files in the respective + # subdirectories, whence taking that dummy file as dependency suffices. + +-date.o: date.c $(objects) box/.last_compiled static/.last_compiled ++date.o: date.c $(objects) math_functions binding_functions + $(CC) -ansi -c date.c +-gapdate.o: date.c $(GAP_objects) box/.last_compiled static/.last_compiled ++gapdate.o: date.c $(GAP_objects) math_functions binding_functions $(CC) -ansi -c -o gapdate.o date.c - Lie.exe: date.o +-Lie.exe: date.o - $(CC) -o Lie.exe $(objects) date.o static/*.o box/*.o -lreadline ++Lie.exe: math_functions binding_functions date.o + $(CC) -o Lie.exe $(LDFLAGS) $(objects) date.o static/*.o box/*.o -lreadline -lncurses chmod g+w Lie.exe Liegap.exe: gapdate.o $(CC) -o Liegap.exe $(GAP_objects) gapdate.o static/*.o box/*.o -@@ -101,8 +117,8 @@ +@@ -101,8 +115,8 @@ noreadline: math_functions binding_functions $(common_objects) print.o chmod g+w Lie.exe $(MAKE) LEARN.ind INFO.ind script INFO.a @@ -110,7 +86,16 @@ diff -u -r -P --new-file --exclude=CVS lie-2.2.2/Makefile lie-2.2.2-1/Makefile INFO.ind: INFO.0 INFO.1 INFO.2 INFO.3 INFO.4 infoind ./infoind -@@ -123,5 +139,8 @@ +@@ -115,7 +129,7 @@ infoind: util/infoind.c + learnind: util/learnind.c + $(MAKE) -C util ../learnind + +-INFO.a: progs/maxsub progs/maxsub0 progs/eqrank ++INFO.a: Lie.exe progs/maxsub progs/maxsub0 progs/eqrank + rm -f INFO.a + ./Lie.exe < progs/maxsub + +@@ -123,5 +137,8 @@ INFO.a: progs/maxsub progs/maxsub0 progs/eqrank clean: $(MAKE) -C box clean $(MAKE) -C static clean @@ -121,9 +106,63 @@ diff -u -r -P --new-file --exclude=CVS lie-2.2.2/Makefile lie-2.2.2-1/Makefile + rm -f debian/lie/usr/bin/Lie.exe + rm -f debian/lie/usr/bin/lie + rm -f debian/lie/usr/share/lie/* -diff -u -r -P --new-file --exclude=CVS lie-2.2.2/make_lie lie-2.2.2-1/make_lie ---- lie-2.2.2/make_lie 1996-09-16 16:19:07.000000000 +0100 -+++ lie-2.2.2-1/make_lie 2006-12-17 13:42:23.000000000 +0000 +diff --git a/debian/lie.1 b/debian/lie.1 +new file mode 100644 +index 0000000..10bf50d +--- /dev/null ++++ b/debian/lie.1 +@@ -0,0 +1,27 @@ ++.TH LIE 1 "December 12, 2006" "" "" ++ ++.SH NAME ++LiE - A computer algebra package for Lie group computations ++.SH SYNOPSIS ++.BR "lie" ++.SH DESCRIPTION ++.B LiE ++LiE is a computer algebra system that is specialised in computations ++involving (reductive) Lie groups and their representations. ++ ++Full documentation about the program and the underlying mathematics ++can be found in /usr/share/doc/lie/manual.dvi. ++ ++Run-time help can be obtained by typing '?' for a list of help entries ++or '?help' for help information. ++ ++See the web page at ++.BR "http://young.sp2mi.univ-poitiers.fr/~marc/LiE/" ++for the CWEBx source code. ++.SH AUTHORS ++LiE was written by Arjeh M. Cohen <amc@win.tue.nl>, Marc van Leeuwen ++<maavl@mathlabo.univ-poitiers.fr> and Bert Lisser. ++.PP ++This manual page was written by Kasper Peeters ++<kasper.peeters@aei.mpg.de>, for the Debian project (but may be used ++by others). +diff --git a/lie b/lie +new file mode 100644 +index 0000000..5a7a906 +--- /dev/null ++++ b/lie +@@ -0,0 +1,4 @@ ++#!/bin/sh ++PTH=`which ${0} | sed -e 's/bin\/lie//'` ++ ++exec ${PTH}/bin/Lie.exe initfile ${PTH}/share/lie +diff --git a/lie_script b/lie_script +index 76f3701..62972c0 100644 +--- a/lie_script ++++ b/lie_script +@@ -1,2 +1,3 @@ +-LD=actual directory gets substituted here +-exec $LD/Lie.exe initfile $LD ++#!/bin/sh ++#LD=actual directory gets substituted here ++exec /usr/bin/Lie.exe initfile /usr/share/lie +diff --git a/make_lie b/make_lie +index 5f059d7..1b5320b 100755 +--- a/make_lie ++++ b/make_lie @@ -1,3 +1,3 @@ #!/bin/sh -sed -e "s!LD=.*!LD=`/bin/pwd`!" <lie_script >lie diff --git a/sci-mathematics/lie/files/parrallelmake-lie-2.2.2.patch b/sci-mathematics/lie/files/parrallelmake-lie-2.2.2.patch deleted file mode 100644 index 5bd54b403..000000000 --- a/sci-mathematics/lie/files/parrallelmake-lie-2.2.2.patch +++ /dev/null @@ -1,52 +0,0 @@ ---- Makefile.orig 2010-08-16 23:59:45.463692224 +1200 -+++ Makefile 2010-08-17 00:00:45.069692939 +1200 -@@ -1,11 +1,11 @@ - srcdir :=$(shell pwd) - --CFLAGS= -O -+CFLAGS?= -O - fixed-flags = -I$(srcdir) -I$(srcdir)/box - all-C-flags:= -ansi $(fixed-flags) $(CFLAGS) - non-ansi-flags := $(fixed-flags) $(CFLAGS) - --CC = gcc # some compiler for ANSI/ISO C -+CC ?= gcc # some compiler for ANSI/ISO C - - # These settings should also be used in subdirectories: - export CC all-C-flags fixed-flags CFLAGS -@@ -49,9 +49,7 @@ - # To 'make all', we first descend into the subdirectories, and afterwards - # return to finish here. - --all: -- $(MAKE) math_functions binding_functions -- $(MAKE) finish -+all: math_functions binding_functions finish - - finish: lie Lie.exe LEARN.ind INFO.ind # do not call 'make finish' directly - -@@ -98,12 +96,12 @@ - # been set to the most recent one of object files in the respective - # subdirectories, whence taking that dummy file as dependency suffices. - --date.o: date.c $(objects) box/.last_compiled static/.last_compiled -+date.o: date.c $(objects) math_functions binding_functions - $(CC) -ansi -c date.c --gapdate.o: date.c $(GAP_objects) box/.last_compiled static/.last_compiled -+gapdate.o: date.c $(GAP_objects) math_functions binding_functions - $(CC) -ansi -c -o gapdate.o date.c - --Lie.exe: date.o -+Lie.exe: math_functions binding_functions date.o - $(CC) -o Lie.exe $(LDFLAGS) $(objects) date.o static/*.o box/*.o -lreadline -lncurses - chmod g+w Lie.exe - Liegap.exe: gapdate.o -@@ -131,7 +129,7 @@ - learnind: util/learnind.c - $(MAKE) -C util ../learnind - --INFO.a: progs/maxsub progs/maxsub0 progs/eqrank -+INFO.a: Lie.exe progs/maxsub progs/maxsub0 progs/eqrank - rm -f INFO.a - ./Lie.exe < progs/maxsub - diff --git a/sci-mathematics/lie/lie-2.2.2.ebuild b/sci-mathematics/lie/lie-2.2.2.ebuild index 1e386d356..173e0715e 100644 --- a/sci-mathematics/lie/lie-2.2.2.ebuild +++ b/sci-mathematics/lie/lie-2.2.2.ebuild @@ -1,15 +1,14 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils toolchain-funcs +inherit toolchain-funcs DESCRIPTION="A Computer algebra package for Lie group computations" -HOMEPAGE="http://www-math.univ-poitiers.fr/~maavl/LiE/" +HOMEPAGE="http://www-math.univ-poitiers.fr/~maavl/LiE/" # no https, invalid certificate SRC_URI="http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/conLiE.tar.gz -> ${P}.tar.gz" -#### Remove the following line when moving this ebuild to the main tree! -RESTRICT="mirror" +S="${WORKDIR}/LiE" LICENSE="LGPL-2.1" ##### See http://packages.debian.org/changelogs/pool/main/l/lie/lie_2.2.2+dfsg-1/lie.copyright @@ -17,20 +16,16 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc" -DEPEND=" +RDEPEND=" + sys-libs/readline:= + sys-libs/ncurses:= +" +DEPEND="${RDEPEND}" +BDEPEND=" sys-devel/bison - sys-libs/readline:0= - sys-libs/ncurses:0=" -RDEPEND="sys-libs/readline:= - sys-libs/ncurses" - -S="${WORKDIR}/LiE" +" -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-make.patch \ - "${FILESDIR}"/parrallelmake-${P}.patch -} +PATCHES=( "${FILESDIR}"/${P}-debian.patch ) src_compile() { emake CC=$(tc-getCC) @@ -38,11 +33,5 @@ src_compile() { src_install() { default - use doc && dodoc "${S}"/manual/* -} - -pkg_postinst() { - elog "This version of the LiE ebuild is still under development." - elog "Help us improve the ebuild in:" - elog "http://bugs.gentoo.org/show_bug.cgi?id=194393" + use doc && dodoc "${S}"/manual/ } diff --git a/sci-mathematics/lie/metadata.xml b/sci-mathematics/lie/metadata.xml index 5041a04a0..f3e755ec1 100644 --- a/sci-mathematics/lie/metadata.xml +++ b/sci-mathematics/lie/metadata.xml @@ -5,5 +5,12 @@ <email>sci-mathematics@gentoo.org</email> <name>Gentoo Mathematics Project</name> </maintainer> - <longdescription>LiE is the name of a software package that enables mathematicians and physicists to perform computations of a Lie group theoretic nature. It focuses on the representation theory of complex semisimple (reductive) Lie groups and algebras, and on the structure of their Weyl groups and root systems.</longdescription> + <longdescription> + LiE is the name of a software package that enables + mathematicians and physicists to perform computations + of a Lie group theoretic nature. It focuses on the + representation theory of complex semisimple (reductive) + Lie groups and algebras, and on the structure of their + Weyl groups and root systems. + </longdescription> </pkgmetadata> diff --git a/sci-mathematics/ltl2ba/Manifest b/sci-mathematics/ltl2ba/Manifest index 4d6528d6b..659c1c6e6 100644 --- a/sci-mathematics/ltl2ba/Manifest +++ b/sci-mathematics/ltl2ba/Manifest @@ -1 +1,3 @@ DIST ltl2ba-1.1.tar.gz 29629 BLAKE2B 06ba7f7b5e3c6b72d2f0ea3b991346c803669e24d66dc38e311109ee08ed6dcc72bfd9f2ebe0f8864b0f80f010a4438029f4f5dbbf0087469ca2d07cdfce6b3f SHA512 8d010e2bb59fa5d682a56a50133865da938fd3bfcde6386184880eec6989bc1b694d6af9146b4b708cefdcdbcf98248f87074b8c973ea8cab65d658b394ccf69 +DIST ltl2ba-1.2.tar.gz 33026 BLAKE2B f19359e33d4eeb4dde75425ed03d940c08f46dd265b1b9c6773807e7dca67fd44f694f685d4153ca786118e336fab736104a865c5d0e9883390fca694f72b492 SHA512 148ffb1b4dbe134b69c6e946a4a9f1a95a809bf36ef3533117eedeceb721dd4c8a3238bbda2de5782a79b7aee70e33adf6ff193917441092a1ccb4e56a53a655 +DIST ltl2ba-1.3.tar.gz 38265 BLAKE2B bd74d9b9e22589ac00fbaa15f745dd6371894f68b50f85507694648274d9391ad3a90cdf1ee6c342abbceb04d0e2eb5d71473d43969b469a933517cfcd1e16c1 SHA512 1bcef13d98879c083dc907939c652e694802ed91c33a5d90bbeb6fc22d6265a0b153932c5fb3f8557aad30582322c16d0be822bf4208f40faf9384b367a84aa6 diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild index 29609c146..6172bb985 100644 --- a/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild +++ b/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild @@ -1,29 +1,31 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 + +inherit flag-o-matic DESCRIPTION="Fast LTL to Buechi Automata Translation" -HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/${PN}/" +HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba" SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="" -DEPEND="" -src_compile() { +src_prepare() { + default sed -i Makefile \ -e "s/CC=gcc/#CC=gcc/g" \ - -e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" + -e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die +} +src_configure() { + append-cflags -fcommon default } src_install() { - dobin ltl2ba || die "dobin failed" + dobin ltl2ba dodoc README } diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild new file mode 100644 index 000000000..0678dcf8e --- /dev/null +++ b/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic + +DESCRIPTION="Fast LTL to Buechi Automata Translation" +HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba" +SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +src_prepare() { + default + sed -i Makefile \ + -e "s/CC=gcc/#CC=gcc/g" \ + -e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die +} + +src_configure() { + append-cflags -fcommon + default +} + +src_install() { + dobin ltl2ba + dodoc README +} diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild new file mode 100644 index 000000000..0678dcf8e --- /dev/null +++ b/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic + +DESCRIPTION="Fast LTL to Buechi Automata Translation" +HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba" +SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +src_prepare() { + default + sed -i Makefile \ + -e "s/CC=gcc/#CC=gcc/g" \ + -e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die +} + +src_configure() { + append-cflags -fcommon + default +} + +src_install() { + dobin ltl2ba + dodoc README +} diff --git a/sci-mathematics/mdp/Manifest b/sci-mathematics/mdp/Manifest deleted file mode 100644 index a1eb88b49..000000000 --- a/sci-mathematics/mdp/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST MDP-3.3.tar.gz 471439 BLAKE2B f16d2075d325ebcfdb9c2628f6568f626f1b9ffe11874b62b878fef07bf557bab14e1912ea196c3b0a73b0eb73518c0d5fa854a593f5f1dddfdb663ffd36d027 SHA512 fdbecd38e86aae970c6091c3ff7cd8e576556bf449051e5d998852e294041587907acc0701d3415059da7aaac73c04803138a04c9990bcc2a168a8f6f83d91cf -DIST MDP-3.5.tar.gz 335420 BLAKE2B ea1a5d941af33220c4d03b4a70d70410b8d7d0ad4f541a1cb07914d745912a766013b551476ad4db39155a4ea998baa98d21f9db312e48434bbd7b622f10677c SHA512 5c4f6264ce566b65d4580bb38be711e93d764b7cf1c507df3e0f9efef23c93646a2ba8aab7de5c3f7c07bee16f9f4ebe1739a780c6dc966da48007d733747c58 diff --git a/sci-mathematics/mdp/mdp-3.3.ebuild b/sci-mathematics/mdp/mdp-3.3.ebuild deleted file mode 100644 index 509639188..000000000 --- a/sci-mathematics/mdp/mdp-3.3.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python3_{4,5} ) - -inherit distutils-r1 - -MY_P="${P/mdp/MDP}" -MY_P="${MY_P/_rc/RC}" - -DESCRIPTION="Data processing framework in python" -HOMEPAGE="http://mdp-toolkit.sourceforge.net/index.html" -SRC_URI="mirror://sourceforge/mdp-toolkit/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND=" - || ( - >=dev-python/numpy-1.1[${PYTHON_USEDEP}] - >=sci-libs/scipy-0.5.2[${PYTHON_USEDEP}] -)" - -S="${WORKDIR}/${MY_P}" - -python_test() { - distutils_install_for_testing - cd "${BUILD_DIR}" || die - "${PYTHON}" -c "import mdp;mdp.test()" || die -} diff --git a/sci-mathematics/mdp/mdp-3.5.ebuild b/sci-mathematics/mdp/mdp-3.5.ebuild deleted file mode 100644 index 6136fc36d..000000000 --- a/sci-mathematics/mdp/mdp-3.5.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python{2_7,3_4,3_5} ) - -inherit distutils-r1 - -MY_P="${P/mdp/MDP}" -MY_P="${MY_P/_rc/RC}" - -DESCRIPTION="Data processing framework in python" -HOMEPAGE="http://mdp-toolkit.sourceforge.net/index.html" -SRC_URI="mirror://sourceforge/mdp-toolkit/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="|| ( - >=dev-python/numpy-1.1[${PYTHON_USEDEP}] - >=sci-libs/scipy-0.5.2[${PYTHON_USEDEP}] - )" - -S="${WORKDIR}/${MY_P}" - -python_test() { - distutils_install_for_testing - cd "${BUILD_DIR}" || die - "${PYTHON}" -c "import mdp;mdp.test()" || die -} diff --git a/sci-mathematics/mdp/mdp-9999.ebuild b/sci-mathematics/mdp/mdp-9999.ebuild deleted file mode 100644 index 9be3d648a..000000000 --- a/sci-mathematics/mdp/mdp-9999.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python{2_7,3_3} ) - -inherit distutils-r1 git-r3 - -MY_P="${P/mdp/MDP}" -MY_P="${MY_P/_rc/RC}" - -DESCRIPTION="Modular data processing framework for python" -HOMEPAGE="http://mdp-toolkit.sourceforge.net/index.html" -SRC_URI="" -EGIT_REPO_URI="git://github.com/mdp-toolkit/mdp-toolkit.git" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="" -RDEPEND="|| ( - >=dev-python/numpy-1.1[${PYTHON_USEDEP}] - >=sci-libs/scipy-0.5.2[${PYTHON_USEDEP}] - )" - -python_test() { - distutils_install_for_testing - cd "${BUILD_DIR}" || die - "${PYTHON}" -c "import mdp;mdp.test()" || die -} diff --git a/sci-mathematics/mdp/metadata.xml b/sci-mathematics/mdp/metadata.xml deleted file mode 100644 index 4a8c55d36..000000000 --- a/sci-mathematics/mdp/metadata.xml +++ /dev/null @@ -1,23 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>tim@cerazone.net</email> - <name>Tim Cera</name> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription lang="en"> -Modular toolkit for Data Processing (MDP) is a Python data processing -framework. Implemented algorithms include: Principal Component Analysis -(PCA), Independent Component Analysis (ICA), Slow Feature Analysis (SFA), -Independent Slow Feature Analysis (ISFA), Growing Neural Gas (GNG), Factor -Analysis, Fisher Discriminant Analysis (FDA), Gaussian Classifiers, and -Restricted Boltzmann Machines. -</longdescription> - <upstream> - <remote-id type="sourceforge">mdp-toolkit</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/netgen/Manifest b/sci-mathematics/netgen/Manifest deleted file mode 100644 index a53b896bc..000000000 --- a/sci-mathematics/netgen/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST netgen-4.9.13.tar.gz 1829916 BLAKE2B f863c0dd4a1df1d0bf14bedc8d5afade7cfcf1209d71f402509bd24989813485051c192456bfb7f102e66991a8d89c7eac72520f9fa6090eea853a597250b445 SHA512 6cfe6ea799f37a35dc74112f5c370fd369277a55965769649c00632eba308061901fd7563fe7eb4b427b0702d39f4f004854da9f02f2e6f11ccd3a72e6b6afa3 -DIST netgen-5.0.0.tar.gz 1835004 BLAKE2B 145d1285ea2989b4b829576ef830bcacf90ada9c2aae47b6e7c1d2a6575696e0dc91d51f47443b69d4e7258d67c1c035e6d730dc77e8c37b4d9669bd804a84d3 SHA512 27f46feaa1cf9d269c4898c093cca404fdc5e5fbfc8c9684d0d2f2ec2f2f9af85dd8b3d3372044f63fca08e1a079fd042fbcdc7b9ca881c38a3cfe67586b34b4 -DIST netgen-5.3.1.tar.gz 1857185 BLAKE2B 943c0d94f9f74d9d83674bde416ad63d2b0b1eb1029d901504d95285530998e03a92b6e71b4d844aab541c3e6a533613f0e90e4343c38f20f28321118b8e73c5 SHA512 6f5b5b8ab47fc3bf57281b26f26b13675aa719146c90a928eda3d704163e20a0a3baf27d520978ec6c4828ee6323eaef65deb851988eefef5d768a9ecad69fc8 diff --git a/sci-mathematics/netgen/files/netgen-5.x-compile-against-occ-6.5.x.patch b/sci-mathematics/netgen/files/netgen-5.x-compile-against-occ-6.5.x.patch deleted file mode 100644 index ce581cee3..000000000 --- a/sci-mathematics/netgen/files/netgen-5.x-compile-against-occ-6.5.x.patch +++ /dev/null @@ -1,28 +0,0 @@ ---- libsrc/occ/Partition_Spliter.cxx.old 2012-11-14 16:14:39.440625195 +0100 -+++ libsrc/occ/Partition_Spliter.cxx 2012-11-14 16:15:20.035646075 +0100 -@@ -1169,8 +1169,8 @@ - for (; j<=nbj && ok; ++j) { - if (Extrema.IsMin(j)) { - hasMin = Standard_True; -- ok = Extrema.Value(j) <= tol; // V6.3 -- // ok = Extrema.SquareDistance(j) <= tol; // V6.5 -+ // ok = Extrema.Value(j) <= tol; // V6.3 -+ ok = Extrema.SquareDistance(j) <= tol; // V6.5 - } - } - } ---- libsrc/occ/Partition_Inter3d.cxx.old 2012-11-14 16:13:11.149581085 +0100 -+++ libsrc/occ/Partition_Inter3d.cxx 2012-11-14 16:14:20.017615214 +0100 -@@ -243,9 +243,9 @@ - Standard_Integer i, nbExt = anExtPS.NbExt(); - Extrema_POnSurf aPOnSurf; - for (i = 1; i <= nbExt; ++i ) -- if (anExtPS.Value( i ) <= TolE) // V6.3 -- // if (anExtPS.SquareDistance( i ) <= TolE) // V6.5 -- { -+ // if (anExtPS.Value( i ) <= TolE) // V6.3 -+ if (anExtPS.SquareDistance( i ) <= TolE) // V6.5 -+ { - aPOnSurf = anExtPS.Point( i ); - break; - } diff --git a/sci-mathematics/netgen/files/netgen-5.x-fedora-fixes.patch b/sci-mathematics/netgen/files/netgen-5.x-fedora-fixes.patch deleted file mode 100644 index 5cb399edb..000000000 --- a/sci-mathematics/netgen/files/netgen-5.x-fedora-fixes.patch +++ /dev/null @@ -1,223 +0,0 @@ -diff -uwrN netgen-5.3.1/libsrc/meshing/meshtype.cpp netgen/libsrc/meshing/meshtype.cpp ---- netgen-5.3.1/libsrc/meshing/meshtype.cpp 2016-02-20 21:55:59.226450843 +0100 -+++ netgen/libsrc/meshing/meshtype.cpp 2016-02-20 23:54:12.293646166 +0100 -@@ -1,4 +1,5 @@ - #include <mystdlib.h> -+#include <float.h> // to get DBL_MIN defined - - #include "meshing.hpp" - -@@ -666,7 +667,8 @@ - - double det = trans.Det(); - -- if (det <= 0) -+ // if (det <= 0) -+ if (det <= DBL_MIN) // avoid FPE - err += 1e12; - else - err += frob * frob / det; -@@ -722,7 +724,8 @@ - - double det = trans(0,0)*trans(1,1)-trans(1,0)*trans(0,1); - -- if (det <= 0) -+ // if (det <= 0) -+ if (det <= DBL_MIN) // avoid FPE - { - dd = 0; - return 1e12; -@@ -806,7 +809,8 @@ - = dtrans(0,0) * trans(1,1) - trans(0,1) * dtrans(1,0) - + trans(0,0) * dtrans(1,1) - dtrans(0,1) * trans(1,0); - -- if (det <= 0) -+ // if (det <= 0) -+ if (det <= DBL_MIN) // avoid FPE - err += 1e12; - else - { -@@ -856,7 +860,8 @@ - frob /= 2; - - double det = trans.Det(); -- if (det <= 0) -+ //if (det <= 0) -+ if (det <= DBL_MIN) // avoid FPE - err += 1e12; - else - err += frob * frob / det; -@@ -1864,7 +1869,8 @@ - case PYRAMID: - { - double noz = 1-p(2); -- if (noz == 0.0) noz = 1e-10; -+ //if (noz == 0.0) noz = 1e-10; -+ if (noz <= DBL_MIN) noz = 1e-10; // avoid FPE - - double xi = p(0) / noz; - double eta = p(1) / noz; -@@ -2513,10 +2519,10 @@ - - MeshingParameters :: MeshingParameters () - { -- optimize3d = "cmdmustm"; -+ optimize3d = (char*)"cmdmustm"; // optimize3d = "cmdmustm"; - //optimize3d = "cmdmstm"; - optsteps3d = 3; -- optimize2d = "smsmsmSmSmSm"; -+ optimize2d = (char*)"smsmsmSmSmSm"; // optimize2d = "smsmsmSmSmSm"; - optsteps2d = 3; - opterrpow = 2; - blockfill = 1; -diff -uwrN netgen-5.3.1/libsrc/meshing/meshtype.hpp netgen/libsrc/meshing/meshtype.hpp ---- netgen-5.3.1/libsrc/meshing/meshtype.hpp 2016-02-20 21:55:59.226450843 +0100 -+++ netgen/libsrc/meshing/meshtype.hpp 2016-02-20 23:54:12.295646166 +0100 -@@ -15,6 +15,7 @@ - Classes for NETGEN - */ - -+class Mesh; // added due to compilation errors on some platforms - - - enum ELEMENT_TYPE { -diff -uwrN netgen-5.3.1/libsrc/meshing/smoothing2.cpp netgen/libsrc/meshing/smoothing2.cpp ---- netgen-5.3.1/libsrc/meshing/smoothing2.cpp 2016-02-20 21:55:59.228450843 +0100 -+++ netgen/libsrc/meshing/smoothing2.cpp 2016-02-20 23:54:12.298646166 +0100 -@@ -361,7 +361,8 @@ - vgrad = 0; - double badness = 0; - -- ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n); -+ //normal already computed: ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n); -+ n = ld.normal; - pp1 = ld.sp1 + x(0) * ld.t1 + x(1) * ld.t2; - - // meshthis -> ProjectPoint (surfi, pp1); -@@ -577,7 +578,8 @@ - vgrad = 0; - badness = 0; - -- ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n); -+ //normal already computed: ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n); -+ n = ld.normal; - - pp1 = ld.sp1 + x(0) * ld.t1 + x(1) * ld.t2; - -@@ -649,7 +651,8 @@ - vgrad = 0; - badness = 0; - -- ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n); -+ //normal already computed: ld.meshthis -> GetNormalVector (ld.surfi, ld.sp1, ld.gi1, n); -+ n = ld.normal; - - // pp1 = sp1; - // pp1.Add2 (x.Get(1), t1, x.Get(2), t2); -diff -uwrN netgen-5.3.1/libsrc/occ/occconstruction.cpp netgen/libsrc/occ/occconstruction.cpp ---- netgen-5.3.1/libsrc/occ/occconstruction.cpp 2016-02-20 21:53:44.420447131 +0100 -+++ netgen/libsrc/occ/occconstruction.cpp 2016-02-20 23:54:12.299646166 +0100 -@@ -28,7 +28,7 @@ - #include <BRepAlgoAPI_Common.hxx> - #include <BRepAlgoAPI_Fuse.hxx> - #include <BRepAlgoAPI_Section.hxx> --#include <BRepOffsetAPI_Sewing.hxx> -+//#include <BRepOffsetAPI_Sewing.hxx> - //#include <BRepAlgo_Sewing.hxx> - #include <BRepOffsetAPI_MakeOffsetShape.hxx> - #include <ShapeFix_Shape.hxx> -diff -uwrN netgen-5.3.1/libsrc/occ/occmeshsurf.cpp netgen/libsrc/occ/occmeshsurf.cpp ---- netgen-5.3.1/libsrc/occ/occmeshsurf.cpp 2016-02-20 21:53:44.421447131 +0100 -+++ netgen/libsrc/occ/occmeshsurf.cpp 2016-02-20 23:54:12.310646166 +0100 -@@ -6,6 +6,7 @@ - #include <meshing.hpp> - #include <GeomLProp_SLProps.hxx> - #include <ShapeAnalysis_Surface.hxx> -+#include <GeomAPI_ProjectPointOnCurve.hxx> // -- moved here from occgeom.hpp - - - namespace netgen -@@ -689,7 +691,7 @@ - } - - newp = hnewp; -- } -+ }//; -- to compile with -Wall -pedantic - - - void OCCRefinementSurfaces :: - - -diff -uwrN netgen-5.3.1/libsrc/occ/Partition_Inter3d.cxx netgen/libsrc/occ/Partition_Inter3d.cxx ---- netgen-5.3.1/libsrc/occ/Partition_Inter3d.cxx 2016-02-20 21:53:44.418447131 +0100 -+++ netgen/libsrc/occ/Partition_Inter3d.cxx 2016-02-20 23:54:12.311646166 +0100 -@@ -243,8 +243,10 @@ - Standard_Integer i, nbExt = anExtPS.NbExt(); - Extrema_POnSurf aPOnSurf; - for (i = 1; i <= nbExt; ++i ) -+ // porting to OCCT6.5.1 - // if (anExtPS.Value( i ) <= TolE) // V6.3 -- if (anExtPS.SquareDistance( i ) <= TolE) // V6.5 -+ // if (anExtPS.SquareDistance( i ) <= TolE) // V6.5 -+ if (anExtPS.SquareDistance( i ) <= TolE * TolE) - { - aPOnSurf = anExtPS.Point( i ); - break; -diff -uwrN netgen-5.3.1/libsrc/occ/Partition_Spliter.cxx netgen/libsrc/occ/Partition_Spliter.cxx ---- netgen-5.3.1/libsrc/occ/Partition_Spliter.cxx 2016-02-20 21:53:44.420447131 +0100 -+++ netgen/libsrc/occ/Partition_Spliter.cxx 2016-02-20 23:54:12.313646166 +0100 -@@ -1169,8 +1169,10 @@ - for (; j<=nbj && ok; ++j) { - if (Extrema.IsMin(j)) { - hasMin = Standard_True; -+ // porting to OCCT6.5.1 - // ok = Extrema.Value(j) <= tol; // V6.3 -- ok = Extrema.SquareDistance(j) <= tol; // V6.5 -+ // ok = Extrema.SquareDistance(j) <= tol; // V6.5 -+ ok = Extrema.SquareDistance(j) <= tol * tol; - } - } - } -diff -uwrN netgen-5.3.1/libsrc/occ/utilities.h netgen/libsrc/occ/utilities.h ---- netgen-5.3.1/libsrc/occ/utilities.h 2016-02-20 21:53:44.421447131 +0100 -+++ netgen/libsrc/occ/utilities.h 2016-02-20 23:54:12.314646166 +0100 -@@ -33,6 +33,7 @@ - - #include <string> - #include <iostream> -+#include <iomanip> - #include <cstdlib> - // #include "SALOME_Log.hxx" - -diff -uwrN netgen-5.3.1/libsrc/stlgeom/stlgeommesh.cpp netgen/libsrc/stlgeom/stlgeommesh.cpp ---- netgen-5.3.1/libsrc/stlgeom/stlgeommesh.cpp 2016-02-20 21:55:59.234450844 +0100 -+++ netgen/libsrc/stlgeom/stlgeommesh.cpp 2016-02-20 23:54:12.315646166 +0100 -@@ -1435,7 +1435,8 @@ - /* - if (!optstring || strlen(optstring) == 0) - { -- mparam.optimize2d = "smcm"; -+ //mparam.optimize2d = (char*)"smcm"; -+ mparam.optimize2d = (char*)"smcm"; - } - else - { -@@ -1453,7 +1454,7 @@ - mesh -> LoadLocalMeshSize (mparam.meshsizefilename); - mesh -> CalcLocalHFromSurfaceCurvature (mparam.grading, - stlparam.resthsurfmeshcurvfac); -- mparam.optimize2d = "cmsmSm"; -+ mparam.optimize2d = "(char*)cmsmSm"; - STLSurfaceOptimization (*stlgeometry, *mesh, mparam); - #ifdef STAT_STREAM - (*statout) << GetTime() << " & "; -@@ -1560,7 +1561,8 @@ - /* - if (!optstring || strlen(optstring) == 0) - { -- mparam.optimize3d = "cmdmstm"; -+ //mparam.optimize3d = "cmdmstm"; -+ mparam.optimize3d = (char*)"cmdmstm"; - } - else - { diff --git a/sci-mathematics/netgen/files/netgen-5.x-includes-fixes.patch b/sci-mathematics/netgen/files/netgen-5.x-includes-fixes.patch deleted file mode 100644 index 650b575c9..000000000 --- a/sci-mathematics/netgen/files/netgen-5.x-includes-fixes.patch +++ /dev/null @@ -1,29 +0,0 @@ -diff -uwrN -x.git netgen-5.3.1/libsrc/include/meshing.hpp netgen/libsrc/include/meshing.hpp ---- netgen-5.3.1/libsrc/include/meshing.hpp 2016-02-21 20:12:55.885186643 +0100 -+++ netgen/libsrc/include/meshing.hpp 2016-02-21 20:09:26.275180871 +0100 -@@ -1 +1 @@ --#include <../meshing/meshing.hpp> -+#include "../meshing/meshing.hpp" -diff -uwrN -x.git netgen-5.3.1/libsrc/include/myadt.hpp netgen/libsrc/include/myadt.hpp ---- netgen-5.3.1/libsrc/include/myadt.hpp 2016-02-21 20:12:55.886186643 +0100 -+++ netgen/libsrc/include/myadt.hpp 2016-02-21 20:09:26.275180871 +0100 -@@ -1 +1 @@ --#include <../general/myadt.hpp> -+#include "../general/myadt.hpp" -diff -uwrN -x.git netgen-5.3.1/libsrc/include/stlgeom.hpp netgen/libsrc/include/stlgeom.hpp ---- netgen-5.3.1/libsrc/include/stlgeom.hpp 2016-02-21 20:12:55.886186643 +0100 -+++ netgen/libsrc/include/stlgeom.hpp 2016-02-21 20:09:26.275180871 +0100 -@@ -1 +1 @@ --#include <../stlgeom/stlgeom.hpp> -+#include "../stlgeom/stlgeom.hpp" -diff -uwrN -x.git netgen-5.3.1/libsrc/meshing/parallelmesh.cpp netgen/libsrc/meshing/parallelmesh.cpp ---- netgen-5.3.1/libsrc/meshing/parallelmesh.cpp 2016-02-21 20:12:55.888186643 +0100 -+++ netgen/libsrc/meshing/parallelmesh.cpp 2016-02-21 20:09:26.276180871 +0100 -@@ -1,6 +1,6 @@ - #ifdef PARALLEL - --#include <meshing.hpp> -+#include "meshing.hpp" - #include "paralleltop.hpp" - - // #define METIS4 diff --git a/sci-mathematics/netgen/files/netgen-5.x-makefiles-fixes.patch b/sci-mathematics/netgen/files/netgen-5.x-makefiles-fixes.patch deleted file mode 100644 index b6c8fd4c1..000000000 --- a/sci-mathematics/netgen/files/netgen-5.x-makefiles-fixes.patch +++ /dev/null @@ -1,412 +0,0 @@ -diff -uwrN -x.git netgen-5.3.1/configure.ac netgen/configure.ac ---- netgen-5.3.1/configure.ac 2016-02-21 21:40:41.852331652 +0100 -+++ netgen/configure.ac 2016-02-21 21:39:31.355329711 +0100 -@@ -14,7 +14,6 @@ - AC_DISABLE_STATIC - - AC_LANG([C++]) --AM_PROG_AR - AC_PROG_CXX - - AC_OPENMP -@@ -36,15 +35,15 @@ - [AC_HELP_STRING([--with-occ=dir],[use OpenCascade installed in directory dir])], - [occdir=$withval] - [occon=true], -- [occdir=/opt/OpenCASCADE] -+ [occdir=$CASROOT] - ) - - - - if test a$occon = atrue ; then - -- AC_SUBST([OCCFLAGS], ["-DOCCGEOMETRY -I$occdir/inc -I/usr/include/opencascade"]) -- AC_SUBST([OCCLIBS], ["-L$occdir/lib -lTKernel -lTKGeomBase -lTKMath -lTKG2d -lTKG3d -lTKXSBase -lTKOffset -lTKFillet -lTKShHealing -lTKMesh -lTKMeshVS -lTKTopAlgo -lTKGeomAlgo -lTKBool -lTKPrim -lTKBO -lTKIGES -lTKBRep -lTKSTEPBase -lTKSTEP -lTKSTL -lTKSTEPAttr -lTKSTEP209 -lTKXDESTEP -lTKXDEIGES -lTKXCAF -lTKLCAF -lFWOSPlugin"]) -+ AC_SUBST([OCCFLAGS], ["-DOCCGEOMETRY -I$occdir/inc"]) -+ AC_SUBST([OCCLIBS], ["-lTKernel -lTKGeomBase -lTKMath -lTKG2d -lTKG3d -lTKXSBase -lTKOffset -lTKFillet -lTKShHealing -lTKMesh -lTKMeshVS -lTKTopAlgo -lTKGeomAlgo -lTKBool -lTKPrim -lTKBO -lTKIGES -lTKBRep -lTKSTEPBase -lTKSTEP -lTKSTL -lTKSTEPAttr -lTKSTEP209 -lTKXDESTEP -lTKXDEIGES -lTKXCAF -lTKLCAF -lFWOSPlugin"]) - - # -lTKDCAF - -@@ -90,18 +89,18 @@ - [AC_HELP_STRING([--disable-gui],[don't build netgen with GUI])], - [if test "$enableval" = yes; then ngguion=true; else ngguion=false; fi]) - --metisdir=/usr/local -+metisdir=/usr - AC_ARG_WITH([metis], - [AC_HELP_STRING([--with-metis=dir],[path to metis 5.x])], - [metisdir=$withval], -- [metisdir=/usr/local] -+ [metisdir=/usr] - ) - - AC_ARG_ENABLE([parallel], - [AC_HELP_STRING([--enable-parallel],[enable mpi parallelization])], -- [AC_SUBST([MPI_INCLUDES], "-I$metisdir/include -DMETIS")] -+ [AC_SUBST([MPI_INCLUDES], "-DMETIS")] - [CXXFLAGS="$CXXFLAGS -DPARALLEL"] -- [AC_SUBST([MPI_LIBS], "-L$metisdir/lib -lmetis")] -+ [AC_SUBST([MPI_LIBS], "-lmetis")] - ) - # -DVTRACE - # -lvt-hyb -diff -uwrN -x.git netgen-5.3.1/libsrc/csg/Makefile.am netgen/libsrc/csg/Makefile.am ---- netgen-5.3.1/libsrc/csg/Makefile.am 2016-02-21 21:40:41.852331652 +0100 -+++ netgen/libsrc/csg/Makefile.am 2016-02-21 21:39:31.355329711 +0100 -@@ -8,24 +8,24 @@ - AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include $(TCL_INCLUDES) - METASOURCES = AUTO - --lib_LTLIBRARIES = libcsg.la -+lib_LTLIBRARIES = libngcsg.la - - --libcsg_la_SOURCES = algprim.cpp brick.cpp \ -+libngcsg_la_SOURCES = algprim.cpp brick.cpp \ - bspline2d.cpp csgeom.cpp csgparser.cpp curve2d.cpp edgeflw.cpp \ - explicitcurve2d.cpp extrusion.cpp gencyl.cpp genmesh.cpp identify.cpp \ - manifold.cpp meshsurf.cpp polyhedra.cpp revolution.cpp singularref.cpp \ - solid.cpp specpoin.cpp spline3d.cpp surface.cpp triapprox.cpp - --libcsg_la_LIBADD = $(top_builddir)/libsrc/meshing/libmesh.la -+libngcsg_la_LIBADD = $(top_builddir)/libsrc/meshing/libngmesh.la - - - - if NGGUI --lib_LTLIBRARIES += libcsgvis.la -+lib_LTLIBRARIES += libngcsgvis.la - --libcsgvis_la_SOURCES = vscsg.cpp csgpkg.cpp --libcsgvis_la_LIBADD = libcsg.la -+libngcsgvis_la_SOURCES = vscsg.cpp csgpkg.cpp -+libngcsgvis_la_LIBADD = libngcsg.la - endif - - # $(top_builddir)/libsrc/geom2d/libgeom2d.la -diff -uwrN -x.git netgen-5.3.1/libsrc/general/Makefile.am netgen/libsrc/general/Makefile.am ---- netgen-5.3.1/libsrc/general/Makefile.am 2016-02-21 21:40:41.852331652 +0100 -+++ netgen/libsrc/general/Makefile.am 2016-02-21 21:39:31.356329711 +0100 -@@ -4,8 +4,8 @@ - - AM_CPPFLAGS = $(MPI_INCLUDES) -I$(top_srcdir)/libsrc/include - METASOURCES = AUTO --noinst_LTLIBRARIES = libgen.la --libgen_la_SOURCES = array.cpp bitarray.cpp dynamicmem.cpp flags.cpp \ -+noinst_LTLIBRARIES = libnggen.la -+libnggen_la_SOURCES = array.cpp bitarray.cpp dynamicmem.cpp flags.cpp \ - hashtabl.cpp mystring.cpp ngexception.cpp optmem.cpp parthreads.cpp \ - profiler.cpp seti.cpp sort.cpp spbita2d.cpp symbolta.cpp table.cpp \ - mpi_interface.cpp gzstream.cpp -diff -uwrN -x.git netgen-5.3.1/libsrc/geom2d/Makefile.am netgen/libsrc/geom2d/Makefile.am ---- netgen-5.3.1/libsrc/geom2d/Makefile.am 2016-02-21 21:40:41.852331652 +0100 -+++ netgen/libsrc/geom2d/Makefile.am 2016-02-21 21:39:31.356329711 +0100 -@@ -4,18 +4,18 @@ - - METASOURCES = AUTO - --lib_LTLIBRARIES = libgeom2d.la -+lib_LTLIBRARIES = libnggeom2d.la - - if NGGUI --lib_LTLIBRARIES += libgeom2dvis.la -+lib_LTLIBRARIES += libnggeom2dvis.la - endif - - - --libgeom2d_la_SOURCES = genmesh2d.cpp geom2dmesh.cpp geometry2d.cpp --libgeom2d_la_LIBADD = $(top_builddir)/libsrc/meshing/libmesh.la -+libnggeom2d_la_SOURCES = genmesh2d.cpp geom2dmesh.cpp geometry2d.cpp -+libnggeom2d_la_LIBADD = $(top_builddir)/libsrc/meshing/libngmesh.la $(MPI_LIBS) - --libgeom2dvis_la_SOURCES = geom2dpkg.cpp vsgeom2d.cpp --libgeom2dvis_la_LIBADD = libgeom2d.la -+libnggeom2dvis_la_SOURCES = geom2dpkg.cpp vsgeom2d.cpp -+libnggeom2dvis_la_LIBADD = libnggeom2d.la -lGL $(MPI_LIBS) - - -diff -uwrN -x.git netgen-5.3.1/libsrc/gprim/Makefile.am netgen/libsrc/gprim/Makefile.am ---- netgen-5.3.1/libsrc/gprim/Makefile.am 2016-02-21 21:40:41.853331652 +0100 -+++ netgen/libsrc/gprim/Makefile.am 2016-02-21 21:39:31.357329711 +0100 -@@ -2,6 +2,6 @@ - - AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include - METASOURCES = AUTO --noinst_LTLIBRARIES = libgprim.la --libgprim_la_SOURCES = adtree.cpp geom2d.cpp geom3d.cpp geomfuncs.cpp \ -+noinst_LTLIBRARIES = libnggprim.la -+libnggprim_la_SOURCES = adtree.cpp geom2d.cpp geom3d.cpp geomfuncs.cpp \ - geomtest3d.cpp transform3d.cpp spline.cpp splinegeometry.cpp -diff -uwrN -x.git netgen-5.3.1/libsrc/interface/Makefile.am netgen/libsrc/interface/Makefile.am ---- netgen-5.3.1/libsrc/interface/Makefile.am 2016-02-21 21:40:41.853331652 +0100 -+++ netgen/libsrc/interface/Makefile.am 2016-02-21 21:39:31.357329711 +0100 -@@ -2,14 +2,14 @@ - - AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include -I$(top_srcdir)/libsrc/interface $(MPI_INCLUDES) $(TCL_INCLUDES) -DOPENGL - METASOURCES = AUTO --lib_LTLIBRARIES = libinterface.la --libinterface_la_SOURCES = nginterface.cpp nginterface_v2.cpp \ -+lib_LTLIBRARIES = libnginterface.la -+libnginterface_la_SOURCES = nginterface.cpp nginterface_v2.cpp \ - read_fnf_mesh.cpp readtetmesh.cpp readuser.cpp writeabaqus.cpp writediffpack.cpp \ - writedolfin.cpp writeelmer.cpp writefeap.cpp writefluent.cpp writegmsh.cpp writejcm.cpp \ - writepermas.cpp writetecplot.cpp writetet.cpp writetochnog.cpp writeuser.cpp \ - wuchemnitz.cpp writegmsh2.cpp writeOpenFOAM15x.cpp - - --libinterface_la_LIBADD = $(top_builddir)/libsrc/meshing/libmesh.la -+libnginterface_la_LIBADD = $(top_builddir)/libsrc/meshing/libngmesh.la - - # libinterface_la_LDFLAGS = -rdynamic -diff -uwrN -x.git netgen-5.3.1/libsrc/linalg/Makefile.am netgen/libsrc/linalg/Makefile.am ---- netgen-5.3.1/libsrc/linalg/Makefile.am 2016-02-21 21:40:41.853331652 +0100 -+++ netgen/libsrc/linalg/Makefile.am 2016-02-21 21:39:31.357329711 +0100 -@@ -1,8 +1,8 @@ - noinst_HEADERS = densemat.hpp linalg.hpp polynomial.hpp vector.hpp opti.hpp - AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include - METASOURCES = AUTO --noinst_LTLIBRARIES = libla.la --libla_la_SOURCES = densemat.cpp polynomial.cpp bfgs.cpp linopt.cpp linsearch.cpp -+noinst_LTLIBRARIES = libngla.la -+libngla_la_SOURCES = densemat.cpp polynomial.cpp bfgs.cpp linopt.cpp linsearch.cpp - - # vector.cpp - -diff -uwrN -x.git netgen-5.3.1/libsrc/meshing/Makefile.am netgen/libsrc/meshing/Makefile.am ---- netgen-5.3.1/libsrc/meshing/Makefile.am 2016-02-21 21:40:41.853331652 +0100 -+++ netgen/libsrc/meshing/Makefile.am 2016-02-21 21:39:31.358329711 +0100 -@@ -15,9 +15,9 @@ - - METASOURCES = AUTO - --lib_LTLIBRARIES = libmesh.la -+lib_LTLIBRARIES = libngmesh.la - --libmesh_la_SOURCES = adfront2.cpp adfront3.cpp bisect.cpp boundarylayer.cpp \ -+libngmesh_la_SOURCES = adfront2.cpp adfront3.cpp bisect.cpp boundarylayer.cpp \ - clusters.cpp curvedelems.cpp delaunay.cpp delaunay2d.cpp \ - geomsearch.cpp global.cpp hprefinement.cpp improve2.cpp \ - improve2gen.cpp improve3.cpp localh.cpp meshclass.cpp \ -@@ -30,8 +30,8 @@ - topology.cpp triarls.cpp validate.cpp zrefine.cpp bcfunctions.cpp \ - parallelmesh.cpp paralleltop.cpp paralleltop.hpp basegeom.cpp - --libmesh_la_LIBADD = $(top_builddir)/libsrc/linalg/libla.la \ -- $(top_builddir)/libsrc/gprim/libgprim.la \ -- $(top_builddir)/libsrc/general/libgen.la \ -- -lz -+libngmesh_la_LIBADD = $(top_builddir)/libsrc/linalg/libngla.la \ -+ $(top_builddir)/libsrc/gprim/libnggprim.la \ -+ $(top_builddir)/libsrc/general/libnggen.la \ -+ $(MPI_LIBS) -lz - -diff -uwrN -x.git netgen-5.3.1/libsrc/occ/Makefile.am netgen/libsrc/occ/Makefile.am ---- netgen-5.3.1/libsrc/occ/Makefile.am 2016-02-21 21:40:41.853331652 +0100 -+++ netgen/libsrc/occ/Makefile.am 2016-02-21 21:39:31.358329711 +0100 -@@ -14,20 +14,20 @@ - - METASOURCES = AUTO - --lib_LTLIBRARIES = libocc.la -+lib_LTLIBRARIES = libngocc.la - - if NGGUI --lib_LTLIBRARIES += liboccvis.la -+lib_LTLIBRARIES += libngoccvis.la - endif - - --libocc_la_SOURCES = Partition_Inter2d.cxx Partition_Inter3d.cxx \ -+libngocc_la_SOURCES = Partition_Inter2d.cxx Partition_Inter3d.cxx \ - Partition_Loop.cxx Partition_Loop2d.cxx Partition_Loop3d.cxx Partition_Spliter.cxx \ - occconstruction.cpp occgenmesh.cpp occgeom.cpp occmeshsurf.cpp - --libocc_la_LIBADD = $(OCCLIBS) -+libngocc_la_LIBADD = $(OCCLIBS) - --liboccvis_la_SOURCES = occpkg.cpp vsocc.cpp --liboccvis_la_LIBADD = libocc.la -+libngoccvis_la_SOURCES = occpkg.cpp vsocc.cpp -+libngoccvis_la_LIBADD = libngocc.la $(TCL_LIB_SPEC) - - -diff -uwrN -x.git netgen-5.3.1/libsrc/stlgeom/Makefile.am netgen/libsrc/stlgeom/Makefile.am ---- netgen-5.3.1/libsrc/stlgeom/Makefile.am 2016-02-21 21:40:41.854331653 +0100 -+++ netgen/libsrc/stlgeom/Makefile.am 2016-02-21 21:39:31.359329711 +0100 -@@ -4,18 +4,18 @@ - AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include $(TCL_INCLUDES) - METASOURCES = AUTO - --lib_LTLIBRARIES = libstl.la -+lib_LTLIBRARIES = libngstl.la - - if NGGUI --lib_LTLIBRARIES += libstlvis.la -+lib_LTLIBRARIES += libngstlvis.la - endif - --libstl_la_SOURCES = meshstlsurface.cpp stlgeom.cpp stlgeomchart.cpp \ -+libngstl_la_SOURCES = meshstlsurface.cpp stlgeom.cpp stlgeomchart.cpp \ - stlgeommesh.cpp stlline.cpp stltool.cpp stltopology.cpp - - --libstlvis_la_SOURCES = stlpkg.cpp vsstl.cpp --libstlvis_la_LIBADD = libstl.la --libstl_la_LIBADD = $(top_builddir)/libsrc/meshing/libmesh.la -+libngstlvis_la_SOURCES = stlpkg.cpp vsstl.cpp -+libngstlvis_la_LIBADD = libngstl.la -lGL $(MPI_LIBS) $(TCL_LIB_SPEC) -+libngstl_la_LIBADD = $(top_builddir)/libsrc/meshing/libngmesh.la $(MPI_LIBS) - # libstlvis_la_LIBADD = libstl.la $(top_builddir)/libsrc/linalg/libla.la - -diff -uwrN -x.git netgen-5.3.1/libsrc/visualization/Makefile.am netgen/libsrc/visualization/Makefile.am ---- netgen-5.3.1/libsrc/visualization/Makefile.am 2016-02-21 21:40:41.854331653 +0100 -+++ netgen/libsrc/visualization/Makefile.am 2016-02-21 21:39:31.359329711 +0100 -@@ -7,11 +7,11 @@ - METASOURCES = AUTO - - if NGGUI --noinst_LTLIBRARIES = libvisual.la -+noinst_LTLIBRARIES = libngvisual.la - endif - - --libvisual_la_SOURCES = meshdoc.cpp mvdraw.cpp \ -+libngvisual_la_SOURCES = meshdoc.cpp mvdraw.cpp \ - vsfieldlines.cpp vsmesh.cpp vssolution.cpp importsolution.cpp - -- -+libngvisual_la_LIBADD = -lGL -diff -uwrN -x.git netgen-5.3.1/libsrc/visualization/Makefile.in netgen/libsrc/visualization/Makefile.in ---- netgen-5.3.1/libsrc/visualization/Makefile.in 2016-02-21 21:40:41.855331653 +0100 -+++ netgen/libsrc/visualization/Makefile.in 2016-02-21 21:39:31.360329711 +0100 -@@ -275,7 +275,7 @@ - visual.hpp vssolution.hpp - - include_HEADERS = soldata.hpp --AM_CPPFLAGS = $(MPI_INCLUDES) -I$(top_srcdir)/libsrc/include -DOPENGL -D$(TOGL_WINDOWINGSYSTEM) $(OCCFLAGS) $(TCL_INCLUDES) -+AM_CPPFLAGS = $(MPI_INCLUDES) -I$(top_srcdir)/libsrc/include -DOPENGL $(OCCFLAGS) $(TCL_INCLUDES) - METASOURCES = AUTO - @NGGUI_TRUE@noinst_LTLIBRARIES = libvisual.la - libvisual_la_SOURCES = meshdoc.cpp mvdraw.cpp \ -diff -uwrN -x.git netgen-5.3.1/ng/Makefile.am netgen/ng/Makefile.am ---- netgen-5.3.1/ng/Makefile.am 2016-02-21 21:40:41.855331653 +0100 -+++ netgen/ng/Makefile.am 2016-02-21 21:39:31.360329711 +0100 -@@ -1,6 +1,6 @@ - include_HEADERS = - --AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include -I$(top_srcdir)/libsrc/interface -DOPENGL -D$(TOGL_WINDOWINGSYSTEM) $(TCL_INCLUDES) $(MPI_INCLUDES) $(FFMPEG_INCLUDES) $(JPEGLIB_INCLUDES) -+AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include -I$(top_srcdir)/libsrc/interface -DOPENGL $(TCL_INCLUDES) $(MPI_INCLUDES) $(FFMPEG_INCLUDES) $(JPEGLIB_INCLUDES) - - - if NGGUI -@@ -17,21 +17,18 @@ - endif - # -lpardiso500-GNU472-X86-64 -lgfortran - --netgen_LDADD = $(top_builddir)/libsrc/visualization/libvisual.la \ -- $(top_builddir)/libsrc/csg/libcsgvis.la \ -- $(top_builddir)/libsrc/csg/libcsg.la \ -- $(top_builddir)/libsrc/interface/libinterface.la \ -- $(top_builddir)/libsrc/meshing/libmesh.la \ -- -L$(TK_BIN_DIR)/Togl1.7 $(TOGLLIBDIR) -lTogl $(LIBGLU) $(TK_LIB_SPEC) $(TCL_LIB_SPEC) $(MPI_LIBS) $(FFMPEG_LIBS) $(JPEGLIB_LIBS) $(PKG_LIBS) $(MKL_LIBS) -- -- --# --# $(top_builddir)/libsrc/occ/liboccvis.la --# $(top_builddir)/libsrc/occ/libocc.la --# $(top_builddir)/libsrc/stlgeom/libstlvis.la --# $(top_builddir)/libsrc/stlgeom/libstl.la --# $(top_builddir)/libsrc/geom2d/libgeom2d.la --# $(top_builddir)/libsrc/geom2d/libgeom2dvis.la -+netgen_LDADD = $(top_builddir)/libsrc/visualization/libngvisual.la \ -+ $(top_builddir)/libsrc/csg/libngcsgvis.la \ -+ $(top_builddir)/libsrc/csg/libngcsg.la \ -+ $(top_builddir)/libsrc/interface/libnginterface.la \ -+ $(top_builddir)/libsrc/meshing/libngmesh.la \ -+ $(top_builddir)/libsrc/occ/libngoccvis.la \ -+ $(top_builddir)/libsrc/occ/libngocc.la \ -+ $(top_builddir)/libsrc/stlgeom/libngstlvis.la \ -+ $(top_builddir)/libsrc/stlgeom/libngstl.la \ -+ $(top_builddir)/libsrc/geom2d/libnggeom2d.la \ -+ $(top_builddir)/libsrc/geom2d/libnggeom2dvis.la \ -+ -L$(TK_BIN_DIR)/Togl1.7 $(TOGLLIBDIR) -lTogl1.7 -ldl -lX11 $(LIBGLU) $(TK_LIB_SPEC) $(TCL_LIB_SPEC) $(MPI_LIBS) $(FFMPEG_LIBS) $(JPEGLIB_LIBS) $(PKG_LIBS) $(MKL_LIBS) - - - # add for static linkage of ngsolve: -diff -uwrN -x.git netgen-5.3.1/ng/Makefile.in netgen/ng/Makefile.in ---- netgen-5.3.1/ng/Makefile.in 2016-02-21 21:40:41.856331653 +0100 -+++ netgen/ng/Makefile.in 2016-02-21 21:39:31.361329711 +0100 -@@ -302,7 +302,7 @@ - include_HEADERS = - AM_CPPFLAGS = -I$(top_srcdir)/libsrc/include \ - -I$(top_srcdir)/libsrc/interface -DOPENGL \ -- -D$(TOGL_WINDOWINGSYSTEM) $(TCL_INCLUDES) $(MPI_INCLUDES) \ -+ $(TCL_INCLUDES) $(MPI_INCLUDES) \ - $(FFMPEG_INCLUDES) $(JPEGLIB_INCLUDES) $(am__append_1) - netgen_SOURCES = demoview.cpp ngappinit.cpp onetcl.cpp parallelfunc.cpp ngpkg.cpp demoview.hpp parallelfunc.hpp togl_1_7.h - @NGMKL_TRUE@MKL_LIBS = -L$(MKLROOT)/lib/intel64 -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lmkl_def -diff -uwrN -x.git netgen-5.3.1/nglib/Makefile.am netgen/nglib/Makefile.am ---- netgen-5.3.1/nglib/Makefile.am 2016-02-21 21:40:41.856331653 +0100 -+++ netgen/nglib/Makefile.am 2016-02-21 21:39:31.362329711 +0100 -@@ -8,15 +8,15 @@ - libnglib_la_SOURCES = nglib.cpp - - libnglib_la_LIBADD = \ -- $(top_builddir)/libsrc/interface/libinterface.la \ -- $(top_builddir)/libsrc/geom2d/libgeom2d.la \ -- $(top_builddir)/libsrc/csg/libcsg.la \ -- $(top_builddir)/libsrc/stlgeom/libstl.la \ -- $(top_builddir)/libsrc/occ/libocc.la \ -- $(top_builddir)/libsrc/meshing/libmesh.la \ -+ $(top_builddir)/libsrc/interface/libnginterface.la \ -+ $(top_builddir)/libsrc/geom2d/libnggeom2d.la \ -+ $(top_builddir)/libsrc/csg/libngcsg.la \ -+ $(top_builddir)/libsrc/stlgeom/libngstl.la \ -+ $(top_builddir)/libsrc/occ/libngocc.la \ -+ $(top_builddir)/libsrc/meshing/libngmesh.la \ - $(OCCLIBS) $(MPI_LIBS) - --libnglib_la_LDFLAGS = -avoid-version -+libnglib_la_LDFLAGS = -release $(PACKAGE_VERSION) - # -rdynamic - - -@@ -25,24 +25,24 @@ - - ng_vol_SOURCES = ng_vol.cpp - ng_vol_LDADD = libnglib.la \ -- $(top_builddir)/libsrc/interface/libinterface.la \ -- $(top_builddir)/libsrc/geom2d/libgeom2d.la \ -- $(top_builddir)/libsrc/csg/libcsg.la \ -- $(top_builddir)/libsrc/stlgeom/libstl.la \ -- $(top_builddir)/libsrc/occ/libocc.la \ -- $(top_builddir)/libsrc/meshing/libmesh.la \ -+ $(top_builddir)/libsrc/interface/libnginterface.la \ -+ $(top_builddir)/libsrc/geom2d/libnggeom2d.la \ -+ $(top_builddir)/libsrc/csg/libngcsg.la \ -+ $(top_builddir)/libsrc/stlgeom/libngstl.la \ -+ $(top_builddir)/libsrc/occ/libngocc.la \ -+ $(top_builddir)/libsrc/meshing/libngmesh.la \ - $(OCCLIBS) $(MPI_LIBS) - - - - ng_stl_SOURCES = ng_stl.cpp - ng_stl_LDADD = libnglib.la \ -- $(top_builddir)/libsrc/interface/libinterface.la \ -- $(top_builddir)/libsrc/geom2d/libgeom2d.la \ -- $(top_builddir)/libsrc/csg/libcsg.la \ -- $(top_builddir)/libsrc/stlgeom/libstl.la \ -- $(top_builddir)/libsrc/occ/libocc.la \ -- $(top_builddir)/libsrc/meshing/libmesh.la \ -+ $(top_builddir)/libsrc/interface/libnginterface.la \ -+ $(top_builddir)/libsrc/geom2d/libnggeom2d.la \ -+ $(top_builddir)/libsrc/csg/libngcsg.la \ -+ $(top_builddir)/libsrc/stlgeom/libngstl.la \ -+ $(top_builddir)/libsrc/occ/libngocc.la \ -+ $(top_builddir)/libsrc/meshing/libngmesh.la \ - $(OCCLIBS) $(MPI_LIBS) - - # ng_occ_SOURCES = ng_occ.cpp diff --git a/sci-mathematics/netgen/files/netgen-5.x-metis-fixes.patch b/sci-mathematics/netgen/files/netgen-5.x-metis-fixes.patch deleted file mode 100644 index cf59613e4..000000000 --- a/sci-mathematics/netgen/files/netgen-5.x-metis-fixes.patch +++ /dev/null @@ -1,102 +0,0 @@ ---- netgen-5.3.1.ORIG/libsrc/meshing/parallelmesh.cpp 2014-08-29 11:54:05.000000000 +0200 -+++ netgen/libsrc/meshing/parallelmesh.cpp 2016-02-20 23:07:00.350568182 +0100 -@@ -14,7 +14,7 @@ - - #if METIS_VER_MAJOR >= 5 - #define METIS5 -- typedef idx_t idxtype; -+ typedef metis::idx_t idxtype; - #else - #define METIS4 - typedef idxtype idx_t; -@@ -794,10 +794,10 @@ - eptr.Append (eind.Size()); - Array<idx_t> epart(ne), npart(nn); - -- int nparts = ntasks-1; -- int edgecut; -+ metis::idx_t nparts = ntasks-1; -+ metis::idx_t edgecut; - -- int ncommon = 3; -+ metis::idx_t ncommon = 3; - METIS_PartMeshDual (&ne, &nn, &eptr[0], &eind[0], NULL, NULL, &ncommon, &nparts, - NULL, NULL, - &edgecut, &epart[0], &npart[0]); -@@ -1029,11 +1029,11 @@ - eptr.Append (eind.Size()); - Array<idx_t> epart(ne), npart(nn); - -- int nparts = ntasks-1; -- int edgecut; -+ metis::idx_t nparts = ntasks-1; -+ metis::idx_t edgecut; - - -- int ncommon = 3; -+ metis::idx_t ncommon = 3; - METIS_PartMeshDual (&ne, &nn, &eptr[0], &eind[0], &nwgt[0], NULL, &ncommon, &nparts, - NULL, NULL, - &edgecut, &epart[0], &npart[0]); -@@ -1266,7 +1266,7 @@ - - for ( int vert = 0; vert < nn; vert++ ) - { -- FlatArray<int> array ( cnt[vert], &adjacency[ xadj[vert] ] ); -+ FlatArray<metis::idx_t> array ( cnt[vert], &adjacency[ xadj[vert] ] ); - BubbleSort(array); - } - -@@ -1318,7 +1318,7 @@ - idxtype *xadj, * adjacency, *v_weights = NULL, *e_weights = NULL; - - int weightflag = 0; -- // int numflag = 0; -+ int numflag = 0; - int nparts = ntasks - 1; - - int options[5]; -@@ -1377,7 +1377,7 @@ - - for ( int el = 0; el < ne; el++ ) - { -- FlatArray<int> array ( cnt[el], &adjacency[ xadj[el] ] ); -+ FlatArray<metis::idx_t> array ( cnt[el], &adjacency[ xadj[el] ] ); - BubbleSort(array); - } - -@@ -1428,8 +1428,8 @@ - void Mesh :: PartDualHybridMesh2D ( ) - { - #ifdef METIS -- int ne = GetNSE(); -- int nv = GetNV(); -+ metis::idx_t ne = GetNSE(); -+ metis::idx_t nv = GetNV(); - - Array<idxtype> xadj(ne+1); - Array<idxtype> adjacency(ne*4); -@@ -1484,18 +1484,18 @@ - - idxtype *v_weights = NULL, *e_weights = NULL; - -- int weightflag = 0; -- // int numflag = 0; -- int nparts = ntasks - 1; -+ metis::idx_t weightflag = 0; -+ metis::idx_t numflag = 0; -+ metis::idx_t nparts = ntasks - 1; - -- int edgecut; -+ metis::idx_t edgecut; - Array<idxtype> part(ne); - - for ( int el = 0; el < ne; el++ ) - BubbleSort (adjacency.Range (xadj[el], xadj[el+1])); - - #ifdef METIS4 -- int options[5]; -+ metis::idx_t options[5]; - options[0] = 0; - METIS_PartGraphKway ( &ne, &xadj[0], &adjacency[0], v_weights, e_weights, &weightflag, - &numflag, &nparts, options, &edgecut, &part[0] ); diff --git a/sci-mathematics/netgen/files/netgen-5.x-missing-define.patch b/sci-mathematics/netgen/files/netgen-5.x-missing-define.patch deleted file mode 100644 index d9d8f99ef..000000000 --- a/sci-mathematics/netgen/files/netgen-5.x-missing-define.patch +++ /dev/null @@ -1,38 +0,0 @@ ---- a/libsrc/occ/Partition_Loop2d.cxx 2012-11-14 21:16:22.876287910 +0100 -+++ b/libsrc/occ/Partition_Loop2d.cxx 2012-11-14 21:22:30.909650554 +0100 -@@ -13,6 +13,7 @@ - - //using namespace std; - #include <climits> -+#include <cmath> - #include "Partition_Loop2d.ixx" - - #include "utilities.h" -@@ -210,7 +211,7 @@ - Cc->D1(uc, PC, CTg1); - if (!isForward) CTg1.Reverse(); - -- Standard_Real anglemin = 3 * PI, tolAng = 1.e-8; -+ Standard_Real anglemin = 3 * M_PI, tolAng = 1.e-8; - - // select an edge whose first derivative is most left of CTg1 - // ie an angle between Tg1 and CTg1 is least -@@ -234,7 +235,7 @@ - // -PI < angle < PI - Standard_Real angle = Tg1.Angle(CTg1); - -- if (PI - Abs(angle) <= tolAng) -+ if (M_PI - Abs(angle) <= tolAng) - { - // an angle is too close to PI; assure that an angle sign really - // reflects an edge position: +PI - an edge is worst, ---- a/configure.ac 2012-11-15 14:55:45.048938870 +0100 -+++ b/configure.ac 2012-11-15 14:55:12.545923777 +0100 -@@ -14,6 +14,7 @@ - AC_DISABLE_STATIC - - AC_LANG([C++]) -+AM_PROG_AR - AC_PROG_CXX - AC_PROG_LIBTOOL - LT_INIT diff --git a/sci-mathematics/netgen/files/netgen-5.x-occ-stl-api-change.patch b/sci-mathematics/netgen/files/netgen-5.x-occ-stl-api-change.patch deleted file mode 100644 index 0452d6b73..000000000 --- a/sci-mathematics/netgen/files/netgen-5.x-occ-stl-api-change.patch +++ /dev/null @@ -1,94 +0,0 @@ ---- a/libsrc/occ/occgeom.cpp 2014-08-29 11:54:03.000000000 +0200 -+++ b/libsrc/occ/occgeom.cpp 2016-02-12 21:14:49.258982206 +0100 -@@ -149,7 +149,7 @@ -
