commit: 1c2a6e7fb4fb1d9205bca1556dd1a63b398d2244 Author: Michael Orlitzky <mjo <AT> gentoo <DOT> org> AuthorDate: Thu Aug 29 16:36:57 2024 +0000 Commit: Michael Orlitzky <mjo <AT> gentoo <DOT> org> CommitDate: Thu Aug 29 17:30:59 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1c2a6e7f
sci-mathematics/gfan: fix startup crash, other improvements AKA steal a few Debian patches. Bug: https://bugs.gentoo.org/717112 Signed-off-by: Michael Orlitzky <mjo <AT> gentoo.org> .../gfan/files/gfan-0.6.2-find-name.patch | 18 +++++ ...gfan-0.6.2-fix-0602ResultantFanProjection.patch | 27 ++++++++ .../files/gfan-0.6.2-fix-spelling-errors.patch | 50 ++++++++++++++ sci-mathematics/gfan/gfan-0.6.2-r5.ebuild | 78 ++++++++++++++++++++++ 4 files changed, 173 insertions(+) diff --git a/sci-mathematics/gfan/files/gfan-0.6.2-find-name.patch b/sci-mathematics/gfan/files/gfan-0.6.2-find-name.patch new file mode 100644 index 000000000000..5e6718e70ed2 --- /dev/null +++ b/sci-mathematics/gfan/files/gfan-0.6.2-find-name.patch @@ -0,0 +1,18 @@ +Description: Properly terminate while loop when finding application name. +Author: Anders Nedergaard Jensen <[email protected]> +Origin: https://bugs.debian.org/950008#17 +Bug-Debian: https://bugs.debian.org/950008 +Forwarded: yes +Last-Update: 2021-11-21 + +--- a/src/application.cpp ++++ b/src/application.cpp +@@ -26,7 +26,7 @@ + { + l--; + } +- while(p[l]!=0 && p[l]!='/'); ++ while(l >= 0 && p[l]!='/'); + + return p+l+1; + } diff --git a/sci-mathematics/gfan/files/gfan-0.6.2-fix-0602ResultantFanProjection.patch b/sci-mathematics/gfan/files/gfan-0.6.2-fix-0602ResultantFanProjection.patch new file mode 100644 index 000000000000..99fe8167398e --- /dev/null +++ b/sci-mathematics/gfan/files/gfan-0.6.2-fix-0602ResultantFanProjection.patch @@ -0,0 +1,27 @@ +Description: Use int64_t instead of signed long int for 64-bit integer typedef + On 32-bit architectures, longs are only 32 bits. The resulting overflow + was causing an infinite loop in the 0602ResultantFanProjection test. +Bug-Debian: https://bugs.debian.org/905300 +Bug-Debian: https://bugs.debian.org/974558 +Author: Doug Torrance <[email protected]> +Last-Update: 2020-11-12 + +(mjo: added missing include) + +--- a/src/vektor.h ++++ b/src/vektor.h +@@ -6,11 +6,12 @@ + #include <assert.h> + #include <algorithm> + #include <complex> ++#include <cstdint> + #include <stdio.h> + + using namespace std; + +-typedef signed long int int64; ++typedef int64_t int64; + + void outOfRange(int i, int n); + + diff --git a/sci-mathematics/gfan/files/gfan-0.6.2-fix-spelling-errors.patch b/sci-mathematics/gfan/files/gfan-0.6.2-fix-spelling-errors.patch new file mode 100644 index 000000000000..08b78c6efcaa --- /dev/null +++ b/sci-mathematics/gfan/files/gfan-0.6.2-fix-spelling-errors.patch @@ -0,0 +1,50 @@ +Descriptions: Fix some spelling errors in output text of the programs +Author: Cédric Boutillier <[email protected]> +Author: Doug Torrance <[email protected]> +Forwarded: yes +Last-Update: 2020-11-13 + +--- a/src/app_scarfisgeneric.cpp ++++ b/src/app_scarfisgeneric.cpp +@@ -24,7 +24,7 @@ + } + const char *helpText() + { +- return "This program takes a matrix as input and checks if it satisfies Scarf's generality conditions. The rows of the matrix are listed on the input. The A1 