- for (exp0.Init (shape, TopAbs_FACE); exp0.More(); exp0.Next())
- {
-- // Variable to hold the colour (if there exists one) of
-+ // Variable to hold the colour (if there exists one) of
- // the current face being processed
- Quantity_Color face_colour;
-
-@@ -190,7 +190,7 @@ - rebuild->Replace(face, newface, Standard_False);
- }
-
-- // Set the original colour of the face to the newly created
-+ // Set the original colour of the face to the newly created
- // face (after the healing process)
- face = TopoDS::Face (exp0.Current());
- face_colours->SetColor(face,face_colour,XCAFDoc_ColorSurf);
-@@ -815,11 +815,11 @@ - face_maxh.SetSize (fmap.Extent());
- face_maxh = mparam.maxh;
-
-- // Philippose - 15/01/2010
-- face_maxh_modified.DeleteAll();
-- face_maxh_modified.SetSize(fmap.Extent());
-+ // Philippose - 15/01/2010
-+ face_maxh_modified.DeleteAll();
-+ face_maxh_modified.SetSize(fmap.Extent());
- face_maxh_modified = 0;
--
-+
-
- // Philippose - 17/01/2009
- face_sel_status.DeleteAll();
-@@ -845,7 +845,7 @@ - cout << "Trying to sew faces ..." << flush;
-
- BRepOffsetAPI_Sewing sewedObj(1);
--
-+
- for (int i = 1; i <= fmap.Extent(); i++)
- {
- TopoDS_Face face = TopoDS::Face (fmap(i));
-@@ -1038,9 +1038,6 @@ - {
- cout << "writing stl..."; cout.flush();
- StlAPI_Writer writer;
-- writer.RelativeMode() = Standard_False;
--
-- writer.SetDeflection(0.02);
- writer.Write(shape,filename);
-
- cout << "done" << endl;
-@@ -1109,7 +1106,7 @@ - }
-
-
-- // For the IGES Reader, all the shapes can be exported as one compund shape
-+ // For the IGES Reader, all the shapes can be exported as one compund shape
- // using the "OneShape" member
- occgeo->shape = reader.OneShape();
- occgeo->face_colours = iges_colour_contents;
-@@ -1187,7 +1184,7 @@ - }
-
-
-- // For the STEP File Reader in OCC, the 1st Shape contains the entire
-+ // For the STEP File Reader in OCC, the 1st Shape contains the entire
- // compound geometry as one shape
- occgeo->shape = step_shape_contents->GetShape(step_shapes.Value(1));
- occgeo->face_colours = step_colour_contents;
-@@ -1218,7 +1215,7 @@ - }
-
- // Philippose - 23/02/2009
-- // Fixed a bug in the OpenCascade XDE Colour handling when
-+ // Fixed a bug in the OpenCascade XDE Colour handling when
- // opening BREP Files, since BREP Files have no colour data.
- // Hence, the face_colours Handle needs to be created as a NULL handle.
- occgeo->face_colours = Handle_XCAFDoc_ColorTool();
-@@ -1236,9 +1233,9 @@ - void OCCGeometry :: Save (string sfilename) const
- {
- const char * filename = sfilename.c_str();
-- if (strlen(filename) < 4)
-+ if (strlen(filename) < 4)
- throw NgException ("illegal filename");
--
-+
- if (strcmp (&filename[strlen(filename)-3], "igs") == 0)
- {
- IGESControl_Writer writer("millimeters", 1);
diff --git a/sci-mathematics/netgen/files/netgen-5.x-parallelmetis4-fix.patch b/sci-mathematics/netgen/files/netgen-5.x-parallelmetis4-fix.patch deleted file mode 100644 index 0170fb8c3..000000000 --- a/sci-mathematics/netgen/files/netgen-5.x-parallelmetis4-fix.patch +++ /dev/null @@ -1,36 +0,0 @@ -diff -uwrN -x.git netgen-5.3.1/libsrc/meshing/parallelmesh.cpp netgen/libsrc/meshing/parallelmesh.cpp ---- netgen-5.3.1/libsrc/meshing/parallelmesh.cpp 2016-02-22 00:22:28.885598956 +0100 -+++ netgen/libsrc/meshing/parallelmesh.cpp 2016-02-22 00:46:17.030638283 +0100 -@@ -962,10 +962,15 @@ - } - - --#ifdef METIS5 -+#ifdef METIS - void Mesh :: ParallelMetis (Array<int> & volume_weights , Array<int> & surface_weights, Array<int> & segment_weights) - { -+ -+ #ifdef METIS5 - PrintMessage (3, "call metis 5 with weights ..."); -+ #else -+ PrintMessage (3, "call metis 4 with weights ..."); -+ #endif - - // cout << "segment_weights " << segment_weights << endl; - // cout << "surface_weights " << surface_weights << endl; -@@ -1034,9 +1039,15 @@ - - - metis::idx_t ncommon = 3; -+ #ifdef METIS5 - METIS_PartMeshDual (&ne, &nn, &eptr[0], &eind[0], &nwgt[0], NULL, &ncommon, &nparts, - NULL, NULL, - &edgecut, &epart[0], &npart[0]); -+ #else -+ int numflag = 0; -+ METIS_PartMeshDual (&ne, &nn, &eptr[0], &eind[0], &numflag, &nparts, -+ &edgecut, &epart[0], &npart[0]); -+ #endif - /* - METIS_PartMeshNodal (&ne, &nn, &eptr[0], &eind[0], NULL, NULL, &nparts, - NULL, NULL, diff --git a/sci-mathematics/netgen/files/netgen.desktop b/sci-mathematics/netgen/files/netgen.desktop deleted file mode 100644 index 714ba53c4..000000000 --- a/sci-mathematics/netgen/files/netgen.desktop +++ /dev/null @@ -1,8 +0,0 @@ -[Desktop Entry] -Name=Netgen -Comment=3D modeling, Mesh generation. -Exec=/usr/bin/netgen -Icon=netgen -Terminal=false -Type=Application -Categories=Graphics; diff --git a/sci-mathematics/netgen/files/netgen.png b/sci-mathematics/netgen/files/netgen.png Binary files differdeleted file mode 100644 index cb2fd8466..000000000 --- a/sci-mathematics/netgen/files/netgen.png +++ /dev/null diff --git a/sci-mathematics/netgen/metadata.xml b/sci-mathematics/netgen/metadata.xml deleted file mode 100644 index a2cd926a4..000000000 --- a/sci-mathematics/netgen/metadata.xml +++ /dev/null @@ -1,14 +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="opencascade"> Enable OpenCASCADE support</flag> - </use> - <upstream> - <remote-id type="sourceforge">netgen-mesher</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/netgen/netgen-4.9.13.ebuild b/sci-mathematics/netgen/netgen-4.9.13.ebuild deleted file mode 100644 index ef4f19b3e..000000000 --- a/sci-mathematics/netgen/netgen-4.9.13.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic multilib versionator - -DESCRIPTION="Automatic 3d tetrahedral mesh generator" -HOMEPAGE="http://www.hpfem.jku.at/netgen/" -SRC_URI="mirror://sourceforge/netgen-mesher/${P}.tar.gz" - -SLOT="0" -LICENSE="LGPL-2.1" -KEYWORDS="~amd64 ~x86" -IUSE="-ffmpeg jpeg -mpi opencascade" - -DEPEND=" - dev-tcltk/tix - dev-tcltk/togl:1.7 - virtual/opengl - x11-libs/libXmu - opencascade? ( sci-libs/opencascade:* ) - ffmpeg? ( media-video/ffmpeg ) - jpeg? ( virtual/jpeg:0= ) - mpi? ( virtual/mpi ) " -RDEPEND="${DEPEND}" -# Note, MPI has not be tested. - -src_configure() { - # This is not the most clever way to deal with these flags - # but --disable-xxx does not seem to work correcly, so... - local myconf="--with-togl=/usr/$(get_libdir)/Togl1.7" - - if use opencascade; then - myconf="${myconf} --enable-occ --with-occ=$CASROOT" - append-ldflags -L$CASROOT/lin/$(get_libdir) - fi - - use mpi && myconf="${myconf} --enable-parallel" - use ffmpeg && myconf="${myconf} --enable-ffmpeg" - use jpeg && myconf="${myconf} --enable-jpeglib" - - append-flags -I/usr/include/togl-1.7 - - econf \ - ${myconf} - - # This would be the more elegant way: -# econf \ -# $(use_enable opencascade occ) \ -# $(use_with opencascade "occ=$CASROOT") \ -# $(use_enable mpi parallel) \ -# $(use_enable ffmpeg) \ -# $(use_enable jpeg jpeglib) -} - -src_install() { - local NETGENDIR="/usr/share/netgen" - - echo -e "NETGENDIR=${NETGENDIR} \nLDPATH=/usr/$(get_libdir)/Togl1.7" > ./99netgen - doenvd 99netgen - - default - mv "${D}"/usr/bin/{*.tcl,*.ocf} "${D}${NETGENDIR}" - - # Install icon and .desktop for menu entry - doicon "${FILESDIR}"/${PN}.png - domenu "${FILESDIR}"/${PN}.desktop -} - -pkg_postinst() { - elog "Please make sure to update your environment variables:" - elog "env-update && source /etc/profile" - elog "Netgen ebuild is still under development." - elog "Help us improve the ebuild in:" - elog "http://bugs.gentoo.org/show_bug.cgi?id=155424" -} diff --git a/sci-mathematics/netgen/netgen-5.0.0.ebuild b/sci-mathematics/netgen/netgen-5.0.0.ebuild deleted file mode 100644 index 2e5d37fde..000000000 --- a/sci-mathematics/netgen/netgen-5.0.0.ebuild +++ /dev/null @@ -1,88 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit autotools eutils flag-o-matic multilib versionator - -MY_PN=${PN}-mesher -MY_PV=$(get_version_component_range 1-2) -DESCRIPTION="NETGEN is an automatic 3d tetrahedral mesh generator" -HOMEPAGE="http://www.hpfem.jku.at/netgen/" -SRC_URI="mirror://sourceforge/project/${MY_PN}/${MY_PN}/${MY_PV}/${P}.tar.gz" - -SLOT="0" -LICENSE="LGPL-2.1" -KEYWORDS="~amd64 ~x86" -IUSE="-ffmpeg jpeg -mpi opencascade" - -DEPEND=" - dev-tcltk/tix - dev-tcltk/togl:1.7 - virtual/opengl - x11-libs/libXmu - opencascade? ( sci-libs/opencascade:* ) - ffmpeg? ( media-video/ffmpeg ) - jpeg? ( virtual/jpeg:0= ) - mpi? ( virtual/mpi ( || ( sci-libs/parmetis sci-libs/metis ) ) ) " -RDEPEND="${DEPEND}" -# Note, MPI has not be tested. - -src_prepare() { - # Adapted from http://sourceforge.net/projects/netgen-mesher/forums/forum/905307/topic/5422824 - epatch "${FILESDIR}/${PN}-5.x-compile-against-occ-6.5.x.patch" - epatch "${FILESDIR}/${PN}-5.x-missing-define.patch" - eautoreconf -} - -src_configure() { - # This is not the most clever way to deal with these flags - # but --disable-xxx does not seem to work correcly, so... - sed -i -e 's:-lTogl:-lTogl1.7:' ng/Makefile.am || die - local myconf="--with-togl=/usr/$(get_libdir)/Togl1.7" - - if use opencascade; then - myconf="${myconf} --enable-occ --with-occ=$CASROOT" - append-ldflags -L$CASROOT/lin/$(get_libdir) - fi - if use mpi; then - myconf="${myconf} --enable-parallel" - append-cppflags -I/usr/include/metis - fi - use ffmpeg && myconf="${myconf} --enable-ffmpeg" - use jpeg && myconf="${myconf} --enable-jpeglib" - append-cppflags -I/usr/include/togl-1.7 - - econf \ - ${myconf} - - # This would be the more elegant way: -# econf \ -# $(use_enable opencascade occ) \ -# $(use_with opencascade "occ=$CASROOT") \ -# $(use_enable mpi parallel) \ -# $(use_enable ffmpeg) \ -# $(use_enable jpeg jpeglib) -} - -src_install() { - local NETGENDIR="/usr/share/netgen" - - echo -e "NETGENDIR=${NETGENDIR} \nLDPATH=/usr/$(get_libdir)/Togl1.7" > ./99netgen - doenvd 99netgen - - default - mv "${D}"/usr/bin/{*.tcl,*.ocf} "${D}${NETGENDIR}" || die - - # Install icon and .desktop for menu entry - doicon "${FILESDIR}"/${PN}.png - domenu "${FILESDIR}"/${PN}.desktop -} - -pkg_postinst() { - elog "Please make sure to update your environment variables:" - elog "env-update && source /etc/profile" - elog "Netgen ebuild is still under development." - elog "Help us improve the ebuild in:" - elog "http://bugs.gentoo.org/show_bug.cgi?id=155424" -} diff --git a/sci-mathematics/netgen/netgen-5.3.1.ebuild b/sci-mathematics/netgen/netgen-5.3.1.ebuild deleted file mode 100644 index 4dd089d1a..000000000 --- a/sci-mathematics/netgen/netgen-5.3.1.ebuild +++ /dev/null @@ -1,119 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools eutils flag-o-matic multilib versionator - -MY_PN=${PN}-mesher -MY_PV=$(get_version_component_range 1-2) -DESCRIPTION="Automatic 3d tetrahedral mesh generator" -HOMEPAGE="http://www.hpfem.jku.at/netgen/" -SRC_URI="mirror://sourceforge/project/${MY_PN}/${MY_PN}/${MY_PV}/${P}.tar.gz" - -SLOT="0" -LICENSE="LGPL-2.1" -KEYWORDS="~amd64 ~x86" -IUSE="-ffmpeg jpeg -mpi opencascade openmp" - -DEPEND=" - dev-lang/tcl:0 - dev-lang/tk:0 - dev-tcltk/tix - dev-tcltk/togl:1.7 - virtual/opengl - x11-libs/libX11 - x11-libs/libXmu - opencascade? ( sci-libs/opencascade:* ) - ffmpeg? ( media-video/ffmpeg ) - jpeg? ( virtual/jpeg:0= ) - mpi? ( virtual/mpi || ( sci-libs/parmetis <sci-libs/metis-5.0 ) opencascade? ( sci-libs/hdf5[mpi] ) ) " -RDEPEND="${DEPEND}" -# Note, MPI has not be tested. - -PATCHES=( - # Adapted from http://sourceforge.net/projects/netgen-mesher/forums/forum/905307/topic/5422824 - "${FILESDIR}"/${PN}-5.x-missing-define.patch - # Adapted from http://pkgs.fedoraproject.org/cgit/rpms/netgen-mesher.git/tree/netgen-5.3.0_metis.patch - "${FILESDIR}"/${PN}-5.x-metis-fixes.patch - "${FILESDIR}"/${PN}-5.x-occ-stl-api-change.patch - # Adapted from http://pkgs.fedoraproject.org/cgit/rpms/netgen-mesher.git/tree/netgen-5.3.1_build.patch - "${FILESDIR}"/${PN}-5.x-makefiles-fixes.patch - # Adapted from http://pkgs.fedoraproject.org/cgit/rpms/netgen-mesher.git/tree/netgen-5.3.0_fixes.patch - "${FILESDIR}"/${PN}-5.x-fedora-fixes.patch - "${FILESDIR}"/${PN}-5.x-includes-fixes.patch - "${FILESDIR}"/${PN}-5.x-parallelmetis4-fix.patch -) - -src_prepare() { - default - if use mpi; then - export CC=mpicc - export CXX=mpic++ - export FC=mpif90 - export F90=mpif90 - export F77=mpif77 - fi - eautoreconf -} - -src_configure() { - # This is not the most clever way to deal with these flags - # but --disable-xxx does not seem to work correcly, so... - local myconf=( --with-togl=/usr/$(get_libdir)/Togl1.7 ) - - myconf+=( $(use_enable openmp) ) - - if use opencascade; then - myconf+=( --enable-occ --with-occ=$CASROOT ) - append-ldflags -L$CASROOT/$(get_libdir) - fi - if use mpi; then - ewarn "*************************************************************************" - ewarn "" - ewarn "MPI has not been tested, you should probably deactivate the mpi use flag" - ewarn "" - ewarn "*************************************************************************" - myconf+=( --enable-parallel ) - append-cppflags -I/usr/include/metis - append-ldflags -L/usr/$(get_libdir)/openmpi/ - fi - use ffmpeg && myconf+=( --enable-ffmpeg ) - use jpeg && myconf+=( --enable-jpeglib ) - append-cppflags -I/usr/include/togl-1.7 - - econf \ - ${myconf[@]} - - # This would be the more elegant way: -# econf \ -# $(use_enable opencascade occ) \ -# $(use_with opencascade "occ=$CASROOT") \ -# $(use_enable mpi parallel) \ -# $(use_enable ffmpeg) \ -# $(use_enable jpeg jpeglib) -} - -src_install() { - local NETGENDIR="/usr/share/netgen" - - echo -e "NETGENDIR=${NETGENDIR} \nLDPATH=/usr/$(get_libdir)/Togl1.7" > ./99netgen - doenvd 99netgen - - default - mv "${D}"/usr/bin/{*.tcl,*.ocf} "${D}${NETGENDIR}" || die - - # Install icon and .desktop for menu entry - doicon "${FILESDIR}"/${PN}.png - domenu "${FILESDIR}"/${PN}.desktop - - prune_libtool_files -} - -pkg_postinst() { - elog "Please make sure to update your environment variables:" - elog "env-update && source /etc/profile" - elog "Netgen ebuild is still under development." - elog "Help us improve the ebuild in:" - elog "http://bugs.gentoo.org/show_bug.cgi?id=155424" -} diff --git a/sci-mathematics/open-axiom/Manifest b/sci-mathematics/open-axiom/Manifest deleted file mode 100644 index a0dc72105..000000000 --- a/sci-mathematics/open-axiom/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST open-axiom-1.4.2.tar.bz2 9862899 BLAKE2B 998961529a9cd632bca0c82b0575ec5f24260e896ef4b74d54160242a7b033680b990a3cf8fa3e4182c27d9bbe998f697bb9c1b47050c2101ab30c62f56e3fe1 SHA512 7db25874c9427e0fe5903f3d9e8ef8d265f132bf839e184efa290795f65b8f1752e8ffd0602142c2260404d79e30793b1cd37a2a25db4a4258d7b7682b8acc1a diff --git a/sci-mathematics/open-axiom/metadata.xml b/sci-mathematics/open-axiom/metadata.xml deleted file mode 100644 index c9b1f5cd4..000000000 --- a/sci-mathematics/open-axiom/metadata.xml +++ /dev/null @@ -1,17 +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> - <longdescription lang="en"> -OpenAxiom is an open source platform for symbolic, algebraic, and -numerical computations. It offers an interactive environment, an expressive -programming language, a compiler, a large set of mathematical libraries of -interest to researchers and practitioners of computational sciences. -</longdescription> - <upstream> - <remote-id type="sourceforge">open-axiom</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/open-axiom/open-axiom-1.4.2.ebuild b/sci-mathematics/open-axiom/open-axiom-1.4.2.ebuild deleted file mode 100644 index 402e19eb2..000000000 --- a/sci-mathematics/open-axiom/open-axiom-1.4.2.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -DESCRIPTION="Symbolic and algebraic computations system" -HOMEPAGE="http://www.open-axiom.org/" -SRC_URI="mirror://sourceforge/project/${PN}/${PV}/${P}.tar.bz2" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="" - -IUSE="X" - -RDEPEND="X? ( x11-libs/libXpm )" -DEPEND="${RDEPEND} - app-text/noweb - >=dev-lisp/sbcl-1.0.22" - -DOCS="MAINTAINERS TODO STYLES" - -src_configure() { - # There is an option to compile with other lisps. However: - # - gcl is getting obsolete and unmaintained and is hard masked - # - could not make it work with ecls - econf \ - --with-lisp=sbcl \ - $(use_with X x) -} - -src_compile() { - # unfortunately could not track down the broken parallel build - # -j5 ok but -j30 sbcl stalled - emake -j1 -} diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest deleted file mode 100644 index d4dff3c12..000000000 --- a/sci-mathematics/petsc/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST petsc-3.10.0.tar.gz 30850631 BLAKE2B 597f2d428f98b785b13b4819dfffe249401ba630873b75f2f65672126affc0f68b387f67dfd53e8a666e6b7fdeee50de1cf35c4934bcf3afc8053382b4874b0f SHA512 67c657dcbb84d8ede391846d0d79f4f312b770c691438b9909a26cfae119629599079c7f6b60a7ff3766be8335c2cede67ea6368949337fd1c5f12cb4f575aa2 -DIST petsc-3.10.4.tar.gz 31115815 BLAKE2B 772943d19acbeb95798d48244a2a2591391a0ac2cf912042b1841e9e62e84f1747b83fde4eabf36df3db88d50ea5164e9cdca1bec7775a4d40936a8b5d03da6e SHA512 f62915bda21b0fef4d4fa5ff6cf1d9607739caad466c97fd4694584ad7e5281442728777b3e63e0c8a37108134f929aff8e1f550993a93910ade25f6dd983466 -DIST petsc-3.8.4.tar.gz 27946435 BLAKE2B c4d71439695855bce0b6bd46ad434142adc9fd7a0d0b899fa5f02b9fefd65926470db02dfe250376416000031b54c230d338d3085472bad3d61a61b9f30f0713 SHA512 c186e143619c12d2175d01046c26221c462091706af0b68515ba1d2c93f97738ec375df7aa0551c5a14c240e80ca744f9d796778f4937a8c8021d64abe1f3b2c -DIST petsc-3.9.4.tar.gz 29400362 BLAKE2B 702dc05c65805e485713289b66561aaf3fc17131f03c58639f7d676cc026b4143f89ff23c58b196ff0817f1207f379e087992475b4ef5d0eac5a049c4c21448f SHA512 daca9d3ecb9f599988c954ce079f8d6b940f48cef5fcdc56b497e67b1226fc7eb70424eb4696ac90f7b9e75967653967702ce8c7f8b0f906328386697121aa9e diff --git a/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch deleted file mode 100644 index 8d0d99330..000000000 --- a/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py -index 219a35b..ad2ed8c 100644 ---- a/config/BuildSystem/config/setCompilers.py -+++ b/config/BuildSystem/config/setCompilers.py -@@ -1385,12 +1385,7 @@ class Configure(config.base.Configure): - for language in languages: - flag = '-L' - self.pushLanguage(language) -- # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options. -- if not Configure.isDarwin(self.log): -- testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,'] -- else: -- testFlags = ['-Wl,-rpath,'] -- # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but f90 & CC do not. -+ testFlags = [] - if self.isSun(self.framework.getCompiler(), self.log): - testFlags.insert(0,'-R') - for testFlag in testFlags: diff --git a/sci-mathematics/petsc/files/petsc-3.8.3-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.8.3-fix_sandbox_violation.patch deleted file mode 100644 index 4f51aee81..000000000 --- a/sci-mathematics/petsc/files/petsc-3.8.3-fix_sandbox_violation.patch +++ /dev/null @@ -1,17 +0,0 @@ -diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py -index 975dc8a..c216941 100644 ---- a/config/PETSc/options/installDir.py -+++ b/config/PETSc/options/installDir.py -@@ -39,12 +39,6 @@ class Configure(config.base.Configure): - if self.framework.argDB['prefix']: - self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix'])) - self.addMakeMacro('PREFIXDIR',self.dir) -- try: -- os.makedirs(os.path.join(self.dir,'PETScTestDirectory')) -- os.rmdir(os.path.join(self.dir,'PETScTestDirectory')) -- except: -- self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs' -- self.installSudo = 'sudo ' - else: - self.dir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) - self.confDir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) diff --git a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch deleted file mode 100644 index 97f8dfed4..000000000 --- a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch +++ /dev/null @@ -1,17 +0,0 @@ -diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py -index 92f190d..047c85b 100644 ---- a/config/PETSc/options/installDir.py -+++ b/config/PETSc/options/installDir.py -@@ -41,12 +41,6 @@ class Configure(config.base.Configure): - self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix'])) - self.petscDir = self.dir - self.petscArch = '' -- try: -- os.makedirs(os.path.join(self.dir,'PETScTestDirectory')) -- os.rmdir(os.path.join(self.dir,'PETScTestDirectory')) -- except: -- self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs' -- self.installSudo = 'sudo ' - else: - self.dir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) - self.petscDir = self.petscdir.dir diff --git a/sci-mathematics/petsc/metadata.xml b/sci-mathematics/petsc/metadata.xml deleted file mode 100644 index 8c9c01d83..000000000 --- a/sci-mathematics/petsc/metadata.xml +++ /dev/null @@ -1,23 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>tamiko@gentoo.org</email> - <name>Matthias Maier</name> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <use> - <flag name="afterimage">Use Afterstep image library (media-libs/libafterimage)</flag> - <flag name="boost">Use boost (dev-libs/boost)</flag> - <flag name="hypre">Use HYPRE (sci-mathematics/hypre) and for preconditioning</flag> - <flag name="complex-scalars">Make scalars complex</flag> - <flag name="metis">Add support for metis (<pkg>sci-libs/parmetis</pkg>)</flag> - <flag name="sparse">Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization</flag> - <flag name="superlu">Use superlu (sci-libs/superlu) for preconditioning</flag> - <flag name="mumps">Add support for mumps (<pkg>sci-libs/mumps</pkg>)</flag> - <flag name="scotch">Add support for scotch (<pkg>sci-libs/scotch</pkg>)</flag> - </use> -</pkgmetadata> diff --git a/sci-mathematics/petsc/petsc-3.10.0.ebuild b/sci-mathematics/petsc/petsc-3.10.0.ebuild deleted file mode 100644 index b67536ef6..000000000 --- a/sci-mathematics/petsc/petsc-3.10.0.ebuild +++ /dev/null @@ -1,196 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator - -MY_P="${PN}-$(replace_version_separator _ -)" - -DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation" -HOMEPAGE="http://www.mcs.anl.gov/petsc/" -SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="afterimage boost complex-scalars cxx debug doc fftw - fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X" - -# hypre and superlu curretly exclude each other due to missing linking to hypre -# if both are enabled -REQUIRED_USE=" - afterimage? ( X ) - complex-scalars? ( !hypre !superlu ) - hdf5? ( mpi ) - hypre? ( cxx mpi !superlu ) - mumps? ( mpi scotch ) - scotch? ( mpi ) - superlu? ( !hypre ) -" - -RDEPEND=" - virtual/blas - virtual/lapack - afterimage? ( media-libs/libafterimage ) - boost? ( dev-libs/boost ) - fftw? ( sci-libs/fftw:3.0[mpi?] ) - hdf5? ( sci-libs/hdf5[mpi?] ) - hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] ) - metis? ( >=sci-libs/parmetis-4 ) - mpi? ( virtual/mpi[cxx?,fortran?] ) - mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack ) - scotch? ( sci-libs/scotch[mpi?] ) - sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 ) - superlu? ( >=sci-libs/superlu-5 ) - X? ( x11-libs/libX11 ) -" - -DEPEND="${RDEPEND} - ${PYTHON_DEPS} - virtual/pkgconfig - dev-util/cmake -" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \ - "${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch -) - -src_prepare() { - default - - sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die -} - -# petsc uses --with-blah=1 and --with-blah=0 to en/disable options -petsc_enable() { - use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0" -} -# add external library: -# petsc_with use_flag libname libdir -# petsc_with use_flag libname include linking_libs -petsc_with() { - local myuse p=${2:-${1}} - if use ${1}; then - myuse="--with-${p}=1" - if [[ $# -ge 4 ]]; then - myuse="${myuse} --with-${p}-include=${EPREFIX}${3}" - shift 3 - myuse="${myuse} --with-${p}-lib=$@" - else - myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}" - fi - else - myuse="--with-${p}=0" - fi - echo ${myuse} -} - -# select between configure options depending on use flag -petsc_select() { - use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4" -} - -src_configure() { - # bug 548498 - # PETSc runs mpi processes during configure that result in a sandbox - # violation by trying to open /proc/mtrr rw. This is not easy to - # mitigate because it happens in libpciaccess.so called by libhwloc.so, - # which is used by libmpi.so. - addpredict /proc/mtrr - # if mpi is built with knem support it needs /dev/knem too - addpredict /dev/knem - - # configureMPITypes with openmpi-2* insists on accessing the scaling - # governor rw. - addpredict /sys/devices/system/cpu/ - - local mylang - local myopt - - use cxx && mylang="cxx" || mylang="c" - use debug && myopt="debug" || myopt="opt" - - # environmental variables expected by petsc during build - - export PETSC_DIR="${S}" - export PETSC_ARCH="linux-gnu-${mylang}-${myopt}" - - if use debug; then - strip-flags - filter-flags -O* - fi - - # C Support on CXX builds is enabled if possible i.e. when not using - # complex scalars (no complex type for both available at the same time) - - econf \ - scrollOutput=1 \ - FFLAGS="${FFLAGS} -fPIC" \ - CFLAGS="${CFLAGS} -fPIC" \ - CXXFLAGS="${CXXFLAGS} -fPIC" \ - LDFLAGS="${LDFLAGS}" \ - --prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \ - --with-shared-libraries \ - --with-single-library \ - --with-clanguage=${mylang} \ - $(use cxx && ! use complex-scalars && echo "with-c-support=1") \ - --with-petsc-arch=${PETSC_ARCH} \ - --with-precision=double \ - --with-gnu-compilers \ - --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \ - $(petsc_enable debug debugging) \ - $(petsc_enable mpi) \ - $(petsc_select mpi cc mpicc $(tc-getCC)) \ - $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \ - $(petsc_enable fortran) \ - $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \ - $(petsc_enable mpi mpi-compilers) \ - $(petsc_select complex-scalars scalar-type complex real) \ - --with-windows-graphics=0 \ - --with-matlab=0 \ - --with-cmake=cmake \ - $(petsc_enable threads pthread) \ - $(petsc_with afterimage afterimage \ - /usr/include/libAfterImage -lAfterImage) \ - $(petsc_with hdf5) \ - $(petsc_with hypre hypre \ - /usr/include/hypre -lHYPRE) \ - $(petsc_with sparse suitesparse) \ - $(petsc_with superlu superlu \ - /usr/include/superlu -lsuperlu) \ - $(petsc_with X x) \ - $(petsc_with X x11) \ - $(petsc_with scotch ptscotch \ - /usr/include/scotch \ - [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \ - $(petsc_with mumps scalapack \ - /usr/include/scalapack -lscalapack) \ - $(petsc_with mumps mumps \ - /usr/include \ - [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \ - --with-imagemagick=0 \ - --with-python=0 \ - $(petsc_with boost) \ - $(petsc_with fftw) -} - -src_install() { - emake DESTDIR="${ED}" install - - # add PETSC_DIR to environmental variables - cat >> 99petsc <<- EOF - PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc - EOF - doenvd 99petsc - - if use doc ; then - dodoc docs/developers.pdf docs/manual.pdf - dohtml -r docs/*.html docs/changes docs/manualpages - fi -} diff --git a/sci-mathematics/petsc/petsc-3.10.4.ebuild b/sci-mathematics/petsc/petsc-3.10.4.ebuild deleted file mode 100644 index bc9a4b110..000000000 --- a/sci-mathematics/petsc/petsc-3.10.4.ebuild +++ /dev/null @@ -1,196 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator - -MY_P="${PN}-$(replace_version_separator _ -)" - -DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation" -HOMEPAGE="http://www.mcs.anl.gov/petsc/" -SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="afterimage boost complex-scalars cxx debug doc fftw - fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X" - -# hypre and superlu curretly exclude each other due to missing linking to hypre -# if both are enabled -REQUIRED_USE=" - afterimage? ( X ) - complex-scalars? ( !hypre !superlu ) - hdf5? ( mpi ) - hypre? ( cxx mpi !superlu ) - mumps? ( mpi scotch ) - scotch? ( mpi ) - superlu? ( !hypre ) -" - -RDEPEND=" - virtual/blas - virtual/lapack - afterimage? ( media-libs/libafterimage ) - boost? ( dev-libs/boost ) - fftw? ( sci-libs/fftw:3.0[mpi?] ) - hdf5? ( sci-libs/hdf5[mpi?] ) - hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] ) - metis? ( >=sci-libs/parmetis-4 ) - mpi? ( virtual/mpi[cxx?,fortran?] ) - mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack ) - scotch? ( sci-libs/scotch[mpi?] ) - sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 ) - superlu? ( >=sci-libs/superlu-5 ) - X? ( x11-libs/libX11 ) -" - -DEPEND="${RDEPEND} - ${PYTHON_DEPS} - virtual/pkgconfig - dev-util/cmake -" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \ - "${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch -) - -src_prepare() { - default - - sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die -} - -# petsc uses --with-blah=1 and --with-blah=0 to en/disable options -petsc_enable() { - use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0" -} -# add external library: -# petsc_with use_flag libname libdir -# petsc_with use_flag libname include linking_libs -petsc_with() { - local myuse p=${2:-${1}} - if use ${1}; then - myuse="--with-${p}=1" - if [[ $# -ge 4 ]]; then - myuse="${myuse} --with-${p}-include=${EPREFIX}${3}" - shift 3 - myuse="${myuse} --with-${p}-lib=$@" - else - myuse="${myuse}" - fi - else - myuse="--with-${p}=0" - fi - echo ${myuse} -} - -# select between configure options depending on use flag -petsc_select() { - use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4" -} - -src_configure() { - # bug 548498 - # PETSc runs mpi processes during configure that result in a sandbox - # violation by trying to open /proc/mtrr rw. This is not easy to - # mitigate because it happens in libpciaccess.so called by libhwloc.so, - # which is used by libmpi.so. - addpredict /proc/mtrr - # if mpi is built with knem support it needs /dev/knem too - addpredict /dev/knem - - # configureMPITypes with openmpi-2* insists on accessing the scaling - # governor rw. - addpredict /sys/devices/system/cpu/ - - local mylang - local myopt - - use cxx && mylang="cxx" || mylang="c" - use debug && myopt="debug" || myopt="opt" - - # environmental variables expected by petsc during build - - export PETSC_DIR="${S}" - export PETSC_ARCH="linux-gnu-${mylang}-${myopt}" - - if use debug; then - strip-flags - filter-flags -O* - fi - - # C Support on CXX builds is enabled if possible i.e. when not using - # complex scalars (no complex type for both available at the same time) - - econf \ - scrollOutput=1 \ - FFLAGS="${FFLAGS} -fPIC" \ - CFLAGS="${CFLAGS} -fPIC" \ - CXXFLAGS="${CXXFLAGS} -fPIC" \ - LDFLAGS="${LDFLAGS}" \ - --prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \ - --with-shared-libraries \ - --with-single-library \ - --with-clanguage=${mylang} \ - $(use cxx && ! use complex-scalars && echo "with-c-support=1") \ - --with-petsc-arch=${PETSC_ARCH} \ - --with-precision=double \ - --with-gnu-compilers \ - --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \ - $(petsc_enable debug debugging) \ - $(petsc_enable mpi) \ - $(petsc_select mpi cc mpicc $(tc-getCC)) \ - $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \ - $(petsc_enable fortran) \ - $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \ - $(petsc_enable mpi mpi-compilers) \ - $(petsc_select complex-scalars scalar-type complex real) \ - --with-windows-graphics=0 \ - --with-matlab=0 \ - --with-cmake=true \ - $(petsc_enable threads pthread) \ - $(petsc_with afterimage afterimage \ - /usr/include/libAfterImage -lAfterImage) \ - $(petsc_with hdf5) \ - $(petsc_with hypre hypre \ - /usr/include/hypre -lHYPRE) \ - $(petsc_with sparse suitesparse) \ - $(petsc_with superlu superlu \ - /usr/include/superlu -lsuperlu) \ - $(petsc_with X x) \ - $(petsc_with X x11) \ - $(petsc_with scotch ptscotch \ - /usr/include/scotch \ - [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \ - $(petsc_with mumps scalapack \ - /usr/include/scalapack -lscalapack) \ - $(petsc_with mumps mumps \ - /usr/include \ - [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \ - --with-imagemagick=0 \ - --with-python=0 \ - $(petsc_with boost) \ - $(petsc_with fftw) -} - -src_install() { - emake DESTDIR="${ED}" install - - # add PETSC_DIR to environmental variables - cat >> 99petsc <<- EOF - PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc - EOF - doenvd 99petsc - - if use doc ; then - dodoc docs/developers.pdf docs/manual.pdf - dohtml -r docs/*.html docs/changes docs/manualpages - fi -} diff --git a/sci-mathematics/petsc/petsc-3.8.4.ebuild b/sci-mathematics/petsc/petsc-3.8.4.ebuild deleted file mode 100644 index c47619aaf..000000000 --- a/sci-mathematics/petsc/petsc-3.8.4.ebuild +++ /dev/null @@ -1,205 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator - -MY_P="${PN}-$(replace_version_separator _ -)" - -DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation" -HOMEPAGE="http://www.mcs.anl.gov/petsc/" -SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="afterimage boost complex-scalars cxx debug doc fftw - fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X" - -# hypre and superlu curretly exclude each other due to missing linking to hypre -# if both are enabled -REQUIRED_USE=" - afterimage? ( X ) - complex-scalars? ( !hypre !superlu ) - hdf5? ( mpi ) - hypre? ( cxx mpi !superlu ) - mumps? ( mpi scotch ) - scotch? ( mpi ) - superlu? ( !hypre ) -" - -RDEPEND=" - virtual/blas - virtual/lapack - afterimage? ( media-libs/libafterimage ) - boost? ( dev-libs/boost ) - fftw? ( sci-libs/fftw:3.0[mpi?] ) - hdf5? ( sci-libs/hdf5[mpi?] ) - hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] ) - metis? ( >=sci-libs/parmetis-4 ) - mpi? ( virtual/mpi[cxx?,fortran?] ) - mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack ) - scotch? ( sci-libs/scotch[mpi?] ) - sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 ) - superlu? ( >=sci-libs/superlu-5 ) - X? ( x11-libs/libX11 ) -" - -DEPEND="${RDEPEND} - ${PYTHON_DEPS} - virtual/pkgconfig - dev-util/cmake -" - -# -# PETSc does not want its Makefiles to be invoked with anything higher than -# -j1. The underlying build system does automatically invoke a parallel -# build. This might not be what you want, but *hey* not your choice. -# -# V=1 enables verbose output with full compiler and linker invocation -# -MAKEOPTS="${MAKEOPTS} -j1 V=1" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \ - "${FILESDIR}"/${PN}-3.8.3-fix_sandbox_violation.patch -) - -src_prepare() { - default - - sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die -} - -# petsc uses --with-blah=1 and --with-blah=0 to en/disable options -petsc_enable() { - use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0" -} -# add external library: -# petsc_with use_flag libname libdir -# petsc_with use_flag libname include linking_libs -petsc_with() { - local myuse p=${2:-${1}} - if use ${1}; then - myuse="--with-${p}=1" - if [[ $# -ge 4 ]]; then - myuse="${myuse} --with-${p}-include=${EPREFIX}${3}" - shift 3 - myuse="${myuse} --with-${p}-lib=$@" - else - myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}" - fi - else - myuse="--with-${p}=0" - fi - echo ${myuse} -} - -# select between configure options depending on use flag -petsc_select() { - use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4" -} - -src_configure() { - # bug 548498 - # PETSc runs mpi processes during configure that result in a sandbox - # violation by trying to open /proc/mtrr rw. This is not easy to - # mitigate because it happens in libpciaccess.so called by libhwloc.so, - # which is used by libmpi.so. - addpredict /proc/mtrr - # if mpi is built with knem support it needs /dev/knem too - addpredict /dev/knem - - # configureMPITypes with openmpi-2* insists on accessing the scaling - # governor rw. - addpredict /sys/devices/system/cpu/ - - local mylang - local myopt - - use cxx && mylang="cxx" || mylang="c" - use debug && myopt="debug" || myopt="opt" - - # environmental variables expected by petsc during build - - export PETSC_DIR="${S}" - export PETSC_ARCH="linux-gnu-${mylang}-${myopt}" - - if use debug; then - strip-flags - filter-flags -O* - fi - - # C Support on CXX builds is enabled if possible i.e. when not using - # complex scalars (no complex type for both available at the same time) - - econf \ - scrollOutput=1 \ - FFLAGS="${FFLAGS} -fPIC" \ - CFLAGS="${CFLAGS} -fPIC" \ - CXXFLAGS="${CXXFLAGS} -fPIC" \ - LDFLAGS="${LDFLAGS}" \ - --prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \ - --with-shared-libraries \ - --with-single-library \ - --with-clanguage=${mylang} \ - $(use cxx && ! use complex-scalars && echo "with-c-support=1") \ - --with-petsc-arch=${PETSC_ARCH} \ - --with-precision=double \ - --with-gnu-compilers \ - --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \ - $(petsc_enable debug debugging) \ - $(petsc_enable mpi) \ - $(petsc_select mpi cc mpicc $(tc-getCC)) \ - $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \ - $(petsc_enable fortran) \ - $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \ - $(petsc_enable mpi mpi-compilers) \ - $(petsc_select complex-scalars scalar-type complex real) \ - --with-windows-graphics=0 \ - --with-matlab=0 \ - --with-cmake=cmake \ - $(petsc_enable threads pthread) \ - $(petsc_with afterimage afterimage \ - /usr/include/libAfterImage -lAfterImage) \ - $(petsc_with hdf5) \ - $(petsc_with hypre hypre \ - /usr/include/hypre -lHYPRE) \ - $(petsc_with sparse suitesparse) \ - $(petsc_with superlu superlu \ - /usr/include/superlu -lsuperlu) \ - $(petsc_with X x) \ - $(petsc_with X x11) \ - $(petsc_with scotch ptscotch \ - /usr/include/scotch \ - [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \ - $(petsc_with mumps scalapack \ - /usr/include/scalapack -lscalapack) \ - $(petsc_with mumps mumps \ - /usr/include \ - [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \ - --with-imagemagick=0 \ - --with-python=0 \ - $(petsc_with boost) \ - $(petsc_with fftw) -} - -src_install() { - emake DESTDIR="${D}/usr/$(get_libdir)/petsc" install - - # add PETSC_DIR to environmental variables - cat >> 99petsc <<- EOF - PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc - EOF - doenvd 99petsc - - if use doc ; then - dodoc docs/developers.pdf docs/manual.pdf - dohtml -r docs/*.html docs/changes docs/manualpages - fi -} diff --git a/sci-mathematics/petsc/petsc-3.9.4.ebuild b/sci-mathematics/petsc/petsc-3.9.4.ebuild deleted file mode 100644 index b67536ef6..000000000 --- a/sci-mathematics/petsc/petsc-3.9.4.ebuild +++ /dev/null @@ -1,196 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator - -MY_P="${PN}-$(replace_version_separator _ -)" - -DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation" -HOMEPAGE="http://www.mcs.anl.gov/petsc/" -SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="afterimage boost complex-scalars cxx debug doc fftw - fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X" - -# hypre and superlu curretly exclude each other due to missing linking to hypre -# if both are enabled -REQUIRED_USE=" - afterimage? ( X ) - complex-scalars? ( !hypre !superlu ) - hdf5? ( mpi ) - hypre? ( cxx mpi !superlu ) - mumps? ( mpi scotch ) - scotch? ( mpi ) - superlu? ( !hypre ) -" - -RDEPEND=" - virtual/blas - virtual/lapack - afterimage? ( media-libs/libafterimage ) - boost? ( dev-libs/boost ) - fftw? ( sci-libs/fftw:3.0[mpi?] ) - hdf5? ( sci-libs/hdf5[mpi?] ) - hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] ) - metis? ( >=sci-libs/parmetis-4 ) - mpi? ( virtual/mpi[cxx?,fortran?] ) - mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack ) - scotch? ( sci-libs/scotch[mpi?] ) - sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 ) - superlu? ( >=sci-libs/superlu-5 ) - X? ( x11-libs/libX11 ) -" - -DEPEND="${RDEPEND} - ${PYTHON_DEPS} - virtual/pkgconfig - dev-util/cmake -" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \ - "${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch -) - -src_prepare() { - default - - sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die -} - -# petsc uses --with-blah=1 and --with-blah=0 to en/disable options -petsc_enable() { - use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0" -} -# add external library: -# petsc_with use_flag libname libdir -# petsc_with use_flag libname include linking_libs -petsc_with() { - local myuse p=${2:-${1}} - if use ${1}; then - myuse="--with-${p}=1" - if [[ $# -ge 4 ]]; then - myuse="${myuse} --with-${p}-include=${EPREFIX}${3}" - shift 3 - myuse="${myuse} --with-${p}-lib=$@" - else - myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}" - fi - else - myuse="--with-${p}=0" - fi - echo ${myuse} -} - -# select between configure options depending on use flag -petsc_select() { - use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4" -} - -src_configure() { - # bug 548498 - # PETSc runs mpi processes during configure that result in a sandbox - # violation by trying to open /proc/mtrr rw. This is not easy to - # mitigate because it happens in libpciaccess.so called by libhwloc.so, - # which is used by libmpi.so. - addpredict /proc/mtrr - # if mpi is built with knem support it needs /dev/knem too - addpredict /dev/knem - - # configureMPITypes with openmpi-2* insists on accessing the scaling - # governor rw. - addpredict /sys/devices/system/cpu/ - - local mylang - local myopt - - use cxx && mylang="cxx" || mylang="c" - use debug && myopt="debug" || myopt="opt" - - # environmental variables expected by petsc during build - - export PETSC_DIR="${S}" - export PETSC_ARCH="linux-gnu-${mylang}-${myopt}" - - if use debug; then - strip-flags - filter-flags -O* - fi - - # C Support on CXX builds is enabled if possible i.e. when not using - # complex scalars (no complex type for both available at the same time) - - econf \ - scrollOutput=1 \ - FFLAGS="${FFLAGS} -fPIC" \ - CFLAGS="${CFLAGS} -fPIC" \ - CXXFLAGS="${CXXFLAGS} -fPIC" \ - LDFLAGS="${LDFLAGS}" \ - --prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \ - --with-shared-libraries \ - --with-single-library \ - --with-clanguage=${mylang} \ - $(use cxx && ! use complex-scalars && echo "with-c-support=1") \ - --with-petsc-arch=${PETSC_ARCH} \ - --with-precision=double \ - --with-gnu-compilers \ - --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \ - $(petsc_enable debug debugging) \ - $(petsc_enable mpi) \ - $(petsc_select mpi cc mpicc $(tc-getCC)) \ - $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \ - $(petsc_enable fortran) \ - $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \ - $(petsc_enable mpi mpi-compilers) \ - $(petsc_select complex-scalars scalar-type complex real) \ - --with-windows-graphics=0 \ - --with-matlab=0 \ - --with-cmake=cmake \ - $(petsc_enable threads pthread) \ - $(petsc_with afterimage afterimage \ - /usr/include/libAfterImage -lAfterImage) \ - $(petsc_with hdf5) \ - $(petsc_with hypre hypre \ - /usr/include/hypre -lHYPRE) \ - $(petsc_with sparse suitesparse) \ - $(petsc_with superlu superlu \ - /usr/include/superlu -lsuperlu) \ - $(petsc_with X x) \ - $(petsc_with X x11) \ - $(petsc_with scotch ptscotch \ - /usr/include/scotch \ - [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \ - $(petsc_with mumps scalapack \ - /usr/include/scalapack -lscalapack) \ - $(petsc_with mumps mumps \ - /usr/include \ - [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \ - --with-imagemagick=0 \ - --with-python=0 \ - $(petsc_with boost) \ - $(petsc_with fftw) -} - -src_install() { - emake DESTDIR="${ED}" install - - # add PETSC_DIR to environmental variables - cat >> 99petsc <<- EOF - PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc - EOF - doenvd 99petsc - - if use doc ; then - dodoc docs/developers.pdf docs/manual.pdf - dohtml -r docs/*.html docs/changes docs/manualpages - fi -} diff --git a/sci-mathematics/pff/Manifest b/sci-mathematics/pff/Manifest deleted file mode 100644 index eabef8165..000000000 --- a/sci-mathematics/pff/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST Float8.4.tgz 352313 SHA256 3436b4521ac8bb24850920f404994579174f5b20d1178d48dbd686ec109ef27c SHA512 4e53aad0a59d6875f071584a34b91029a51e8d797e2f5c1a51c772973b241ebda093463532653dbc54245bd03b2414d648648670c6658547c908403cbe6d1275 WHIRLPOOL 2bfe679b50a5ccb6aec88403a85766b774a416c56d94dd640d00577a35d2d3a06b7d91795285ba0e57c17f6bdcc19d71ffa2a7ab5f796b4e2e2366c195f557b5 diff --git a/sci-mathematics/pff/metadata.xml b/sci-mathematics/pff/metadata.xml deleted file mode 100644 index 0c97b245d..000000000 --- a/sci-mathematics/pff/metadata.xml +++ /dev/null @@ -1,14 +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> - <longdescription> -PFF (Preuves Formelles sur les Flottants = Formal Proofs about Floats) -is a repository of a Coq library about floating-point arithmetic. It -contains both definitions and proofs of basic facts, old and new -properties and algorithms. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/pff/pff-8.4.ebuild b/sci-mathematics/pff/pff-8.4.ebuild deleted file mode 100644 index 951b49edc..000000000 --- a/sci-mathematics/pff/pff-8.4.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -DESCRIPTION="Library for reasoning about floating point numbers in coq" -HOMEPAGE="http://lipforge.ens-lyon.fr/www/pff/" -SRC_URI="http://lipforge.ens-lyon.fr/frs/download.php/165/Float${PV}.tgz" - -LICENSE="LGPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="sci-mathematics/coq" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/Float${PV}" - -src_prepare() { - sed -i Makefile \ - -e "s|\`\$(COQC) -where\`/user-contrib|\$(DSTROOT)/\`\$(COQC) -where\`/user-contrib|g" \ - -e "s|VOFILESINC=\$(filter \$(wildcard \./\*),\$(VOFILES))|VOFILESINC:=\$(filter-out ,\$(VOFILES))|g" -} - -src_compile(){ - default -} - -src_install(){ - emake install DSTROOT="${D}" -} diff --git a/sci-mathematics/pulp/Manifest b/sci-mathematics/pulp/Manifest index e47e45371..9d87e82b0 100644 --- a/sci-mathematics/pulp/Manifest +++ b/sci-mathematics/pulp/Manifest @@ -1 +1,2 @@ -DIST PuLP-1.5.6.zip 9105984 BLAKE2B 0a6b41abca5dfe12db9b09f37f6deb3093ebd0b25244960eab83acdb7d1bf7d10c0983845f254e103be650d1f5f3a6657a4ffcc7bb4501043d865e37e9101f38 SHA512 9feed42d7943d1d9ef8484a99184bd695303a1b0f00b7dfaa65f67fe07b1fa24a67d83a0de1bd664e59cda614c9810ab28b84e2606fb3701e4d336d2a2d93c6f +DIST pulp-2.7.0.gh.tar.gz 28000854 BLAKE2B d2ec0f2e795ffc93051189e236ddefc92c1e0fbfc825f8bd32b6f8569c1e0ec290acaa418e93768587238ff25c3ae9a4d27457c7e5eb0635fc919ebb80b3de3b SHA512 be89eaeaac81cb79f6533b8764283f1f4ba85570f7626db6fa3e760124a26dcc1ee3ff3b293c67de2ed48083fe611ae0ca93db83da801456a34fe7cff816ba61 +DIST pulp-2.8.0.gh.tar.gz 31434075 BLAKE2B 65d0abc19d7677818dab3417c4ada9e171357c3e568ab23d224417287a6b28d41b0c82771e293d8793f5bc70ea84510538e2c84b1409aabd85517f7d1881a0ed SHA512 28fcec6d5c47778a46e8ea3316884a1f22777de9b692a47c3222c1aedc27106f711d19f6ce7af97b07322f947fc76cafa69e2c6636c7cc6d96ca19e96a766e8d diff --git a/sci-mathematics/pulp/metadata.xml b/sci-mathematics/pulp/metadata.xml index ce584d233..c86c3b501 100644 --- a/sci-mathematics/pulp/metadata.xml +++ b/sci-mathematics/pulp/metadata.xml @@ -7,5 +7,6 @@ </maintainer> <upstream> <remote-id type="pypi">PuLP</remote-id> + <remote-id type="github">coin-or/pulp</remote-id> </upstream> </pkgmetadata> diff --git a/sci-mathematics/pulp/pulp-1.5.6-r1.ebuild b/sci-mathematics/pulp/pulp-1.5.6-r1.ebuild deleted file mode 100644 index 88878fdcc..000000000 --- a/sci-mathematics/pulp/pulp-1.5.6-r1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python{2_7,3_4} pypy ) - -inherit distutils-r1 - -MY_PN="PuLP" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="Create MPS/LP files, call solvers, and present results" -HOMEPAGE="http://pulp-or.googlecode.com/" -SRC_URI="mirror://pypi/P/PuLP/${MY_P}.zip" - -LICENSE="BSD-2" -KEYWORDS="~amd64" -SLOT="0" -IUSE="examples" - -DEPEND="dev-python/setuptools" -RDEPEND=" - dev-python/setuptools - dev-python/pyparsing - sci-libs/coinor-cbc - >=sci-mathematics/glpk-4.35" - -S="${WORKDIR}/${MY_P}" - -python_prepare_all() { - rm -rf ./src/pulp/solverdir/cbc* || die - distutils-r1_python_prepare_all -} - -python_install_all() { - use examples && EXAMPLES=( examples/. ) - distutils-r1_python_install_all -} diff --git a/sci-mathematics/pulp/pulp-2.7.0.ebuild b/sci-mathematics/pulp/pulp-2.7.0.ebuild new file mode 100644 index 000000000..641a91622 --- /dev/null +++ b/sci-mathematics/pulp/pulp-2.7.0.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Create MPS/LP files, call solvers, and present results" +HOMEPAGE="https://coin-or.github.io/pulp/" +SRC_URI="https://github.com/coin-or/${PN}/archive/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD-2" +KEYWORDS="~amd64 ~x86" +SLOT="0" + +distutils_enable_tests setup.py +# ToDo: package theme +#distutils_enable_sphinx doc/source dev-python/sphinx_glpi_theme diff --git a/sci-mathematics/pulp/pulp-2.8.0.ebuild b/sci-mathematics/pulp/pulp-2.8.0.ebuild new file mode 100644 index 000000000..9a5cee909 --- /dev/null +++ b/sci-mathematics/pulp/pulp-2.8.0.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Create MPS/LP files, call solvers, and present results" +HOMEPAGE="https://coin-or.github.io/pulp/" +SRC_URI="https://github.com/coin-or/${PN}/archive/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD-2" +KEYWORDS="~amd64 ~x86" +SLOT="0" + +distutils_enable_tests setup.py +# ToDo: package theme +#distutils_enable_sphinx doc/source dev-python/sphinx_glpi_theme diff --git a/sci-mathematics/ripser/Manifest b/sci-mathematics/ripser/Manifest new file mode 100644 index 000000000..5b2d33259 --- /dev/null +++ b/sci-mathematics/ripser/Manifest @@ -0,0 +1 @@ +DIST ripser-1.1.tar.gz 3253697 BLAKE2B 8c1fccfabfd1db22e386b14707d1e078281921f6c353ce406bb35d37a8453a0e93e7423d8a52ee61d15a62d65708f070614a4ba4d3e13bc45f5d8aeb22d78997 SHA512 22bbce287abbf3cf5594e6dd1d5b754ea4707d21a9711ed9646a6c06715861ff0c79bb6090be5031c8e093ac586d9c3110e6aba84c5fabeefb165d4bc729705c diff --git a/sci-mathematics/ripser/files/ripser-Makefile.patch b/sci-mathematics/ripser/files/ripser-Makefile.patch new file mode 100644 index 000000000..e8135fd27 --- /dev/null +++ b/sci-mathematics/ripser/files/ripser-Makefile.patch @@ -0,0 +1,51 @@ +diff --git a/Makefile b/Makefile +index ab410bd..cb0a1c1 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,15 +1,35 @@ +-build: ripser ++TARGET = ripser + ++DESTDIR ?= + +-all: ripser ripser-coeff ripser-debug ++prefix ?= /usr/local ++exec_prefix ?= $(prefix) ++bindir ?= $(exec_prefix)/bin + ++CFLAGS += -std=c++11 -Wall -Wextra -Wpedantic -Wstrict-overflow ++ ++ifeq ($(INDICATE_PROGRESS),1) ++ CFLAGS += -D INDICATE_PROGRESS ++endif ++ ++ifeq ($(USE_GOOGLE_HASHMAP),1) ++ CFLAGS += -D USE_GOOGLE_HASHMAP ++endif ++ ++ifeq ($(NDEBUG),1) ++ CFLAGS += -D NDEBUG ++endif ++ ++build: all ++ ++all: ripser ripser-coeff + + ripser: ripser.cpp +- c++ -std=c++11 -Wall ripser.cpp -o ripser -Ofast -D NDEBUG ++ $(CXX) $(CFLAGS) $(CXXFLAGS) ripser.cpp -o ripser + + ripser-coeff: ripser.cpp +- c++ -std=c++11 -Wall ripser.cpp -o ripser-coeff -Ofast -D NDEBUG -D USE_COEFFICIENTS +- +-ripser-debug: ripser.cpp +- c++ -std=c++11 -Wall ripser.cpp -o ripser-debug -g ++ $(CXX) $(CFLAGS) $(CXXFLAGS) -D USE_COEFFICIENTS ripser.cpp -o ripser-coeff + ++install: all ++ install -d ${DESTDIR}${bindir} ++ install -m 755 ripser ripser-coeff ${DESTDIR}$(bindir) + + clean: +- rm -f ripser ripser-coeff ripser-debug ++ rm -f ripser ripser-coeff diff --git a/sci-mathematics/ripser/metadata.xml b/sci-mathematics/ripser/metadata.xml new file mode 100644 index 000000000..05f38b851 --- /dev/null +++ b/sci-mathematics/ripser/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@aisha.cc</email> + <name>Aisha Tammy</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <use> + <flag name="progress">print progress of calculations in console</flag> + <flag name="sparsehash">use google sparsehash for storage</flag> + </use> + <upstream> + <remote-id type="github">Ripser/ripser</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-mathematics/ripser/ripser-1.1.ebuild b/sci-mathematics/ripser/ripser-1.1.ebuild new file mode 100644 index 000000000..809faa019 --- /dev/null +++ b/sci-mathematics/ripser/ripser-1.1.ebuild @@ -0,0 +1,33 @@ +# Copyright 2019-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +DESCRIPTION="efficient computation of Vietoris-Rips persistence barcodes" +HOMEPAGE="https://github.com/Ripser/ripser" +SRC_URI="https://github.com/Ripser/ripser/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +KEYWORDS="~amd64" + +LICENSE="MIT" +SLOT="0" +IUSE="debug progress sparsehash" + +BDEPEND=" + sparsehash? ( dev-cpp/sparsehash ) +" + +PATCHES=( + "${FILESDIR}/ripser-Makefile.patch" +) + +src_compile() { + emake USE_GOOGLE_HASHMAP=$(usex sparsehash 1 0) \ + INDICATE_PROGRESS=$(usex progress 1 0) \ + NDEBUG=$(usex debug 0 1)\ + all +} + +src_install() { + emake prefix="/usr" DESTDIR="${D}" install +} diff --git a/sci-mathematics/scilab-bin/Manifest b/sci-mathematics/scilab-bin/Manifest new file mode 100644 index 000000000..6029dc30e --- /dev/null +++ b/sci-mathematics/scilab-bin/Manifest @@ -0,0 +1,2 @@ +DIST scilab-2023.1.0.bin.x86_64-linux-gnu.tar.xz 182801620 BLAKE2B 19847145a8d70550afa77591854aa651ee5fe23f9998eee21c11acdd4112397fb5e2e82c6bc7edbc2f808048f70905dc0df37db00c43b5794bf304e9a0807ca4 SHA512 af0f71d270513f283ac732e2004094854a117ce4550c5ab579eda5c5ec52bde76a8fa5dd7649db84d68d43124524342f2fdc5f1ba269a60a3930c578ef3391f8 +DIST scilab-6.1.1.bin.linux-x86_64.tar.gz 215840619 BLAKE2B dcfb88f2488cf26371c5beee1e905a33e4c6fc343bb490bb43a73334960f0c13df7d372841949a46d7dc5b6c0a404e6648828104717274518a8ff905a0ae15ad SHA512 ed386e01869cfac3d12881ddb4ae0258bb02e1d4a919a82405dbedce77406c04269883b6e1456dbad52551217307a7baebbb355a699168b77810263f5e357895 diff --git a/sci-mathematics/scilab-bin/metadata.xml b/sci-mathematics/scilab-bin/metadata.xml new file mode 100644 index 000000000..dc2f8c0b5 --- /dev/null +++ b/sci-mathematics/scilab-bin/metadata.xml @@ -0,0 +1,15 @@ +<?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> + <longdescription lang="en"> + Scilab is a matrix-based scientific software package. Scilab contains + hundreds of built-in mathematical functions, rich data structures + (including polynomials, rationals,linear systems, lists, etc...) and + comes with a number of specific toolboxes for control, signal + processing, ... + </longdescription> +</pkgmetadata> diff --git a/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild b/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild new file mode 100644 index 000000000..83d189b8a --- /dev/null +++ b/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit xdg + +MY_PN="${PN//-bin}" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Scientific software package for numerical computations" +HOMEPAGE="https://www.scilab.org/" +SRC_URI="https://www.scilab.org/download/${PV}/${MY_P}.bin.x86_64-linux-gnu.tar.xz" +S="${WORKDIR}/${P//-bin}" + +LICENSE="GPL-2 Apache-2.0 sun-bcla-jhall jing MPL-1.0 MIT" +SLOT="0" +KEYWORDS="-* ~amd64" + +# Bundled dependencies not packaged in ::gentoo +# sci-libs/hdf5[cxx]:0/9 +# libgluegen.so (in ::sci) +# libjogl_desktop.so (in ::sci) +# libOpenXLSX.so (in ::sci) +# +# Bundled dependencies in ::gentoo +# dev-lang/tcl +# dev-libs/openssl:0/1.1 +# dev-libs/newt +# dev-libs/libpcre +# net-misc/curl +# sci-libs/amd +# sci-libs/arpack +# sci-libs/camd +# sci-libs/ccolamd +# sci-libs/cholmod +# sci-libs/colamd +# sci-libs/fftw:3.0/3 +# sci-libs/lapack +# sci-libs/matio +# sci-libs/openblas +# sci-libs/umfpack + +RDEPEND=" + sys-libs/ncurses-compat + virtual/jre:1.8 +" + +QA_PREBUILT=( "opt/${MY_PN}/*" ) + +src_prepare() { + default + local SCILAB_HOME="/opt/${MY_PN}" + # fix the .pc file to reflect the dirs where we are installing stuff + sed -i -e "/^prefix=/c prefix=${SCILAB_HOME}" lib/pkgconfig/scilab.pc || die + + # move appdata to metainfo + mv share/appdata share/metainfo || die +} + +src_install() { + local SCILAB_HOME="/opt/${MY_PN}" + dodir "${SCILAB_HOME}" + + # make convenience symlinks in PATH + for file in bin/*; do + dosym "../${MY_PN}/${file}" "/opt/${file}" + done + + # copy all the things + cp -r "${S}/"* "${ED}/${SCILAB_HOME}" || die + + # move out dekstop, icons etc + dodir /usr/share + mv "${ED}/${SCILAB_HOME}/share/"{metainfo,applications,icons,locale,mime} "${ED}/usr/share/" || die + dodir /usr/lib64/pkgconfig + mv "${ED}/${SCILAB_HOME}/lib/pkgconfig/scilab.pc" "${ED}/usr/lib64/pkgconfig/" || die +} diff --git a/sci-mathematics/scilab-bin/scilab-bin-6.1.1.ebuild b/sci-mathematics/scilab-bin/scilab-bin-6.1.1.ebuild new file mode 100644 index 000000000..07b7da8ee --- /dev/null +++ b/sci-mathematics/scilab-bin/scilab-bin-6.1.1.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit xdg + +MY_PN="${PN//-bin}" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Scientific software package for numerical computations" +HOMEPAGE="https://www.scilab.org/" +SRC_URI="https://www.scilab.org/download/${PV}/${MY_P}.bin.linux-x86_64.tar.gz" +S="${WORKDIR}/${P//-bin}" + +LICENSE="GPL-2 Apache-2.0 sun-bcla-jhall jing MPL-1.0 MIT" +SLOT="0" +KEYWORDS="-* ~amd64" + +# Bundled dependencies not packaged in ::gentoo +# sci-libs/hdf5[cxx]:0/9 +# libgluegen.so (in ::sci) +# libjogl_desktop.so (in ::sci) +# libOpenXLSX.so (in ::sci) +# +# Bundled dependencies in ::gentoo +# dev-lang/tcl +# dev-libs/openssl:0/1.1 +# dev-libs/newt +# dev-libs/libpcre +# net-misc/curl +# sci-libs/amd +# sci-libs/arpack +# sci-libs/camd +# sci-libs/ccolamd +# sci-libs/cholmod +# sci-libs/colamd +# sci-libs/fftw:3.0/3 +# sci-libs/lapack +# sci-libs/matio +# sci-libs/openblas +# sci-libs/umfpack + +RDEPEND=" + sys-libs/ncurses-compat + virtual/jre:1.8 +" + +QA_PREBUILT=( "opt/${MY_PN}/*" ) + +src_prepare() { + default + local SCILAB_HOME="/opt/${MY_PN}" + # fix the .pc file to reflect the dirs where we are installing stuff + sed -i -e "/^prefix=/c prefix=${SCILAB_HOME}" lib/pkgconfig/scilab.pc || die + + # move appdata to metainfo + mv share/appdata share/metainfo || die +} + +src_install() { + local SCILAB_HOME="/opt/${MY_PN}" + dodir "${SCILAB_HOME}" + + # make convenience symlinks in PATH + for file in bin/*; do + dosym "../${MY_PN}/${file}" "/opt/${file}" + done + + # copy all the things + cp -r "${S}/"* "${ED}/${SCILAB_HOME}" || die + + # move out dekstop, icons etc + dodir /usr/share + mv "${ED}/${SCILAB_HOME}/share/"{metainfo,applications,icons,locale,mime} "${ED}/usr/share/" || die + dodir /usr/lib64/pkgconfig + mv "${ED}/${SCILAB_HOME}/lib/pkgconfig/scilab.pc" "${ED}/usr/lib64/pkgconfig/" || die +} diff --git a/sci-mathematics/scilab/Manifest b/sci-mathematics/scilab/Manifest deleted file mode 100644 index 0253bcef2..000000000 --- a/sci-mathematics/scilab/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST scilab-5.5.2-src.tar.gz 69626327 BLAKE2B 6180bb91d878e646838a085894dcf6da7127b60788a234f1900dc19b6a981af789c10e78f08ed1357fbec82b32d0fe0ba4b8ffe3350ac4a9f5ee0843bbb3b177 SHA512 7f00ac837e36b5524a9c9a3106bdaefebb71559eb2932b2a16e4fac53fa1f9e66b87eabf98b3006ede25f8ab1d16d6ef1c7561ed29b67ddb42c98610fa72fe79 diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-accessviolation.patch b/sci-mathematics/scilab/files/scilab-5.5.2-accessviolation.patch deleted file mode 100644 index a7e5c6d5f..000000000 --- a/sci-mathematics/scilab/files/scilab-5.5.2-accessviolation.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -urN scilab-5.5.0-orig/bin/scilab scilab-5.5.0/bin/scilab ---- a/bin/scilab 2014-07-12 15:24:17.105686656 -0400 -+++ b/bin/scilab 2014-07-12 15:25:29.307725409 -0400 -@@ -647,17 +647,6 @@ - GTK_MODULES=$(echo $GTK_MODULES | sed s/gnomebreakpad//g) - export GTK_MODULES - --# libEGL may be partially supported by the closed-source NVIDIA driver. --# Until they release an EGL driver, we force the egl_glx driver. --# http://bugzilla.scilab.org/show_bug.cgi?id=12940 --if test -x /usr/bin/glxinfo; then -- NVIDIA_GLX_VENDOR=$(/usr/bin/glxinfo |grep "NVIDIA Corporation") -- if test ! -z "$NVIDIA_GLX_VENDOR"; then -- EGL_DRIVER=egl_glx -- export EGL_DRIVER -- fi --fi -- - if test $SCIVERBOSE -ne 0; then - echo "SCI : $SCI" - echo "SCIBIN : $SCIBIN" diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-batik-1.8.patch b/sci-mathematics/scilab/files/scilab-5.5.2-batik-1.8.patch deleted file mode 100644 index 007d530ad..000000000 --- a/sci-mathematics/scilab/files/scilab-5.5.2-batik-1.8.patch +++ /dev/null @@ -1,99 +0,0 @@ -From: Bryan Gardiner <bog@khumba.net> -Project-Bug-URL: https://bugzilla.scilab.org/show_bug.cgi?id=13813 -Gentoo-Bug-URL: https://github.com/gentoo-science/sci/pull/456 - -Updates Scilab to build against (and require) Batik >=1.8, fixing an API change -with SAXSVGDocumentFactory being moved. This is not tested beyond "yes Scilab -still links to Batik to export SVGs," as I'm not sure of a good test case, and -it's awaiting upstream review. - ---- a/configure -+++ b/configure -@@ -16600,8 +16600,8 @@ $as_echo "$as_me: WARNING: Could not find or use the Java package/jar batik used - fi - - -- { $as_echo "$as_me:${as_lineno-$LINENO}: checking minimal version (1.7) of batik" >&5 --$as_echo_n "checking minimal version (1.7) of batik... " >&6; } -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking minimal version (1.8) of batik" >&5 -+$as_echo_n "checking minimal version (1.8) of batik... " >&6; } - saved_ac_java_classpath=$ac_java_classpath - export ac_java_classpath="$BATIK:$ac_java_classpath" - if test "x" == "x"; then -@@ -16614,7 +16614,7 @@ import org.apache.batik.Version; - - public class conftest { - public static void main(String[] argv) { -- String minVersion="1.7"; -+ String minVersion="1.8"; - - System.out.println(Version.getVersion()); - if (compare(minVersion, Version.getVersion()) > 0) { -@@ -16663,7 +16663,7 @@ EOF - STDOUT=`cat conftest.java.output` - fi - echo "configure: CLASSPATH was $CLASSPATH" >&5 -- as_fn_error $? "Wrong version of batik. Expected at least 1.7. Found $STDOUT" "$LINENO" 5 -+ as_fn_error $? "Wrong version of batik. Expected at least 1.8. Found $STDOUT" "$LINENO" 5 - fi - fi - if test -f conftest.java.output; then -@@ -16673,7 +16673,7 @@ EOF - echo "configure: failed program was:" >&5 - cat conftest.java >&5 - echo "configure: CLASSPATH was $CLASSPATH" >&5 -- as_fn_error $? "Wrong version of batik. Expected at least 1.7. Found $STDOUT" "$LINENO" 5 -+ as_fn_error $? "Wrong version of batik. Expected at least 1.8. Found $STDOUT" "$LINENO" 5 - fi - - else -@@ -16686,7 +16686,7 @@ import org.apache.batik.Version; - - public class conftest { - public static void main(String[] argv) { -- String minVersion="1.7"; -+ String minVersion="1.8"; - - System.out.println(Version.getVersion()); - if (compare(minVersion, Version.getVersion()) != 0) { -@@ -16735,7 +16735,7 @@ EOF - STDOUT=`cat conftest.java.output` - fi - echo "configure: CLASSPATH was $CLASSPATH" >&5 -- as_fn_error $? "Wrong version of batik. Expected exact version 1.7. Found $STDOUT" "$LINENO" 5 -+ as_fn_error $? "Wrong version of batik. Expected exact version 1.8. Found $STDOUT" "$LINENO" 5 - fi - fi - if test -f conftest.java.output; then -@@ -16745,7 +16745,7 @@ EOF - echo "configure: failed program was:" >&5 - cat conftest.java >&5 - echo "configure: CLASSPATH was $CLASSPATH" >&5 -- as_fn_error $? "Wrong version of batik. Expected exact version 1.7. Found $STDOUT" "$LINENO" 5 -+ as_fn_error $? "Wrong version of batik. Expected exact version 1.8. Found $STDOUT" "$LINENO" 5 - fi - - fi ---- a/configure.ac -+++ b/configure.ac -@@ -1038,7 +1038,7 @@ interface for JOGL2 - or libGL (OpenGL library) are installed and if the version - BATIK=$PACKAGE_JAR_FILE - fi - AC_SUBST(BATIK) -- AC_JAVA_CHECK_VERSION_PACKAGE([batik],[import org.apache.batik.Version;],$BATIK,[1.7],[Version.getVersion()]) -+ AC_JAVA_CHECK_VERSION_PACKAGE([batik],[import org.apache.batik.Version;],$BATIK,[1.8],[Version.getVersion()]) - - # Commons I/O library - AC_JAVA_CHECK_PACKAGE([commons-io],[org.apache.commons.io.output.CountingOutputStream],[Commons I/O library]) ---- a/modules/graph/src/java/org/scilab/modules/graph/utils/ScilabGraphUtils.java -+++ b/modules/graph/src/java/org/scilab/modules/graph/utils/ScilabGraphUtils.java -@@ -28,7 +28,7 @@ import org.apache.batik.bridge.DocumentLoader; - import org.apache.batik.bridge.GVTBuilder; - import org.apache.batik.bridge.UserAgent; - import org.apache.batik.bridge.UserAgentAdapter; --import org.apache.batik.dom.svg.SAXSVGDocumentFactory; -+import org.apache.batik.anim.dom.SAXSVGDocumentFactory; - import org.apache.batik.gvt.GraphicsNode; - import org.apache.batik.util.XMLResourceDescriptor; - import org.scilab.forge.jlatexmath.ParseException; - diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-fix-random-runtime-failure.patch b/sci-mathematics/scilab/files/scilab-5.5.2-fix-random-runtime-failure.patch deleted file mode 100644 index da7b6e485..000000000 --- a/sci-mathematics/scilab/files/scilab-5.5.2-fix-random-runtime-failure.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -urN scilab-orig/modules/api_scilab/src/cpp/api_double.cpp scilab/modules/api_scilab/src/cpp/api_double.cpp ---- a/modules/api_scilab/src/cpp/api_double.cpp 2012-08-06 23:26:31.342617365 -0400 -+++ b/modules/api_scilab/src/cpp/api_double.cpp 2012-08-06 23:27:34.838621420 -0400 -@@ -497,7 +497,7 @@ - /*--------------------------------------------------------------------------*/ - int createScalarDouble(void* _pvCtx, int _iVar, double _dblReal) - { -- return createCommonScalarDouble(_pvCtx, _iVar, 0, _dblReal, NULL); -+ return createCommonScalarDouble(_pvCtx, _iVar, 0, _dblReal, 0); - } - /*--------------------------------------------------------------------------*/ - int createScalarComplexDouble(void* _pvCtx, int _iVar, double _dblReal, double _dblImg) diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-followlinks.patch b/sci-mathematics/scilab/files/scilab-5.5.2-followlinks.patch deleted file mode 100644 index a3f60bee7..000000000 --- a/sci-mathematics/scilab/files/scilab-5.5.2-followlinks.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/m4/java.m4 2014-02-11 23:43:03.030430258 -0500 -+++ b/m4/java.m4 2014-02-11 23:43:54.008428766 -0500 -@@ -839,7 +839,7 @@ - for jar in "$jardir/$1.jar" "$jardir/lib$1.jar" "$jardir/lib$1-java.jar" "$jardir/$1*.jar"; do - - # TODO check the behaviour when spaces -- jars_resolved=`ls $jar 2>/dev/null` -+ jars_resolved=$(realpath $(ls $jar 2>/dev/null) 2>/dev/null) - for jar_resolved in $jars_resolved; do # If several jars matches - if test -e "$jar_resolved"; then - export ac_java_classpath="$jar_resolved:$ac_java_classpath" diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-fop-2.0.patch b/sci-mathematics/scilab/files/scilab-5.5.2-fop-2.0.patch deleted file mode 100644 index 18bdaac1d..000000000 --- a/sci-mathematics/scilab/files/scilab-5.5.2-fop-2.0.patch +++ /dev/null @@ -1,38 +0,0 @@ -From: Bryan Gardiner <bog@khumba.net> -Project-Bug-URL: https://bugzilla.scilab.org/show_bug.cgi?id=14009 -Gentoo-Bug-URL: https://github.com/gentoo-science/sci/pull/456 - -Updates Scilab to build against FOP >=2.0. This is not tested, as I'm not sure -of a test case, and it's awaiting upstream review. - ---- a/modules/helptools/src/java/org/scilab/modules/helptools/FopConverter.java -+++ b/modules/helptools/src/java/org/scilab/modules/helptools/FopConverter.java -@@ -43,10 +43,10 @@ public class FopConverter extends ContainerConverter { - String fileName = outputDirectory + "/" + baseName + "." + format.name().toLowerCase(); - - try { -- FopFactory fopFactory = FopFactory.newInstance(); -+ FopFactory fopFactory = -+ FopFactory.newInstance(new File(System.getenv("SCI") + "/modules/helptools/etc/fopconf.xml")); - fopFactory.addElementMapping(new JLaTeXMathElementMapping()); - fopFactory.getXMLHandlerRegistry().addXMLHandler(new JLaTeXMathXMLHandler()); -- fopFactory.setUserConfig(new File(System.getenv("SCI") + "/modules/helptools/etc/fopconf.xml")); - - // Step 3: Construct fop with desired output format - OutputStream out = new BufferedOutputStream(new FileOutputStream(fileName)); ---- a/modules/scinotes/src/java/org/scilab/modules/scinotes/utils/CodeExporter.java -+++ b/modules/scinotes/src/java/org/scilab/modules/scinotes/utils/CodeExporter.java -@@ -114,11 +114,11 @@ public class CodeExporter extends FOCodeConverter { - * @param format the page format - */ - public void convert(String code, int[] lineNumberArray, String fileName, String type, String title, PageFormat format) { -- FopFactory fopFactory = FopFactory.newInstance(); - OutputStream out = null; - - try { -- fopFactory.setUserConfig(new File(ScilabConstants.SCI + "/modules/helptools/etc/fopconf.xml")); -+ FopFactory fopFactory = -+ FopFactory.newInstance(new File(ScilabConstants.SCI + "/modules/helptools/etc/fopconf.xml")); - FOUserAgent userAgent = fopFactory.newFOUserAgent(); - userAgent.setProducer(CREATOR); - userAgent.setTitle(title); diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-freehep.patch b/sci-mathematics/scilab/files/scilab-5.5.2-freehep.patch deleted file mode 100644 index 46825cb29..000000000 --- a/sci-mathematics/scilab/files/scilab-5.5.2-freehep.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -uNr scilab-5.5.2-orig/configure.ac scilab-5.5.2/configure.ac ---- a/configure.ac 2016-06-05 12:30:06.582735449 -0400 -+++ b/configure.ac 2016-06-05 12:31:29.706708157 -0400 -@@ -1024,7 +1024,7 @@ - AC_SUBST(FREEHEP_IO) - - # Freehep Util -- AC_JAVA_CHECK_PACKAGE([freehep-util],[org.freehep.util.StringUtilities],[Freehep Util]) -+ AC_JAVA_CHECK_PACKAGE([freehep-graphicsbase],[org.freehep.graphicsbase.util.UserProperties],[Freehep Util]) - FREEHEP_UTIL=$PACKAGE_JAR_FILE - AC_SUBST(FREEHEP_UTIL) - fi diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-gluegen.patch b/sci-mathematics/scilab/files/scilab-5.5.2-gluegen.patch deleted file mode 100644 index d75c31e9a..000000000 --- a/sci-mathematics/scilab/files/scilab-5.5.2-gluegen.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/modules/gui/src/java/org/scilab/modules/gui/SwingView.java 2014-03-24 22:38:00.928934500 -0400 -+++ b/modules/gui/src/java/org/scilab/modules/gui/SwingView.java 2014-03-24 22:37:33.947567043 -0400 -@@ -157,7 +157,7 @@ - - static { - try { -- System.loadLibrary("gluegen2-rt"); -+ System.loadLibrary("gluegen-rt"); - } catch (Exception e) { - System.err.println(e); - } diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-java-heap.patch b/sci-mathematics/scilab/files/scilab-5.5.2-java-heap.patch deleted file mode 100644 index ca17e52a6..000000000 --- a/sci-mathematics/scilab/files/scilab-5.5.2-java-heap.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/etc/jvm_options.xml 2014-02-12 00:05:34.323390688 -0500 -+++ b/etc/jvm_options.xml 2014-02-12 00:05:53.977390112 -0500 -@@ -22,7 +22,7 @@ - <!-- ENABLE Just In Time java compiler --> - <option value="-Djava.compiler=JIT"/> - <!-- Set Java Heap space to 256mb --> -- <option value="-Xmx256m"/> -+ <option value="-Xmx512m"/> - <!-- Avoid jvm to handle sigint (& other signals) --> - <option value="-Xrs"/> - diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-missinglib.patch b/sci-mathematics/scilab/files/scilab-5.5.2-missinglib.patch deleted file mode 100644 index 25b281820..000000000 --- a/sci-mathematics/scilab/files/scilab-5.5.2-missinglib.patch +++ /dev/null @@ -1,11 +0,0 @@ -diff -urN scilab-5.5.1-orig/Makefile.am scilab-5.5.1/Makefile.am ---- a/Makefile.am 2014-10-09 18:22:21.994610695 -0400 -+++ b/Makefile.am 2014-10-09 18:24:28.208333575 -0400 -@@ -74,6 +74,7 @@ - if NEED_JAVA - scilab_bin_LDADD += \ - $(top_builddir)/modules/console/libsciconsole.la \ -+ $(top_builddir)/modules/console/libsciconsole-minimal.la \ - $(top_builddir)/modules/jvm/libscijvm.la \ - $(top_builddir)/modules/commons/libscicommons.la - else diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-nogui.patch b/sci-mathematics/scilab/files/scilab-5.5.2-nogui.patch deleted file mode 100644 index f83fa31d0..000000000 --- a/sci-mathematics/scilab/files/scilab-5.5.2-nogui.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- a/Makefile.in 2014-01-09 22:29:06.534469383 -0500 -+++ b/Makefile.in 2014-01-09 22:29:40.368471544 -0500 -@@ -2247,8 +2247,8 @@ - @BUILD_HELP_TRUE@ done; \ - @BUILD_HELP_TRUE@ fi - # Also install scirenderer.jar --@EXTERNAL_SCIRENDERER_FALSE@ $(mkinstalldirs) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER) --@EXTERNAL_SCIRENDERER_FALSE@ $(INSTALL_DATA) $(top_builddir)/$(PATHTOSCIRENDERER)/$(SCIRENDERERJAR) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER)/ -+@EXTERNAL_SCIRENDERER_FALSE@@NEED_JAVA_TRUE@ $(mkinstalldirs) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER) -+@EXTERNAL_SCIRENDERER_FALSE@@NEED_JAVA_TRUE@ $(INSTALL_DATA) $(top_builddir)/$(PATHTOSCIRENDERER)/$(SCIRENDERERJAR) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER)/ - - .PHONY: macros localization doc - diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-xmlgraphics-common-2.0.patch b/sci-mathematics/scilab/files/scilab-5.5.2-xmlgraphics-common-2.0.patch deleted file mode 100644 index 4d90f30c7..000000000 --- a/sci-mathematics/scilab/files/scilab-5.5.2-xmlgraphics-common-2.0.patch +++ /dev/null @@ -1,91 +0,0 @@ -From: Bryan Gardiner <bog@khumba.net> -Project-Bug-URL: https://bugzilla.scilab.org/show_bug.cgi?id=13724 -Gentoo-Bug-URL: https://github.com/gentoo-science/sci/pull/456 - -Updates Scilab 5.5.2 to build against xmlgraphics-common >=2.0. This is not -tested, as I'm not sure of a test case, and a similar patch (where the -super.processShape calls are passed cached=true) is already awaiting upstream -review. - ---- a/modules/graphic_export/src/java/org/scilab/modules/graphic_export/Export.java -+++ b/modules/graphic_export/src/java/org/scilab/modules/graphic_export/Export.java -@@ -857,7 +857,7 @@ public class Export { - } - - @Override -- public int processShape(Shape s) throws IOException { -+ public int processShape(Shape s, boolean cached) throws IOException { - if (s instanceof Ellipse2D.Double) { - Ellipse2D.Double ell = (Ellipse2D.Double) s; - if (ell.height == ell.width) { -@@ -880,10 +880,10 @@ public class Export { - buffer.append("[").append(gen.formatDouble(coords[0])).append(" ").append(gen.formatDouble(coords[1])); - it.next(); - } else { -- return super.processShape(s); -+ return super.processShape(s, cached); - } - } else { -- return super.processShape(s); -+ return super.processShape(s, cached); - } - - for (; !it.isDone(); it.next()) { -@@ -891,7 +891,7 @@ public class Export { - if (type == PathIterator.SEG_LINETO) { - buffer.append(" ").append(gen.formatDouble(coords[0])).append(" ").append(gen.formatDouble(coords[1])); - } else { -- return super.processShape(s); -+ return super.processShape(s, cached); - } - } - buffer.append("] DP"); -@@ -899,7 +899,7 @@ public class Export { - return PathIterator.WIND_NON_ZERO; - } - -- return super.processShape(s); -+ return super.processShape(s, cached); - } - }; - g2d.setGraphicContext(new GraphicContext()); -@@ -1029,7 +1029,7 @@ public class Export { - } - - @Override -- public int processShape(Shape s) throws IOException { -+ public int processShape(Shape s, boolean cached) throws IOException { - if (s instanceof Ellipse2D.Double) { - Ellipse2D.Double ell = (Ellipse2D.Double) s; - if (ell.height == ell.width) { -@@ -1052,10 +1052,10 @@ public class Export { - buffer.append("[").append(gen.formatDouble(coords[0])).append(" ").append(gen.formatDouble(coords[1])); - it.next(); - } else { -- return super.processShape(s); -+ return super.processShape(s, cached); - } - } else { -- return super.processShape(s); -+ return super.processShape(s, cached); - } - - for (; !it.isDone(); it.next()) { -@@ -1063,7 +1063,7 @@ public class Export { - if (type == PathIterator.SEG_LINETO) { - buffer.append(" ").append(gen.formatDouble(coords[0])).append(" ").append(gen.formatDouble(coords[1])); - } else { -- return super.processShape(s); -+ return super.processShape(s, cached); - } - } - buffer.append("] DP"); -@@ -1071,7 +1071,7 @@ public class Export { - return PathIterator.WIND_NON_ZERO; - } - -- return super.processShape(s); -+ return super.processShape(s, cached); - } - - }; diff --git a/sci-mathematics/scilab/files/scilab.bash_completion b/sci-mathematics/scilab/files/scilab.bash_completion deleted file mode 100644 index c289e8632..000000000 --- a/sci-mathematics/scilab/files/scilab.bash_completion +++ /dev/null @@ -1,54 +0,0 @@ -# Scilab completion -# Scilab ( http://www.scilab.org/ ) - This file is part of Scilab -# Copyright (C) DIGITEO - 2010 - Sylvestre Ledru -# This file must be used under the terms of the CeCILL. -# This source file is licensed as described in the file COPYING, which -# you should have received as part of this distribution. The terms -# are also available at -# http://www.cecill.info/licences/Licence_CeCILL_V2-en.txt - -_scilab() -{ - local cur prev options - COMPREPLY=() - cur=${COMP_WORDS[COMP_CWORD]} - prev=${COMP_WORDS[COMP_CWORD-1]} - - # List all options. Note that - options='-ns -nb -nw -nwni -nogui -debug -debug-kdbg -d -display -profiling -profiling-visu -l -mem -version -e -f -nouserstartup -args -mem -h --help' - - # Loop on the arguments to manage conflicting options - for (( i=0; i < ${#COMP_WORDS[@]}-1; i++ )); do - #exclude some mutually exclusive options - [[ ${COMP_WORDS[i]} == '-nwni' ]] && options=${options/-nw} - [[ ${COMP_WORDS[i]} == '-nw' ]] && options=${options/-nwni} - [[ ${COMP_WORDS[i]} == '-e' ]] && options=${options/-f} - done - - case "$1" in - *scilab-cli*) - # Option -nw is not available - options=${options/-nw} - ;; - esac - - case $prev in - -f) - _filedir '@(sci|sce|SCI|SCE|tst|TST)' - return 0 - ;; - -e|-l|-d|-display|-mem) - cur=${cur#[\"\']} - eqext='=' - ;; - - *) - COMPREPLY=( $( compgen -W "$options" | grep "^$cur" ) ) - ;; - esac - - return 0 -} -complete -F _scilab $filenames scilab scilab-cli scilab-adv-cli - - diff --git a/sci-mathematics/scilab/files/scilab.xml b/sci-mathematics/scilab/files/scilab.xml deleted file mode 100644 index 8594e7bdc..000000000 --- a/sci-mathematics/scilab/files/scilab.xml +++ /dev/null @@ -1,13 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info"> - <mime-type type="text/x-sci"> - <comment>Scilab Function</comment> - <sub-class-of type="text/plain"/> - <glob pattern="*.sci"/> - </mime-type> - <mime-type type="text/x-sce"> - <comment>Scilab Script</comment> - <sub-class-of type="text/plain"/> - <glob pattern="*.sce"/> - </mime-type> -</mime-info> diff --git a/sci-mathematics/scilab/metadata.xml b/sci-mathematics/scilab/metadata.xml deleted file mode 100644 index ef72c6a0f..000000000 --- a/sci-mathematics/scilab/metadata.xml +++ /dev/null @@ -1,24 +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> - <longdescription lang="en"> -Scilab is a matrix-based scientific software package. Scilab contains -hundreds of built-in mathematical functions, rich data structures -(including polynomials, rationals,linear systems, lists, etc...) and -comes with a number of specific toolboxes for control, signal -processing, ... -</longdescription> - <use> - <flag name="gui">Build the Java base graphical interface</flag> - <flag name="umfpack">Adds support for sparse solving -with <pkg>sci-libs/umfpack</pkg></flag> - <flag name="matio">Enable support for MATLAB file through <pkg>sci-libs/matio</pkg></flag> - <flag name="xcos">Enable building hybrid dynamic systems modeler and -simulator Xcos</flag> - <flag name="emf">Add suport for exporting to emf files</flag> - </use> -</pkgmetadata> diff --git a/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild b/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild deleted file mode 100644 index c655c1324..000000000 --- a/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild +++ /dev/null @@ -1,290 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -JAVA_PKG_OPT_USE="gui" -VIRTUALX_REQUIRED="manual" - -inherit autotools bash-completion-r1 check-reqs eutils flag-o-matic \ - fortran-2 java-pkg-opt-2 pax-utils toolchain-funcs virtualx xdg-utils - -DESCRIPTION="Scientific software package for numerical computations" -HOMEPAGE="http://www.scilab.org/" -SRC_URI="http://www.scilab.org/download/${PV}/${P}-src.tar.gz" - -LICENSE="CeCILL-2.1" -SLOT="0" -KEYWORDS="" -IUSE="bash-completion debug doc emf fftw +gui +matio mpi nls openmp - static-libs test tk +umfpack +xcos" -REQUIRED_USE="xcos? ( gui ) doc? ( gui )" - -RESTRICT="test" - -IUSE_L10N="fr zh zh ru ca de es pt ja it uk pl cs" -L10N_DOC="fr pt ja ru" - -map_lang() { - local lang=${1/_/-} - case $1 in - # Retain the following, which have a specific subtag - de_*|en_*|pt_*|zh_*) ;; - # Consider all other xx_XX as duplicates of the generic xx tag - *_*) lang=${1%%_*} ;; - esac - echo ${lang} -} - -prev_l= -for l in ${IUSE_L10N}; do - l=$(map_lang ${l}) - [[ ${l} != "${prev_l}" ]] && IUSE+=" l10n_${l}" - prev_l=${l} -done -unset l prev_l - -CDEPEND=" - dev-libs/libpcre - dev-libs/libxml2:2 - sci-libs/hdf5[mpi=] - >=sci-libs/arpack-3 - sys-devel/gettext - sys-libs/ncurses:0= - sys-libs/readline:0= - virtual/lapack - emf? ( - dev-java/freehep-graphicsio:0 - dev-java/freehep-graphicsio-emf:0 - dev-java/freehep-graphics2d:0 - dev-java/freehep-io:0 - dev-java/freehep-graphicsbase:0 - ) - fftw? ( sci-libs/fftw:3.0 ) - gui? ( - dev-java/avalon-framework:4.2 - >=dev-java/batik-1.8-r2:1.8 - dev-java/commons-io:1 - dev-java/commons-logging:0 - >=dev-java/flexdock-1.2.4:0 - >=dev-java/fop-2.0:0 - =dev-java/gluegen-2.2.4:2.2 - dev-java/javahelp:0 - dev-java/jeuclid-core:0 - dev-java/jgoodies-looks:2.6 - >=dev-java/jlatexmath-1.0.3:1 - >=dev-java/jlatexmath-fop-1.0.3:1 - =dev-java/jogl-2.2.4:2.2 - >=dev-java/jrosetta-1.0.4:0 - dev-java/skinlf:0 - dev-java/xmlgraphics-commons:2 - virtual/opengl - xcos? ( dev-java/jgraphx:2.5 ) - ) - matio? ( >=sci-libs/matio-1.5 ) - tk? ( dev-lang/tk:0= ) - umfpack? ( sci-libs/umfpack )" - -RDEPEND="${CDEPEND} - gui? ( >=virtual/jre-1.5 )" - -DEPEND="${CDEPEND} - virtual/pkgconfig - debug? ( dev-util/lcov ) - gui? ( - >=virtual/jdk-1.6 - doc? ( app-text/docbook-xsl-stylesheets - dev-java/xml-commons-external:1.4 - dev-java/saxon:9 ) - xcos? ( dev-lang/ocaml ) - ) - test? ( - dev-java/junit:4 - gui? ( ${VIRTUALX_DEPEND} ) )" - -DOCS=( "ACKNOWLEDGEMENTS" "README_Unix" "Readme_Visual.txt" ) - -PATCHES=( - "${FILESDIR}/${P}-followlinks.patch" - "${FILESDIR}/${P}-gluegen.patch" - "${FILESDIR}/${P}-fix-random-runtime-failure.patch" - "${FILESDIR}/${P}-accessviolation.patch" - "${FILESDIR}/${P}-missinglib.patch" - "${FILESDIR}/${P}-batik-1.8.patch" - "${FILESDIR}/${P}-fop-2.0.patch" - "${FILESDIR}/${P}-xmlgraphics-common-2.0.patch" - "${FILESDIR}/${P}-freehep.patch" -) - -pkg_pretend() { - use doc && CHECKREQS_MEMORY="512M" check-reqs_pkg_pretend -} - -pkg_setup() { - if use openmp; then - if [[ $(tc-getCC) == *gcc* ]] && ! tc-has-openmp; then - ewarn "You are using a gcc without OpenMP capabilities" - die "Need an OpenMP capable compiler" - fi - FORTRAN_NEED_OPENMP=1 - fi - FORTRAN_STANDARD="77 90" - fortran-2_pkg_setup - #bug 8053 - unset F77 - java-pkg-opt-2_pkg_setup - - ALL_L10N="en_US" - ALL_L10N_DOC="en_US" - for l in ${IUSE_L10N}; do - use l10n_${l} && ALL_L10N="${ALL_L10N} ${l}" - done - for l in ${L10N_DOC}; do - use l10n_${l} && ALL_L10N_DOC="${ALL_L10N_DOC} ${l}" - done - export ALL_L10N ALL_L10N_DOC -} - -src_prepare() { - default - - # works for me on x86, but users are having - # trouble without see #282 on github - append-ldflags $(no-as-needed) - - # increases java heap to 512M when building docs (sync with cheqreqs above) - use doc && eapply "${FILESDIR}/${P}-java-heap.patch" - - # use the L10N variable that we set - sed -i -e "/^ALL_LINGUAS=/d" -e "/^ALL_LINGUAS_DOC=/d" -i configure.ac ||die - - # make sure the DOCBOOK_ROOT variable is set - sed -i -e "s/xsl-stylesheets-\*/xsl-stylesheets/g" bin/scilab* || die - - # remove self closing <br /> (error our with javadoc8) - # already upstream commit 2103082c - find . -name '*.java' -exec sed -i "s|<br />|<BR>|" {} \; ||die - - #add specific gentoo java directories - if use gui; then - sed -i -e "s|/usr/lib/jogl2|/usr/lib/jogl-2.2|" \ - -e "s|/usr/lib64/jogl2|/usr/lib64/jogl-2.2|" configure.ac || die - sed -i -e "s|/usr/lib/gluegen2|/usr/lib/gluegen-2.2|" \ - -e "s|/usr/lib64/gluegen2|/usr/lib64/gluegen-2.2|" \ - -e "s|AC_CHECK_LIB(\[gluegen2-rt|AC_CHECK_LIB([gluegen-rt|" \ - configure.ac || die - - sed -i -e "s/jogl2/jogl-2.2/" -e "s/gluegen2/gluegen-2.2/" \ - etc/librarypath.xml || die - fi - - mkdir jar || die - pushd jar >/dev/null - if use gui; then - java-pkg_jar-from jlatexmath-1,flexdock,skinlf - java-pkg_jar-from jgoodies-looks-2.6,jrosetta - java-pkg_jar-from avalon-framework-4.2,jeuclid-core - java-pkg_jar-from xmlgraphics-commons-2,commons-io-1 - java-pkg_jar-from jogl-2.2 jogl-all.jar jogl2.jar - java-pkg_jar-from gluegen-2.2 gluegen-rt.jar gluegen2-rt.jar - java-pkg_jar-from fop fop.jar - java-pkg_jar-from javahelp jhall.jar - java-pkg_jar-from jlatexmath-fop-1 - use xcos && java-pkg_jar-from jgraphx-2.5 - if use doc; then - java-pkg_jar-from --build-only batik-1.8 batik-all.jar - java-pkg_jar-from --build-only saxon-9 saxon.jar saxon9he.jar - java-pkg_jar-from --build-only xml-commons-external-1.4 xml-apis-ext.jar - fi - fi - if use emf; then - java-pkg_jar-from freehep-graphicsio-emf,freehep-graphics2d - java-pkg_jar-from freehep-graphicsio,freehep-io,freehep-graphicsbase - fi - if use test; then - java-pkg_jar-from junit-4 junit.jar junit4.jar - java-pkg_jar-from ant-junit - fi - popd - - java-pkg-opt-2_src_prepare - eautoconf -} - -src_configure() { - if use gui; then - export JAVA_HOME="$(java-config -O)" - else - unset JAVAC - fi - - export BLAS_LIBS="$($(tc-getPKG_CONFIG) --libs blas)" - export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" - export F77_LDFLAGS="${LDFLAGS}" - - econf \ - --enable-relocatable \ - --disable-rpath \ - --with-docbook="${EPREFIX}/usr/share/sgml/docbook/xsl-stylesheets" \ - --disable-static-system-lib \ - $(use_enable debug) \ - $(use_enable debug code-coverage) \ - $(use_enable debug debug-C) \ - $(use_enable debug debug-CXX) \ - $(use_enable debug debug-fortran) \ - $(use_enable debug debug-java) \ - $(use_enable debug debug-linker) \ - $(use_enable doc build-help) \ - $(use_enable nls) \ - $(use_enable nls build-localization) \ - $(use_enable static-libs static) \ - $(use_enable test compilation-tests) \ - $(use_with emf) \ - $(use_with fftw) \ - $(use_with gui) \ - $(use_with gui javasci) \ - $(use_with matio) \ - $(use_with openmp) \ - $(use_with tk) \ - $(use_with umfpack) \ - $(use_with xcos) \ - $(use_with xcos modelica) \ - $(use_with mpi) -} - -src_compile() { - addpredict /proc/mtrr - default - pax-mark m .libs/scilab-bin - use doc && emake doc -} - -src_test() { - if use gui; then - Xemake check - else - emake check - fi -} - -src_install() { - default - prune_libtool_files --all - rm -rf "${D}"/usr/share/scilab/modules/*/tests ||die - use bash-completion && newbashcomp "${FILESDIR}"/"${PN}".bash_completion "${PN}" - echo "SEARCH_DIRS_MASK=${EPREFIX}/usr/$(get_libdir)/scilab" \ - > 50-"${PN}" - insinto /etc/revdep-rebuild && doins "50-${PN}" -} - -pkg_postinst() { - xdg_mimeinfo_database_update - einfo "If you are using the NVIDIA binary drivers, and run into graphics" - einfo "crashes, you may try to run scilab as follows:" - einfo "EGL_DRIVER=egl_glx scilab" - einfo "See upstream http://bugzilla.scilab.org/show_bug.cgi?id=12940" -} - -pkg_postrm() { - xdg_mimeinfo_database_update -} diff --git a/sci-mathematics/slepc/Manifest b/sci-mathematics/slepc/Manifest deleted file mode 100644 index 8f4488e93..000000000 --- a/sci-mathematics/slepc/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST slepc-3.10.0.tar.gz 4565134 BLAKE2B 88546893525d1744b37d2190ba57c49c0c59022cc43b235f6fa91a4ff57b077ac114ce6e2cd72fee74cb35cb271821ccc7fc511dc5a2432fe436f2bf57fb69f4 SHA512 f182c5e612f1aa5ca436bcb0ad812f216f6e5eaebf16683cab5c8fba63d29ffd55c9fb69377dd9bce3b32f3e6dec4a681face5d960ed1c78bb78cdc0ffe913d9 -DIST slepc-3.10.2.tar.gz 4566198 BLAKE2B 3699f350871f1b48fe024ae55a4b27f3cd41558fc86968e9a54502fe5807a807e1aad5b8f6ed38d3eeac06aa41ccd298f03525441fed35927ed174410eec24d0 SHA512 07eacc8532dfdd8976fbffa0fc5664c377816f42ccba9bdcdc3f11fdc26557b0c86ed16c4d56f089837ef46206b82d99b97f782367137d16af2dae2b2250954f -DIST slepc-3.8.2.tar.gz 4305725 BLAKE2B 7a8a0281cea19fb3c4b45ad98c277acff9d743c45e44af0600fe69c03b25d168994782daee01da7edb584adc1fce75badc6786752f70c1a751b59181b43476b3 SHA512 4d2cbcdd9ecc5e7fca10df85c0248874f379df4c7c5f6158e6896e9d5beced69c8755baf706418cd46dc2a82872a916d244b92b9fef4a7d6e8213d4899729a3e -DIST slepc-3.9.0.tar.gz 4473419 BLAKE2B 1d64dc0ed0fd8617c6d17dcc53064ad3ceca8fd5392ea37ff82923c7d5c6740eaabdfc2b033f5e773e62c28d5e21cb3403d3f3b01c578f154aa9be80dbf6e97f SHA512 490403e42a2f02f56db7a9edda1c6f4d7454f6c14645ee12511a8a0551de5ea238d39dde4a5b854f82cc161582c73a5bf392b07c9161bb9a89e600ad53e28909 diff --git a/sci-mathematics/slepc/metadata.xml b/sci-mathematics/slepc/metadata.xml deleted file mode 100644 index 046ec6c8f..000000000 --- a/sci-mathematics/slepc/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="person"> - <email>tamiko@gentoo.org</email> - <name>Matthias Maier</name> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <use> - <flag name="complex-scalars">Make scalars complex</flag> - </use> -</pkgmetadata> diff --git a/sci-mathematics/slepc/slepc-3.10.0.ebuild b/sci-mathematics/slepc/slepc-3.10.0.ebuild deleted file mode 100644 index 5bd6c4b95..000000000 --- a/sci-mathematics/slepc/slepc-3.10.0.ebuild +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils flag-o-matic python-any-r1 toolchain-funcs versionator - -DESCRIPTION="Scalable Library for Eigenvalue Problem Computations" -HOMEPAGE="http://slepc.upv.es/" -SRC_URI="http://slepc.upv.es/download/distrib/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="complex-scalars doc mpi" - -PETSC_PV="$(get_version_component_range 1-2 ${PV})" -RDEPEND=" - =sci-mathematics/petsc-${PETSC_PV}*:=[mpi=,complex-scalars=] - sci-libs/arpack[mpi=] - mpi? ( virtual/mpi ) -" - -DEPEND="${RDEPEND} - ${PYTHON_DEPS} - virtual/pkgconfig - dev-util/cmake -" - -MAKEOPTS="${MAKEOPTS} -j1 V=1" - -src_prepare() { - default - - sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die -} - -src_configure() { - # *sigh* - addpredict "${PETSC_DIR}"/.nagged - - # Make sure that the environment is set up correctly: - unset PETSC_DIR - unset PETSC_ARCH - unset SLEPC_DIR - source "${EPREFIX}"/etc/env.d/99petsc - export PETSC_DIR - - # configure is a custom python script and doesn't want to have default - # configure arguments that we set with econf - ./configure \ - --prefix="${EPREFIX}/usr/$(get_libdir)/slepc" \ - --with-arpack=1 \ - --with-arpack-dir="${EPREFIX}/usr/$(get_libdir)" \ - --with-arpack-flags="$(usex mpi "-lparpack,-larpack" "-larpack")" - -} - -src_install() { - emake SLEPC_DESTDIR="${D}/usr/$(get_libdir)/slepc" install - - # add PETSC_DIR to environmental variables - cat >> 99slepc <<- EOF - SLEPC_DIR=${EPREFIX}/usr/$(get_libdir)/slepc - EOF - doenvd 99slepc - - if use doc ; then - dodoc docs/slepc.pdf - dohtml -r docs/*.html docs/manualpages - fi -} diff --git a/sci-mathematics/slepc/slepc-3.10.2.ebuild b/sci-mathematics/slepc/slepc-3.10.2.ebuild deleted file mode 100644 index 2009090c1..000000000 --- a/sci-mathematics/slepc/slepc-3.10.2.ebuild +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils flag-o-matic python-any-r1 toolchain-funcs versionator - -DESCRIPTION="Scalable Library for Eigenvalue Problem Computations" -HOMEPAGE="http://slepc.upv.es/" -SRC_URI="http://slepc.upv.es/download/distrib/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="complex-scalars doc mpi" - -PETSC_PV="$(get_version_component_range 1-2 ${PV})" -RDEPEND=" - =sci-mathematics/petsc-${PETSC_PV}*:=[mpi=,complex-scalars=] - sci-libs/arpack[mpi=] - mpi? ( virtual/mpi ) -" - -DEPEND="${RDEPEND} - ${PYTHON_DEPS} - virtual/pkgconfig - dev-util/cmake -" - -MAKEOPTS="${MAKEOPTS} -j1 V=1" - -src_prepare() { - default - - sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die -} - -src_configure() { - # *sigh* - addpredict "${PETSC_DIR}"/.nagged - - # Make sure that the environment is set up correctly: - unset PETSC_DIR - unset PETSC_ARCH - unset SLEPC_DIR - source "${EPREFIX}"/etc/env.d/99petsc - export PETSC_DIR - - # configure is a custom python script and doesn't want to have default - # configure arguments that we set with econf - ./configure \ - --prefix="${EPREFIX}/usr/$(get_libdir)/slepc" \ - --with-arpack=1 \ - --with-arpack-dir="${EPREFIX}/usr/$(get_libdir)" \ - --with-arpack-flags="$(usex mpi "-lparpack,-larpack" "-larpack")" - -} - -src_install() { - emake SLEPC_DESTDIR="${D}/usr/$(get_libdir)/slepc" install - - # add PETSC_DIR to environmental variables - cat >> 99slepc <<- EOF - SLEPC_DIR=${EPREFIX}/usr/$(get_libdir)/slepc - EOF - doenvd 99slepc - - if use doc ; then - dodoc docs/slepc.pdf - dohtml -r docs/*.html docs/manualpages - fi -} diff --git a/sci-mathematics/slepc/slepc-3.8.2.ebuild b/sci-mathematics/slepc/slepc-3.8.2.ebuild deleted file mode 100644 index 5bd6c4b95..000000000 --- a/sci-mathematics/slepc/slepc-3.8.2.ebuild +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils flag-o-matic python-any-r1 toolchain-funcs versionator - -DESCRIPTION="Scalable Library for Eigenvalue Problem Computations" -HOMEPAGE="http://slepc.upv.es/" -SRC_URI="http://slepc.upv.es/download/distrib/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="complex-scalars doc mpi" - -PETSC_PV="$(get_version_component_range 1-2 ${PV})" -RDEPEND=" - =sci-mathematics/petsc-${PETSC_PV}*:=[mpi=,complex-scalars=] - sci-libs/arpack[mpi=] - mpi? ( virtual/mpi ) -" - -DEPEND="${RDEPEND} - ${PYTHON_DEPS} - virtual/pkgconfig - dev-util/cmake -" - -MAKEOPTS="${MAKEOPTS} -j1 V=1" - -src_prepare() { - default - - sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die -} - -src_configure() { - # *sigh* - addpredict "${PETSC_DIR}"/.nagged - - # Make sure that the environment is set up correctly: - unset PETSC_DIR - unset PETSC_ARCH - unset SLEPC_DIR - source "${EPREFIX}"/etc/env.d/99petsc - export PETSC_DIR - - # configure is a custom python script and doesn't want to have default - # configure arguments that we set with econf - ./configure \ - --prefix="${EPREFIX}/usr/$(get_libdir)/slepc" \ - --with-arpack=1 \ - --with-arpack-dir="${EPREFIX}/usr/$(get_libdir)" \ - --with-arpack-flags="$(usex mpi "-lparpack,-larpack" "-larpack")" - -} - -src_install() { - emake SLEPC_DESTDIR="${D}/usr/$(get_libdir)/slepc" install - - # add PETSC_DIR to environmental variables - cat >> 99slepc <<- EOF - SLEPC_DIR=${EPREFIX}/usr/$(get_libdir)/slepc - EOF - doenvd 99slepc - - if use doc ; then - dodoc docs/slepc.pdf - dohtml -r docs/*.html docs/manualpages - fi -} diff --git a/sci-mathematics/slepc/slepc-3.9.0.ebuild b/sci-mathematics/slepc/slepc-3.9.0.ebuild deleted file mode 100644 index 5bd6c4b95..000000000 --- a/sci-mathematics/slepc/slepc-3.9.0.ebuild +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils flag-o-matic python-any-r1 toolchain-funcs versionator - -DESCRIPTION="Scalable Library for Eigenvalue Problem Computations" -HOMEPAGE="http://slepc.upv.es/" -SRC_URI="http://slepc.upv.es/download/distrib/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="complex-scalars doc mpi" - -PETSC_PV="$(get_version_component_range 1-2 ${PV})" -RDEPEND=" - =sci-mathematics/petsc-${PETSC_PV}*:=[mpi=,complex-scalars=] - sci-libs/arpack[mpi=] - mpi? ( virtual/mpi ) -" - -DEPEND="${RDEPEND} - ${PYTHON_DEPS} - virtual/pkgconfig - dev-util/cmake -" - -MAKEOPTS="${MAKEOPTS} -j1 V=1" - -src_prepare() { - default - - sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die -} - -src_configure() { - # *sigh* - addpredict "${PETSC_DIR}"/.nagged - - # Make sure that the environment is set up correctly: - unset PETSC_DIR - unset PETSC_ARCH - unset SLEPC_DIR - source "${EPREFIX}"/etc/env.d/99petsc - export PETSC_DIR - - # configure is a custom python script and doesn't want to have default - # configure arguments that we set with econf - ./configure \ - --prefix="${EPREFIX}/usr/$(get_libdir)/slepc" \ - --with-arpack=1 \ - --with-arpack-dir="${EPREFIX}/usr/$(get_libdir)" \ - --with-arpack-flags="$(usex mpi "-lparpack,-larpack" "-larpack")" - -} - -src_install() { - emake SLEPC_DESTDIR="${D}/usr/$(get_libdir)/slepc" install - - # add PETSC_DIR to environmental variables - cat >> 99slepc <<- EOF - SLEPC_DIR=${EPREFIX}/usr/$(get_libdir)/slepc - EOF - doenvd 99slepc - - if use doc ; then - dodoc docs/slepc.pdf - dohtml -r docs/*.html docs/manualpages - fi -} diff --git a/sci-mathematics/tisean/Manifest b/sci-mathematics/tisean/Manifest deleted file mode 100644 index 3139928c2..000000000 --- a/sci-mathematics/tisean/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST TISEAN_3.0.1.tar.gz 876454 BLAKE2B 5d1fb099fb28650d0a93b53ef52f332257ab87046f3ad4823c8c2b64e282ff681d839a193cec52a6a7b3934cdd1abaf5359e2954a501790f8fa06d61d49f41d9 SHA512 7c69f4189d0aeaadcd5d558f672bd2db0f4aa8d43bb390e54d283ae4a7a562446f909d46426da3de058c99ec54c84e8d7a69cec82a9b1772a946f5a7a5861f33 diff --git a/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch b/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch deleted file mode 100644 index dc86d1f16..000000000 --- a/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch +++ /dev/null @@ -1,752 +0,0 @@ -From 377911cf0ba30428e8e6095162ac9d63689838b8 Mon Sep 17 00:00:00 2001 -From: Rainer Hegger <hegger@theochem.uni-frankfurt.de> -Date: Thu, 16 Apr 2015 15:49:31 +0200 -Subject: [PATCH] Collected changes over the last years - ---- - configure | 22 +++++----- - docs/docs_c/corr.html | 5 +++ - docs/docs_c/lfo-ar.html | 2 +- - docs/docs_c/lyap_spec.html | 4 +- - docs/tutorial/ex1.html | 2 +- - docs/tutorial/ex2.html | 10 ++--- - docs/tutorial/ex3.html | 2 +- - source_c/corr.c | 28 +++++++++--- - source_c/false_nearest.c | 10 ++++- - source_c/histogram.c | 55 +++++++++++++++--------- - source_c/lzo-run.c | 2 +- - source_c/mem_spec.c | 5 ++- - source_c/mutual.c | 105 +++++++++++++++++++++++++++++---------------- - source_c/polynom.c | 7 ++- - source_c/polynomp.c | 2 +- - source_c/xcor.c | 2 +- - source_f/cluster.f | 3 +- - 17 files changed, 172 insertions(+), 94 deletions(-) - -diff --git a/configure b/configure -index c27cf28..095e16d 100755 ---- a/configure -+++ b/configure -@@ -35,17 +35,17 @@ verbose= - x_includes=NONE - x_libraries=NONE - bindir='bin' --sbindir='${exec_prefix}/sbin' --libexecdir='${exec_prefix}/libexec' --datadir='${prefix}/share' --sysconfdir='${prefix}/etc' --sharedstatedir='${prefix}/com' --localstatedir='${prefix}/var' --libdir='${exec_prefix}/lib' --includedir='${prefix}/include' -+sbindir='sbin' -+libexecdir='libexec' -+datadir='share' -+sysconfdir='etc' -+sharedstatedir='com' -+localstatedir='var' -+libdir='lib' -+includedir='include' - oldincludedir='/usr/include' --infodir='${prefix}/info' --mandir='${prefix}/man' -+infodir='info' -+mandir='man' - - # Initialize some other variables. - subdirs= -@@ -1020,7 +1020,7 @@ fi - - - --for fff in "$FC" f77 g77 "f77 +U77" "f77 -q -f -B108 -lU77"; do -+for fff in "$FC" f77 g77 gfortran "f77 +U77" "f77 -q -f -B108 -lU77"; do - if test -z "$fff"; then - continue - fi -diff --git a/docs/docs_c/corr.html b/docs/docs_c/corr.html -index 8b2eb8c..f2aa4f2 100644 ---- a/docs/docs_c/corr.html -+++ b/docs/docs_c/corr.html -@@ -57,6 +57,11 @@ <h2 align=center>Usage:</h2> - <td>100 - </tr> - <tr> -+<th>-s# -+<td>calculate the correlation only every #-th step -+<td>1 -+</tr> -+<tr> - <th>-n - <td>don't use normalization to standard deviation - <td>not set -diff --git a/docs/docs_c/lfo-ar.html b/docs/docs_c/lfo-ar.html -index 59263b6..11a9b4e 100644 ---- a/docs/docs_c/lfo-ar.html -+++ b/docs/docs_c/lfo-ar.html -@@ -117,7 +117,7 @@ <h2 align=center>Description of the Output:</h2> - The output consists of 5 columns for each neighborhood size:</b> - <ul> - <li> neighborhood size (units of the data) --<li> relative forecast error ((forecast error)/(variance of the data)) -+<li> relative forecast error ((forecast error)/(standard deviation of data)) - <li> fraction of points for which neighbors were found for this neighborhood - size - <li> average number of neighbors found per point -diff --git a/docs/docs_c/lyap_spec.html b/docs/docs_c/lyap_spec.html -index ab67d84..189482a 100644 ---- a/docs/docs_c/lyap_spec.html -+++ b/docs/docs_c/lyap_spec.html -@@ -58,7 +58,9 @@ <h2 align=center>Usage:</h2> - --> - <tr> - <th>-r# --<td>minimal neighborhood size -+<td>minimal neighborhood size. This option dominates -k. This means -+ that if -r is set and more than -k neighbors are found, the number -+ of neighbors will not be reduced to the value given with -k. - <td>not set - </tr> - <tr> -diff --git a/docs/tutorial/ex1.html b/docs/tutorial/ex1.html -index e77be7b..660811b 100644 ---- a/docs/tutorial/ex1.html -+++ b/docs/tutorial/ex1.html -@@ -146,7 +146,7 @@ - variable <font color=blue>x </font> of the logistic equation for - various parameter values (e.g.: <font color=green> - gnuplot> plot '< henon -B0 -A2 -l10000 | histogram -b100' with --hist</font>). When a sufficiently long transient has been -+histeps</font>). When a sufficiently long transient has been - discarded, such a histogram is the approximation to the invaraint - measure on the bins of the histogram. Verify numerically:<br> - <ul> -diff --git a/docs/tutorial/ex2.html b/docs/tutorial/ex2.html -index 5324a15..a0fbb11 100644 ---- a/docs/tutorial/ex2.html -+++ b/docs/tutorial/ex2.html -@@ -82,7 +82,7 @@ - the two histograms, you thus should shift the one with respect to the - other by the mean value of the data:<br> - <font color=green> --set data style histep<br> -+set style data histep<br> - plot '< histogram amplitude.dat' u ($1-.146):2,'< histogram - ar.dat' </font> - <br>Result: The data sets are differnt: the distribution of <font -@@ -95,7 +95,7 @@ - <a href="../docs_f/spectrum.html">spectrum</a>) of both of them:<br> - <font color=red> corr amplitude.dat -D500 -o<br> - corr ar.dat -D500 -o</font><br> --<font color=green>set data style lines</font><br> -+<font color=green>set style data lines</font><br> - <font color=green> plot 'ar.dat.cor','amplitude.dat.cor'</font><br> - <font color=red>spectrum amplitude.dat -o<br> - spectrum ar.dat -o</font><br> -@@ -150,7 +150,7 @@ - <ul> - <li> compute the false nearest neighbour statistics - (<a href="../docs_c/false_nearest.html">false_nearest</a>):<br> --<font color=red> false_nearest amplitude.dat -M8 -d8 -o -+<font color=red> false_nearest amplitude.dat -M1,8 -d8 -o - -t200 -f5 </font><br> - Study the output, <font color=blue>amplitude.dat.fnn</font>, and - observe the invariance of the result (namely that the embedding dimension -@@ -158,9 +158,9 @@ - <br><br> - - <li> Use the zeorth-order predictor --(<a href="../docs_c/zeroth.html">zeroth</a>) -+(<a href="../docs_c/lzo-test.html">zeroth</a>) - on amplitude.dat and on ar.dat.<br> --<font color=red> zeroth amplitude.dat -m1,4 -d8 -o -+<font color=red> lzo-test amplitude.dat -m1,4 -d8 -o - -s250<br> - zeroth ar.dat -m1,4 -d8 -o - -s250</font><br> -diff --git a/docs/tutorial/ex3.html b/docs/tutorial/ex3.html -index 91735dd..2894689 100644 ---- a/docs/tutorial/ex3.html -+++ b/docs/tutorial/ex3.html -@@ -196,7 +196,7 @@ - <font color=red> ll-ar optimal.dat -d10 -m3 -i2000 -s1 -o</font>,<br> - and compare the results:<br> - <font color=green> --set data style linespoints<br> -+set style data linespoints<br> - plot 'whatisit.dat.ll', 'whatisit.dat.ll' u 1:3,'optimal.dat.ll', - 'optimal.dat.ll' u 1:3</font><br> - <br> -diff --git a/source_c/corr.c b/source_c/corr.c -index 06da07a..4c79b9a 100644 ---- a/source_c/corr.c -+++ b/source_c/corr.c -@@ -30,7 +30,7 @@ - char *format,*outfile=NULL,stout=1,normalize=1; - unsigned int column=1; - unsigned int verbosity=0xff; --unsigned long tau=100,length=ULONG_MAX,exclude=0; -+unsigned long tau=100,step=1,length=ULONG_MAX,exclude=0; - double *array; - double av,var; - char *infile=NULL; -@@ -48,6 +48,8 @@ void show_options(char *progname) - fprintf(stderr,"\t-x # of lines to be ignored [default 0]\n"); - fprintf(stderr,"\t-c column to read [default is 1]\n"); - fprintf(stderr,"\t-D corrlength [default is 100]\n"); -+ fprintf(stderr,"\t-s # calculate the correlation only every #-th step " -+ "[default is 1]\n"); - fprintf(stderr,"\t-n don\'t normalize to the variance" - " of the data [not set]\n"); - fprintf(stderr,"\t-o output_file [default is 'datafile'.cor; no -o" -@@ -72,6 +74,8 @@ void scan_options(int argc,char **argv) - sscanf(out,"%u",&column); - if ((out=check_option(argv,argc,'D','u')) != NULL) - sscanf(out,"%lu",&tau); -+ if ((out=check_option(argv,argc,'s','u')) != NULL) -+ sscanf(out,"%lu",&step); - if ((out=check_option(argv,argc,'n','n')) != NULL) - normalize=0; - if ((out=check_option(argv,argc,'V','u')) != NULL) -@@ -88,16 +92,17 @@ double corr(long i) - long j; - double c=0.0; - -- for (j=0;j<(length-i);j++) -+ for (j=0;j<(length-i);j++) { - c += array[j]*array[j+i]; -+ } - -- return c/(length-i); -+ return c/(double)(length-i); - } - - int main(int argc,char** argv) - { -- char stdi=0; -- long i; -+ char stdi=0,done=0; -+ unsigned long i; - FILE *fout=NULL; - - if (scan_help(argc,argv)) -@@ -157,14 +162,25 @@ int main(int argc,char** argv) - else - var=1.0; - -- for (i=0;i<=tau;i++) -+ for (i=0;i<=tau;i += step) - if (!stout) { - fprintf(fout,"%ld %e\n",i,corr(i)/var); - fflush(fout); -+ if (i == tau) done=1; - } - else { - fprintf(stdout,"%ld %e\n",i,corr(i)/var); - fflush(stdout); -+ if (i == tau) done=1; -+ } -+ if (!done) -+ if (!stout) { -+ fprintf(fout,"%ld %e\n",tau,corr(tau)/var); -+ fflush(fout); -+ } -+ else { -+ fprintf(stdout,"%ld %e\n",tau,corr(tau)/var); -+ fflush(stdout); - } - if (!stout) - fclose(fout); -diff --git a/source_c/false_nearest.c b/source_c/false_nearest.c -index f8a16e9..f5eed04 100644 ---- a/source_c/false_nearest.c -+++ b/source_c/false_nearest.c -@@ -21,6 +21,7 @@ - /*Changes: - 12/10/05: It's multivariate now - 12/16/05: Scaled <eps> and sigma(eps) -+ 03/08/09: delay was missing in delay embedding of univariate case - */ - - #include <stdio.h> -@@ -37,7 +38,7 @@ char *infile=NULL; - char stdo=1,dimset=0; - char *column=NULL; - unsigned long length=ULONG_MAX,exclude=0,theiler=0; --unsigned int delay=1,maxdim=5,minemb=1; -+unsigned int delay=1,maxdim=6,minemb=1; - unsigned int comp=1,maxemb=5; - unsigned int verbosity=0xff; - double rt=2.0; -@@ -226,6 +227,11 @@ int main(int argc,char **argv) - series=(double**)get_multi_series(infile,&length,exclude,&comp,column, - dimset,verbosity); - -+ if ((maxemb*delay+1) >= length) { -+ fprintf(stderr,"Not enough points!\n"); -+ exit(FALSE_NEAREST_NOT_ENOUGH_POINTS); -+ } -+ - for (i=0;i<comp;i++) { - rescale_data(series[i],length,&min,&ind_inter); - variance(series[i],length,&av,&ind_var); -@@ -259,7 +265,7 @@ int main(int argc,char **argv) - for (i=0;i<maxdim;i++) { - if (comp == 1) { - vcomp[i]=0; -- vemb[i]=i; -+ vemb[i]=i*delay; - } - else { - vcomp[i]=i%comp; -diff --git a/source_c/histogram.c b/source_c/histogram.c -index 6ab9f02..a45576d 100644 ---- a/source_c/histogram.c -+++ b/source_c/histogram.c -@@ -17,10 +17,8 @@ - * along with TISEAN; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - */ --/*Author: Rainer Hegger. Last modified Dec 6, 2005*/ --/*Changes: -- 12/06/05: shift output x value to center of interval --*/ -+/*Author: Rainer Hegger. Last modified May 16, 2014*/ -+ - #include <math.h> - #include <limits.h> - #include <stdio.h> -@@ -28,7 +26,7 @@ - #include <string.h> - #include "routines/tsa.h" - --#define WID_STR "Makes a histogram of the data" -+#define WID_STR "Creates a histogram of a onedimensional dataset" - - unsigned long length=ULONG_MAX; - unsigned long base=50; -@@ -36,15 +34,10 @@ unsigned long exclude=0; - unsigned int column=1; - unsigned int verbosity=0xff; - double size; --char my_stdout=1,gotsize=0; -+char my_stdout=1,gotsize=0,density=0; - char *outfile=NULL; - char *infile=NULL; - --double *series; --double average,var; --double min,max; --long *box; -- - void show_options(char *progname) - { - what_i_do(progname,WID_STR); -@@ -57,6 +50,8 @@ void show_options(char *progname) - fprintf(stderr,"\t-x # of lines to ignore [default %ld]\n",exclude); - fprintf(stderr,"\t-c column to read [default %d]\n",column); - fprintf(stderr,"\t-b # of intervals [default %ld]\n",base); -+ fprintf(stderr,"\t-D output densities not relative frequencies" -+ " [default not set]\n"); - fprintf(stderr,"\t-o output file [default 'datafile'.dat ;" - " If no -o is given: stdout]\n"); - fprintf(stderr,"\t-V verbosity level [default 1]\n\t\t" -@@ -80,6 +75,8 @@ void scan_options(int n,char **str) - sscanf(out,"%lu",&base); - if ((out=check_option(str,n,'V','u')) != NULL) - sscanf(out,"%u",&verbosity); -+ if ((out=check_option(str,n,'D','n')) != NULL) -+ density=1; - if ((out=check_option(str,n,'o','o')) != NULL) { - my_stdout=0; - if (strlen(out) > 0) -@@ -92,6 +89,10 @@ int main(int argc,char **argv) - char stdi=0; - unsigned long i,j; - double x,norm,size=1.0,size2=1.0; -+ double min,max; -+ double *series; -+ double average,var; -+ long *box; - FILE *fout; - - if (scan_help(argc,argv)) -@@ -123,24 +124,36 @@ int main(int argc,char **argv) - - series=(double*)get_series(infile,&length,exclude,column,verbosity); - variance(series,length,&average,&var); -- rescale_data(series,length,&min,&max); -- -- -+ -+ min=max=series[0]; -+ for (i=1;i<length;i++) { -+ if (series[i] < min) min=series[i]; -+ else if (series[i] > max) max=series[i]; -+ } -+ max -= min; -+ -+ for (i=0;i<length;i++) -+ series[i]=(series[i]-min); -+ - if (base > 0) { - check_alloc(box=(long*)malloc(sizeof(long)*base)); - for (i=0;i<base;i++) - box[i]=0; - size=1./base; -- size2=size/2.0; -+ size2=(1.0-size/2.0)*max; - for (i=0;i<length;i++) { -- if (series[i] > (1.0-size2)) -- series[i]=1.0-size2; -- j=(long)(series[i]*base); -+ if (series[i] > size2) -+ series[i]=size2; -+ j=(long)(series[i]*base/max); - box[j]++; - } - } - -- norm=1.0/(double)length; -+ if (!density) -+ norm=1.0/(double)length; -+ else -+ norm=1.0/(double)length*(double)base/max; -+ - if (!my_stdout) { - fout=fopen(outfile,"w"); - if (verbosity&VER_INPUT) -@@ -150,7 +163,7 @@ int main(int argc,char **argv) - fprintf(fout,"#standard deviation= %e\n",var); - for (i=0;i<base;i++) { - x=(double)(i*size); -- fprintf(fout,"%e %e\n",(x+size2)*max+min,(double)box[i]*norm); -+ fprintf(fout,"%e %e\n",(x+size/2.0)*max+min,(double)box[i]*norm); - } - fclose(fout); - } -@@ -162,7 +175,7 @@ int main(int argc,char **argv) - fprintf(stdout,"#standard deviation= %e\n",var); - for (i=0;i<base;i++) { - x=(double)(i*size); -- fprintf(stdout,"%e %e\n",(x+size2)*max+min,(double)box[i]*norm); -+ fprintf(stdout,"%e %e\n",(x+size/2.0)*max+min,(double)box[i]*norm); - fflush(stdout); - } - } -diff --git a/source_c/lzo-run.c b/source_c/lzo-run.c -index 5393e9f..bc54fb5 100644 ---- a/source_c/lzo-run.c -+++ b/source_c/lzo-run.c -@@ -49,7 +49,7 @@ unsigned int MINN=50; - unsigned int **indexes; - unsigned long LENGTH=ULONG_MAX,FLENGTH=1000,exclude=0; - unsigned long seed=0x9074325L; --double EPS0=1.e-3,EPSF=1.2,Q=10.0; -+double EPS0=1.e-3,EPSF=1.2,Q=0.0; - - double **mat,*vec,*hsum,*newav; - -diff --git a/source_c/mem_spec.c b/source_c/mem_spec.c -index a38fcfd..9821488 100644 ---- a/source_c/mem_spec.c -+++ b/source_c/mem_spec.c -@@ -22,6 +22,7 @@ - Feb 19, 2007: changed meaning of -f flag and added -P flag to be - consistent with spectrum - Dec 5, 2006: Seg fault when poles > length; -+ Mar 15, 2007: normalization now the same as in spectrum - */ - #include <stdio.h> - #include <string.h> -@@ -216,7 +217,7 @@ int main(int argc,char **argv) - fdt=i/(2.0*out); - pow_spec=powcoef(fdt,cof); - fprintf(fout,"%e %e\n",fdt*samplingrate, -- pm/pow_spec/sqrt((double)length)); -+ pm/pow_spec/(double)length); - fflush(fout); - } - fclose(fout); -@@ -233,7 +234,7 @@ int main(int argc,char **argv) - fdt=i/(2.0*out); - pow_spec=powcoef(fdt,cof); - fprintf(stdout,"%e %e\n",fdt*samplingrate, -- pm/pow_spec/*/sqrt((double)length)*/); -+ pm/pow_spec/(double)length); - } - } - -diff --git a/source_c/mutual.c b/source_c/mutual.c -index fbea470..0496e92 100644 ---- a/source_c/mutual.c -+++ b/source_c/mutual.c -@@ -17,7 +17,7 @@ - * along with TISEAN; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - */ --/*Author: Rainer Hegger. Last modified, Sep 20, 2000 */ -+/*Author: Rainer Hegger. Last modified, Jul 13, 2010 */ - #include <stdio.h> - #include <stdlib.h> - #include <math.h> -@@ -26,16 +26,17 @@ - #include "routines/tsa.h" - - #define WID_STR "Estimates the time delayed mutual information\n\t\ --of the data set" -+of one or two data columns" - - --char *file_out=NULL,stout=1; -+char *file_out=NULL,stout=1,dimset=0; - char *infile=NULL; - unsigned long length=ULONG_MAX,exclude=0; --unsigned int column=1; -+unsigned int dim=1; - unsigned int verbosity=0xff; - long partitions=16,corrlength=20; --long *array,*h1,*h11,**h2; -+long **array,*h1,*h11,**h2; -+char *column=NULL; - - void show_options(char *progname) - { -@@ -48,7 +49,7 @@ void show_options(char *progname) - " means stdin\n"); - fprintf(stderr,"\t-l # of points to be used [Default is all]\n"); - fprintf(stderr,"\t-x # of lines to be ignored [Default is 0]\n"); -- fprintf(stderr,"\t-c column to read [Default is 1]\n"); -+ fprintf(stderr,"\t-c columns to read [Default is 1]\n"); - fprintf(stderr,"\t-b # of boxes [Default is 16]\n"); - fprintf(stderr,"\t-D max. time delay [Default is 20]\n"); - fprintf(stderr,"\t-o output file [-o without name means 'datafile'.mut;" -@@ -69,8 +70,8 @@ void scan_options(int n,char** in) - sscanf(out,"%lu",&length); - if ((out=check_option(in,n,'x','u')) != NULL) - sscanf(out,"%lu",&exclude); -- if ((out=check_option(in,n,'c','u')) != NULL) -- sscanf(out,"%u",&column); -+ if ((out=check_option(in,n,'c','s')) != NULL) -+ column=out; - if ((out=check_option(in,n,'b','u')) != NULL) - sscanf(out,"%lu",&partitions); - if ((out=check_option(in,n,'D','u')) != NULL) -@@ -86,7 +87,7 @@ void scan_options(int n,char** in) - - double make_cond_entropy(long t) - { -- long i,j,hi,hii,count=0; -+ long i,j,hi,hii,count=0,start,stop; - double hpi,hpj,pij,cond_ent=0.0,norm; - - for (i=0;i<partitions;i++) { -@@ -94,15 +95,23 @@ double make_cond_entropy(long t) - for (j=0;j<partitions;j++) - h2[i][j]=0; - } -- for (i=0;i<length;i++) -- if (i >= t) { -- hii=array[i]; -- hi=array[i-t]; -- h1[hi]++; -- h11[hii]++; -- h2[hi][hii]++; -- count++; -- } -+ if (t < 0) { -+ start=0; -+ stop=length+t; -+ } -+ else { -+ start=t; -+ stop=length; -+ } -+ -+ for (i=start;i<stop;i++) { -+ hii=array[0][i]; -+ hi=array[1][i+t]; -+ h1[hi]++; -+ h11[hii]++; -+ h2[hi][hii]++; -+ count++; -+ } - - norm=1.0/(double)count; - cond_ent=0.0; -@@ -127,8 +136,8 @@ double make_cond_entropy(long t) - int main(int argc,char** argv) - { - char stdi=0; -- long tau,i; -- double *series,min,interval,shannon; -+ long tau,i,j; -+ double **series,min1,min2,interval1,interval2,shannon,condent; - FILE *file; - - if (scan_help(argc,argv)) -@@ -140,7 +149,7 @@ int main(int argc,char** argv) - what_i_do(argv[0],WID_STR); - #endif - -- infile=search_datafile(argc,argv,&column,verbosity); -+ infile=search_datafile(argc,argv,NULL,verbosity); - if (infile == NULL) - stdi=1; - -@@ -158,20 +167,44 @@ int main(int argc,char** argv) - if (!stout) - test_outfile(file_out); - -- series=(double*)get_series(infile,&length,exclude,column,verbosity); -- rescale_data(series,length,&min,&interval); -+ if (column == NULL) { -+ series=(double**)get_multi_series(infile,&length,exclude,&dim,"", -+ dimset,verbosity); -+ } -+ else { -+ series=(double**)get_multi_series(infile,&length,exclude,&dim,column, -+ dimset,verbosity); -+ } - - check_alloc(h1=(long *)malloc(sizeof(long)*partitions)); - check_alloc(h11=(long *)malloc(sizeof(long)*partitions)); - check_alloc(h2=(long **)malloc(sizeof(long *)*partitions)); - for (i=0;i<partitions;i++) - check_alloc(h2[i]=(long *)malloc(sizeof(long)*partitions)); -- check_alloc(array=(long *)malloc(sizeof(long)*length)); -- for (i=0;i<length;i++) -- if (series[i] < 1.0) -- array[i]=(long)(series[i]*(double)partitions); -- else -- array[i]=partitions-1; -+ check_alloc(array=(long **)malloc(sizeof(long*)*2)); -+ check_alloc(array[0]=(long *)malloc(sizeof(long)*length)); -+ check_alloc(array[1]=(long *)malloc(sizeof(long)*length)); -+ if (dim == 1) { -+ rescale_data(series[0],length,&min1,&interval1); -+ for (i=0;i<length;i++) -+ if (series[0][i] < 1.0) -+ array[0][i]=array[1][i]=(long)(series[0][i]*(double)partitions); -+ else -+ array[0][i]=array[1][i]=partitions-1; -+ free(series[0]); -+ } -+ else { -+ rescale_data(series[0],length,&min1,&interval1); -+ rescale_data(series[1],length,&min2,&interval2); -+ for (j=0;j<2;j++) { -+ for (i=0;i<length;i++) -+ if (series[j][i] < 1.0) -+ array[j][i]=(long)(series[j][i]*(double)partitions); -+ else -+ array[j][i]=partitions-1; -+ free(series[j]); -+ } -+ } - free(series); - - shannon=make_cond_entropy(0); -@@ -182,10 +215,9 @@ int main(int argc,char** argv) - file=fopen(file_out,"w"); - if (verbosity&VER_INPUT) - fprintf(stderr,"Opened %s for writing\n",file_out); -- fprintf(file,"#shannon= %e\n",shannon); -- fprintf(file,"%d %e\n",0,shannon); -- for (tau=1;tau<=corrlength;tau++) { -- fprintf(file,"%ld %e\n",tau,make_cond_entropy(tau)); -+ for (tau=-corrlength;tau<=corrlength;tau++) { -+ condent=make_cond_entropy(tau); -+ fprintf(file,"%ld %e %e\n",tau,condent,condent/log((double)partitions)); - fflush(file); - } - fclose(file); -@@ -193,10 +225,9 @@ int main(int argc,char** argv) - else { - if (verbosity&VER_INPUT) - fprintf(stderr,"Writing to stdout\n"); -- fprintf(stdout,"#shannon= %e\n",shannon); -- fprintf(stdout,"%d %e\n",0,shannon); -- for (tau=1;tau<=corrlength;tau++) { -- fprintf(stdout,"%ld %e\n",tau,make_cond_entropy(tau)); -+ for (tau=-corrlength;tau<=corrlength;tau++) { -+ condent=make_cond_entropy(tau); -+ fprintf(stdout,"%ld %e %e\n",tau,condent,condent/log((double)partitions)); - fflush(stdout); - } - } -diff --git a/source_c/polynom.c b/source_c/polynom.c -index bc57ba8..6448f49 100644 ---- a/source_c/polynom.c -+++ b/source_c/polynom.c -@@ -20,6 +20,8 @@ - /*Author: Rainer Hegger*/ - /* Changes: - 6/30/2006: Norm of the errors was wrong -+ 6/5/2008: Norm was still wrong. Now its given as an absolute value in -+ units of the data - */ - #include <stdio.h> - #include <stdlib.h> -@@ -265,6 +267,7 @@ int main(int argc,char **argv) - - series=(double*)get_series(infile,&LENGTH,exclude,COLUMN,verbosity); - variance(series,LENGTH,&av,&std_dev); -+ - for (i=0;i<LENGTH;i++) - series[i] /= std_dev; - -@@ -307,11 +310,11 @@ int main(int argc,char **argv) - - in_error=make_error((unsigned long)0,INSAMPLE); - -- fprintf(file,"#average insample error= %e\n",sqrt(in_error)); -+ fprintf(file,"#average insample error= %e\n",sqrt(in_error)*std_dev); - - if (INSAMPLE < LENGTH) { - out_error=make_error(INSAMPLE,LENGTH); -- fprintf(file,"#average out of sample error= %e\n",sqrt(out_error)); -+ fprintf(file,"#average out of sample error= %e\n",sqrt(out_error)*std_dev); - } - - if (CAST) -diff --git a/source_c/polynomp.c b/source_c/polynomp.c -index 6021e19..5b32e58 100644 ---- a/source_c/polynomp.c -+++ b/source_c/polynomp.c -@@ -239,7 +239,7 @@ int main(int argc,char **argv) - fclose(file); - - dummy=(double**)get_multi_series(parin,&plength,0LU, -- &dim,"",(char)"1",verbosity); -+ &dim,"",1,verbosity); - - check_alloc(order=(unsigned int**)malloc(sizeof(int*)*plength)); - for (i=0;i<plength;i++) { -diff --git a/source_c/xcor.c b/source_c/xcor.c -index ec1ed7f..8f50609 100644 ---- a/source_c/xcor.c -+++ b/source_c/xcor.c -@@ -30,7 +30,7 @@ given as two columns of one file." - - char *columns=NULL,*outfile=NULL,stout=1; - unsigned long length=ULONG_MAX,exclude=0; --long tau=100; -+unsigned long tau=100; - unsigned int verbosity=0xff; - double *array1,*array2; - char *infile=NULL; -diff --git a/source_f/cluster.f b/source_f/cluster.f -index 61357ff..d564fc7 100644 ---- a/source_f/cluster.f -+++ b/source_f/cluster.f -@@ -47,7 +47,8 @@ - d(i,j)=dij - np=max(i,j,np) - goto 1 -- 999 if(iv_io(iverb).eq.1) write(0,'(a,i)') "matrix size ", np -+c 999 if(iv_io(iverb).eq.1) write(0,'(a,i)') "matrix size ", np -+ 999 if(iv_io(iverb).eq.1) write(0,*) "matrix size ", np - dmean=0 - nd=0 - do 20 i=1,np diff --git a/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch b/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch deleted file mode 100644 index 7f80f6276..000000000 --- a/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch +++ /dev/null @@ -1,57 +0,0 @@ -diff --git a/Makefile.in b/Makefile.in -index c1f3e0c..60f9720 100644 ---- a/Makefile.in -+++ b/Makefile.in -@@ -9,8 +9,8 @@ HAVE_NR = @HAVE_NR@ - - all: - @head -20 README -- -if test -n "${FC}"; then (cd source_f && $(MAKE) $@); fi -- -if test -n "${CC}"; then (cd source_c && $(MAKE) $@); fi -+ $(MAKE) -C source_f $@ -+ $(MAKE) -C source_c $@ - - install: do_install missing - @echo "******************************************************************" -diff --git a/source_c/Makefile.in b/source_c/Makefile.in -index 1ab10e4..2efb803 100644 ---- a/source_c/Makefile.in -+++ b/source_c/Makefile.in -@@ -23,10 +23,10 @@ LOADLIBS = routines/libddtsa.a -lm - all: $(ALL) - - routines/libddtsa.a: -- (cd routines && $(MAKE)) -+ $(MAKE) -C routines - - $(ALL): routines/libddtsa.a *.c -- -$(CC) $(CFLAGS) $(COPTS) -o $@ $@.c $(LOADLIBS) -+ -$(CC) $(LDFLAGS) $(CFLAGS) $(COPTS) -o $@ $@.c $(LOADLIBS) - - install: all - -for bin in $(ALL); do $(INSTALL) $$bin $(BINDIR); done -diff --git a/source_f/Makefile.in b/source_f/Makefile.in -index 6525b72..e45eea7 100644 ---- a/source_f/Makefile.in -+++ b/source_f/Makefile.in -@@ -37,17 +37,17 @@ istdio.o: istdio_temp.f - $(FC) $(FFLAGS) -c istdio.f -o istdio.o - - $(BINS): libtsa.a libsla.a *.f -- -$(FC) $(FFLAGS) -o $@ $@.f $(LOADLIBES) $(LDFLAGS) -+ -$(FC) $(LDFLAGS) $(FFLAGS) -o $@ $@.f $(LOADLIBES) - - libtsa.a: $(INC) - $(AR) $(ARFLAGS) libtsa.a $? - $(RANLIB) libtsa.a - - libsla.a: slatec/*.f -- (cd slatec && $(MAKE)) -+ $(MAKE) -C slatec - - Randomize: libtsa.a libsla.a -- -(cd randomize && $(MAKE)) -+ $(MAKE) -C randomize - - clean: - @rm -f istdio.f diff --git a/sci-mathematics/tisean/metadata.xml b/sci-mathematics/tisean/metadata.xml deleted file mode 100644 index 02d26ebf3..000000000 --- a/sci-mathematics/tisean/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>jlec@gentoo.org</email> - <name>Justin Lecher (jlec)</name> - </maintainer> - <upstream> - <remote-id type="github">heggus/Tisean</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/tisean/tisean-3.0.1.ebuild b/sci-mathematics/tisean/tisean-3.0.1.ebuild deleted file mode 100644 index f43138ee6..000000000 --- a/sci-mathematics/tisean/tisean-3.0.1.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs - -MY_P="Tisean_${PV}" - -DESCRIPTION="Time series analytics with theory of non-liner deterministic dynamical systems" -HOMEPAGE=" - https://github.com/heggus/Tisean - http://www.mpipks-dresden.mpg.de/%7Etisean/Tisean_3.0.1/index.html" -SRC_URI="http://www.mpipks-dresden.mpg.de/~tisean/TISEAN_3.0.1.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - tc-export FC CC - epatch \ - "${FILESDIR}"/${P}-gentoo.patch \ - "${FILESDIR}"/${P}-backport.patch -} - -src_configure() { - econf \ - --prefix="${ED}/usr" -} - -src_install() { - # TODO: fix file collisions with: - # media-gfx/graphviz: /usr/bin/cluster - # media-gfx/imagemagick: /usr/bin/compare - dodir /usr/bin - default -} - -pkg_postinst() { - optfeature "plotting support" sci-visualization/gnuplot -} diff --git a/sci-mathematics/ufc/Manifest b/sci-mathematics/ufc/Manifest deleted file mode 100644 index 2a3e180a7..000000000 --- a/sci-mathematics/ufc/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST ufc-1.4.2.tar.gz 560547 SHA256 7f67e67c1e51753cbc0755db4122e2ece585af53a7869ddb670ee6aae7f2ff91 SHA512 6737e2125d7551d893c2034ad0fb5e623c51524510b072f3ad11c1851313d6c67c71bef14426f0a29ca3e92f821b9b320f1dbe7d98ba936a393b29a98ee89ece WHIRLPOOL d5fa9db8f07108b7345c8435915779ec6a5d8535c30f5b28b4173254fe1fbe9824a422d56eb21f33a513fa84b784c72854186b3149c8a70d55ab62971505c211 -DIST ufc-2.3.0.tar.gz 93771 BLAKE2B 6cbe24bf66da9300e9d4eed09aae15c15e8b92549c1dd18f4499d2debb873a7d1adf04c14498c8618e377418cdb81bbee6b9a3c7ec3efc85ab314b287ee7d692 SHA512 b60a7641fcd694466e0388989e8405ebb1cb2e15320dede45c1edc1fb80ea320e5177bdbed826b3a54c8e7fcd68180bc13fb18f458b2e3fca8af9f4994b51ad6 diff --git a/sci-mathematics/ufc/metadata.xml b/sci-mathematics/ufc/metadata.xml deleted file mode 100644 index 062f16a24..000000000 --- a/sci-mathematics/ufc/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> - <longdescription lang="en"> -UFC (Unified Form-assembly Code) is a unified framework for finite element assembly. More precisely, it defines a fixed interface for communicating low level routines (functions) for evaluating and assembling finite element variational forms. The UFC interface consists of a single header file ufc.h that specifies a C++ interface that must be implemented by code that complies with the UFC specification. -</longdescription> - <upstream> - <remote-id type="bitbucket">fenics-project/ufc-deprecated</remote-id> - <remote-id type="launchpad">ufc</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/ufc/ufc-1.4.2.ebuild b/sci-mathematics/ufc/ufc-1.4.2.ebuild deleted file mode 100644 index 90700be9b..000000000 --- a/sci-mathematics/ufc/ufc-1.4.2.ebuild +++ /dev/null @@ -1,19 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit cmake-utils - -DESCRIPTION="Unified framework for finite element assembly" -HOMEPAGE="http://launchpad.net/ufc" -SRC_URI="http://launchpad.net/${PN}/trunk/${PV}/+download/${P}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64" - -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" diff --git a/sci-mathematics/ufc/ufc-2.3.0.ebuild b/sci-mathematics/ufc/ufc-2.3.0.ebuild deleted file mode 100644 index bf9b9330b..000000000 --- a/sci-mathematics/ufc/ufc-2.3.0.ebuild +++ /dev/null @@ -1,18 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit cmake-utils - -DESCRIPTION="Unified framework for finite element assembly" -HOMEPAGE="https://bitbucket.org/fenics-project/${PN}-deprecated/" -SRC_URI="https://bitbucket.org/fenics-project/${PN}-deprecated/downloads/${P}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" diff --git a/sci-mathematics/why/Manifest b/sci-mathematics/why/Manifest deleted file mode 100644 index 9b986a8e8..000000000 --- a/sci-mathematics/why/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST why-2.34.tar.gz 4019877 BLAKE2B f7f26b993ffb6b47b5822ad555d55e766738a7f158797408af79a1b90b5becc87f14581b569981e37d3fbf6cd120fd1c9bf1b10b48cc057acc4c92458bb65cb7 SHA512 e4abf6573cff52fcfe5c6b867ec15f6f65a88c9892143681b74e3a35caa870acdf04fdda6fc67790af608975bb688c6ec14fc12f2e44b319abdd262ac59384a7 diff --git a/sci-mathematics/why/files/why-flocq23.patch b/sci-mathematics/why/files/why-flocq23.patch deleted file mode 100644 index b54d85a38..000000000 --- a/sci-mathematics/why/files/why-flocq23.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- lib/coq/WhyFloats.v.orig 2014-03-17 16:01:46.000000000 -0600 -+++ lib/coq/WhyFloats.v 2014-04-21 15:39:55.680771647 -0600 -@@ -108,7 +108,7 @@ - generalize (Zeq_bool_eq _ _ H1). clear. - rewrite Fcalc_digits.Z_of_nat_S_digits2_Pnat. - intros H. --apply (Fcalc_digits.Zpower_gt_Zdigits Fcalc_digits.radix2 (Zpos prec) (Zpos m)). -+apply (Fcore_digits.Zpower_gt_Zdigits Fcalc_digits.radix2 (Zpos prec) (Zpos m)). - revert H. - unfold FLT_exp. - generalize (Fcore_digits.Zdigits radix2 (Zpos m)). diff --git a/sci-mathematics/why/metadata.xml b/sci-mathematics/why/metadata.xml deleted file mode 100644 index 70e1eb45f..000000000 --- a/sci-mathematics/why/metadata.xml +++ /dev/null @@ -1,25 +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@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription> -Why is a software verification platform. It contains a general-purpose -verification condition generator (VCG) which is used as a back-end -by other verification tools but it can also be used directly to verify -programs. It also provides Krakatoa, a tool or the verification of Java -programs and Caduceus, a tool for the verification of C programs. -</longdescription> - <use> - <flag name="apron">Use <pkg>sci-mathematics/apron</pkg> library for -abstract interpretation</flag> - <flag name="coq">Add <pkg>sci-mathematics/coq</pkg> support</flag> - <flag name="float">Add <pkg>sci-mathematics/flocq</pkg> support</flag> - <flag name="gappa">Add <pkg>sci-mathematics/gappalib-coq</pkg> support</flag> - <flag name="frama-c">Add <pkg>sci-mathematics/frama-c</pkg> support</flag> - <flag name="pff">Add <pkg>sci-mathematics/pff</pkg> support</flag> - <flag name="why3">Add <pkg>sci-mathematics/why3</pkg> support</flag> - </use> -</pkgmetadata> diff --git a/sci-mathematics/why/why-2.34.ebuild b/sci-mathematics/why/why-2.34.ebuild deleted file mode 100644 index 4851cd7c9..000000000 --- a/sci-mathematics/why/why-2.34.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit autotools eutils - -DESCRIPTION="Why is a software verification platform" -HOMEPAGE="http://why.lri.fr/" -SRC_URI="http://why.lri.fr/download/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="apron coq doc examples float gappa frama-c gtk pff why3" - -DEPEND=">=dev-lang/ocaml-3.12.1 - >=dev-ml/ocamlgraph-1.5 - gtk? ( >=dev-ml/lablgtk-2.14 ) - apron? ( sci-mathematics/apron ) - coq? ( sci-mathematics/coq ) - gappa? ( sci-mathematics/gappalib-coq ) - pff? ( sci-mathematics/pff ) - frama-c? ( >=sci-mathematics/frama-c-20140301 ) - float? ( sci-mathematics/flocq ) - why3? ( sci-mathematics/why3 )" -RDEPEND="${DEPEND}" - -DOCS=( CHANGES README Version ) - -src_prepare() { - sed -i Makefile.in \ - -e "s/DESTDIR =.*//g" \ - -e "s/@COQLIB@/\$(DESTDIR)\/@COQLIB@/g" || die - - #to build with apron-0.9.10 - sed -i configure.in \ - -e "s/pvs/sri-pvs/g" \ - -e "s/oct_caml/octMPQ_caml/g" \ - -e "s/box_caml/boxMPQ_caml/g" \ - -e "s/polka_caml/polkaMPQ_caml/g" || die - - epatch "${FILESDIR}"/why-flocq23.patch - eautoreconf -} - -src_configure() { - econf $(use_enable apron) PATH="/usr/bin:$PATH" -} - -src_compile(){ - MAKEOPTS+=" -j1" - emake DESTDIR="/" -} - -src_install(){ - default - - doman doc/why.1 - - if use doc; then - dodoc doc/manual.ps - fi - - if use examples; then - insinto /usr/share/doc/${PF} - doins -r examples examples-c - fi -} diff --git a/sci-mathematics/why3/Manifest b/sci-mathematics/why3/Manifest deleted file mode 100644 index 6ba945696..000000000 --- a/sci-mathematics/why3/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST why3-0.83.tar.gz 5347628 BLAKE2B d405eec88a66312f6f39ab64e121650256395c01396d47b1b18d68cb5a501cc60698d5498df3a25ccd780f6ff592ffb5a5f9f1fd2ac6fe252213b1df42480b0f SHA512 e1c4d462986835aa0e9a1ca117e4c3bbaf307b45b6de03da6ea8dd706770b8d9894031ea22ec732dfa7340d613b023ab499837203a132db5f138e51596e64177 diff --git a/sci-mathematics/why3/metadata.xml b/sci-mathematics/why3/metadata.xml deleted file mode 100644 index 5f92771c1..000000000 --- a/sci-mathematics/why3/metadata.xml +++ /dev/null @@ -1,24 +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> - <longdescription> -Why3 is a platform for deductive program verification. It provides -a rich language for specification and programming, called WhyML, -and relies on external theorem provers, both automated and interactive, -to discharge verification conditions. Why3 comes with a standard -library of logical theories (integer and real arithmetic, Boolean -operations, sets and maps, etc.) and basic programming data structures -(arrays, queues, hash tables, etc.). A user can write WhyML programs -directly and get correct-by-construction OCaml programs through an -automated extraction mechanism. WhyML is also used as an intermediate -language for the verification of C, Java, or Ada programs. -</longdescription> - <use> - <flag name="float">Add <pkg>sci-mathematics/flocq</pkg> support</flag> - <flag name="frama-c">Enable Frama-C plugin</flag> - </use> -</pkgmetadata> diff --git a/sci-mathematics/why3/why3-0.83.ebuild b/sci-mathematics/why3/why3-0.83.ebuild deleted file mode 100644 index ac914306c..000000000 --- a/sci-mathematics/why3/why3-0.83.ebuild +++ /dev/null @@ -1,59 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils - -DESCRIPTION=" Why3 is a platform for deductive program verification" -HOMEPAGE="http://why3.lri.fr/" -SRC_URI="https://gforge.inria.fr/frs/download.php/33490/${P}.tar.gz" - -LICENSE="LGPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="float frama-c doc examples" - -DEPEND=">=dev-lang/ocaml-3.12.1 - dev-ml/zarith - sci-mathematics/coq - frama-c? ( >=sci-mathematics/frama-c-20140301 ) - float? ( sci-mathematics/flocq ) - doc? ( dev-tex/rubber )" -RDEPEND="${DEPEND}" - -DOCS=( CHANGES README Version ) - -src_prepare() { - mv doc/why.1 doc/why3.1 || die - sed -i configure.in -e "s/\"pvs\"/\"sri-pvs\"/g" || die - sed -i configure -e "s/\"pvs\"/\"sri-pvs\"/g" || die - sed -i Makefile.in -e "s:DESTDIR =::g" \ - -e "s:\$(RUBBER) --warn all --pdf manual.tex:makeindex manual.tex; \$(RUBBER) --warn all --pdf manual.tex; cd ..:g" || die -} - -src_configure() { - econf $(use_enable frama-c) -} - -src_compile() { - MAKEOPTS+=" -j1" - - default - if use doc; then - emake doc/manual.pdf - fi -} - -src_install(){ - default - - doman doc/why3.1 - if use doc; then - dodoc doc/manual.pdf - fi - if use examples; then - insinto /usr/share/doc/${PF} - doins -r examples - fi -} diff --git a/sci-mathematics/z3/Manifest b/sci-mathematics/z3/Manifest deleted file mode 100644 index 5232371ed..000000000 --- a/sci-mathematics/z3/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST z3-4.3.1.tar.xz 1841796 BLAKE2B 50049ad94c1a35559b6f064daef73366d1b1756842f4eda67fd0f835b769e2e991369a54ad4976958dd1288eb2bfbdfe8ee44abbe932afdd15d58acc5346da55 SHA512 ccffb07c6468911685db28030e012a6504c2ce5d50b33163cfac0f12bdbd25b5365b39e61ad514ede01bc138cbc7004de6a9efa6264bc5d2f9fc8db63c989c91 diff --git a/sci-mathematics/z3/metadata.xml b/sci-mathematics/z3/metadata.xml deleted file mode 100644 index ae9640ffb..000000000 --- a/sci-mathematics/z3/metadata.xml +++ /dev/null @@ -1,8 +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@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-mathematics/z3/z3-4.3.1.ebuild b/sci-mathematics/z3/z3-4.3.1.ebuild deleted file mode 100644 index 751fc10ad..000000000 --- a/sci-mathematics/z3/z3-4.3.1.ebuild +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools flag-o-matic python-r1 toolchain-funcs vcs-snapshot - -DESCRIPTION="An efficient theorem prover" -HOMEPAGE="http://z3.codeplex.com/" -SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" - -SLOT="0" -LICENSE="MIT" -KEYWORDS="~amd64 ~x86" -IUSE="gmp" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - gmp? ( dev-libs/gmp:0 )" -DEPEND="${RDEPEND}" - -pkg_setup() { - if [[ ${MERGE_TYPE} != binary ]]; then - if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then - ewarn "Please use an openmp compatible compiler" - ewarn "like >gcc-4.2 with USE=openmp" - die "Openmp support missing in compiler" - fi - fi -} - -src_prepare() { - sed \ - -e 's:-O3::g' \ - -e 's:-fomit-frame-pointer::' \ - -e 's:-msse2::g' \ - -e 's:-msse::g' \ - -e "/LINK_EXTRA_FLAGS/s:@LDFLAGS@:-lrt $(usex gmp -lgmp):g" \ - -e 's:t@\$:t\$:g' \ - -i scripts/*mk* || die - - append-ldflags -fopenmp - - eautoreconf -} - -src_configure() { - python_export_best - econf \ - --host="" \ - --with-python="${PYTHON}" \ - $(use_with gmp) \ - SLIBFLAGS=" -Wl,-soname,lib${PN}.so.0.1 " - ${EPYTHON} scripts/mk_make.py || die -} - -src_compile() { - emake \ - --directory="build" \ - CXX=$(tc-getCXX) \ - LINK="$(tc-getCXX) ${LDFLAGS}" \ - LINK_FLAGS="${LDFLAGS}" -} - -src_install() { - doheader src/api/z3*.h src/api/c++/z3*.h - dolib.so build/*.so - dobin build/z3 - - python_foreach_impl python_domodule src/api/python/*.py -} diff --git a/sci-mathematics/z3/z3-9999.ebuild b/sci-mathematics/z3/z3-9999.ebuild deleted file mode 100644 index 589751a60..000000000 --- a/sci-mathematics/z3/z3-9999.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools flag-o-matic git-r3 python-r1 toolchain-funcs - -DESCRIPTION="An efficient theorem prover" -HOMEPAGE="http://z3.codeplex.com/" -SRC_URI="" -EGIT_REPO_URI="https://git01.codeplex.com/z3" -EGIT_MIN_CLONE_TYPE=single - -SLOT="0" -LICENSE="MIT" -KEYWORDS="" -IUSE="gmp" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - gmp? ( dev-libs/gmp:0 )" -# A new curl is needed because codeplex has a bug and early version of libcurl -# will cause a failed git clone. -DEPEND="${RDEPEND} - >=net-misc/curl-7.33" - -pkg_setup() { - if [[ ${MERGE_TYPE} != binary ]]; then - if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then - ewarn "Please use an openmp compatible compiler" - ewarn "like >gcc-4.2 with USE=openmp" - die "Openmp support missing in compiler" - fi - fi -} - -src_prepare() { - sed \ - -e 's:-O3::g' \ - -e 's:-fomit-frame-pointer::' \ - -e 's:-msse2::g' \ - -e 's:-msse::g' \ - -e "/LINK_EXTRA_FLAGS/s:@LDFLAGS@:-lrt $(usex gmp -lgmp):g" \ - -e 's:t@\$:t\$:g' \ - -i scripts/*mk* || die - - append-ldflags -fopenmp - - eautoreconf -} - -src_configure() { - python_export_best - econf \ - --host="" \ - --with-python="${PYTHON}" \ - $(use_with gmp) \ - SLIBFLAGS=" -Wl,-soname,lib${PN}.so.0.1 " - ${EPYTHON} scripts/mk_make.py || die -} - -src_compile() { - emake \ - --directory="build" \ - CXX=$(tc-getCXX) \ - LINK="$(tc-getCXX) ${LDFLAGS}" \ - LINK_FLAGS="${LDFLAGS}" -} - -src_install() { - doheader src/api/z3*.h src/api/c++/z3*.h - dolib.so build/*.so - dobin build/z3 - - python_foreach_impl python_domodule src/api/python/*.py -} |