condition is that there exists a strictly poistive vector in the co-kernel of the matrix. The A2 condition is that te maximal minors of the matrix are non-zero. A3\n"; ++ return "This program takes a matrix as input and checks if it satisfies Scarf's generality conditions. The rows of the matrix are listed on the input. The A1 condition is that there exists a strictly poistive vector in the co-kernel of the matrix. The A2 condition is that the maximal minors of the matrix are non-zero. A3\n"; + } + ScarfIsGenericApplication() + { +--- a/src/app_symmetries.cpp ++++ b/src/app_symmetries.cpp +@@ -35,7 +35,7 @@ + } + SymmetriesApplication(): + optionSymmetry("--symmetry","Specify subgroup to be searched for permutations keeping the ideal fixed."), +- optionTorusSymmetry("--symsigns","Specify for each generator of the group specified wiht --symmetry an element of ${-1,+1}^n$ which by its multiplication on the variables together with the permutation is expected to keep the ideal fixed.") ++ optionTorusSymmetry("--symsigns","Specify for each generator of the group specified with --symmetry an element of ${-1,+1}^n$ which by its multiplication on the variables together with the permutation is expected to keep the ideal fixed.") + { + registerOptions(); + } +--- a/src/app_representatives.cpp ++++ b/src/app_representatives.cpp +@@ -24,7 +24,7 @@ + } + const char *helpText() + { +- return "This program computes takes generaters for a subgroup of S_n and a list of n-dimensional integer vectors. The output is a list of vectors, one from each orbit of elements of the list. \n"; ++ return "This program computes takes generators for a subgroup of S_n and a list of n-dimensional integer vectors. The output is a list of vectors, one from each orbit of elements of the list. \n"; + } + RepresentativesApplication() + { +--- a/src/tropical2.cpp ++++ b/src/tropical2.cpp +@@ -271,7 +271,7 @@ + PolynomialSet r(theRing); + if(theRing.getNumberOfVariables()!=weight.size()) + { +- cerr << "Error: Number of varaibles in polynomial ring "<<theRing.getNumberOfVariables()<< " length of weight vector " << weight.size() <<endl; ++ cerr << "Error: Number of variables in polynomial ring "<<theRing.getNumberOfVariables()<< " length of weight vector " << weight.size() <<endl; + assert(0); + } + diff --git a/sci-mathematics/gfan/gfan-0.6.2-r5.ebuild b/sci-mathematics/gfan/gfan-0.6.2-r5.ebuild new file mode 100644 index 000000000000..47fbcc3b8e1d --- /dev/null +++ b/sci-mathematics/gfan/gfan-0.6.2-r5.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Compute Groebner fans and tropical varieties" +HOMEPAGE="https://users-math.au.dk/~jensen/software/gfan/gfan.html"; +SRC_URI="https://users-math.au.dk/~jensen/software/${PN}/${PN}${PV}.tar.gz"; + +S="${WORKDIR}/${PN}${PV}" + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="~amd64 ~arm ~riscv ~x86 ~amd64-linux ~x86-linux" +IUSE="doc" + +BDEPEND="doc? ( virtual/latex-base )" +DEPEND="dev-libs/gmp:0=[cxx(+)] + sci-libs/cddlib:0=" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-0.6.2-testsuite.patch" + "${FILESDIR}/${PN}-0.6.2-Makefile.patch" + "${FILESDIR}/${PN}-0.6.2-fix-0602ResultantFanProjection.patch" + "${FILESDIR}/${PN}-0.6.2-fix-spelling-errors.patch" + "${FILESDIR}/${PN}-0.6.2-find-name.patch" +) + +pkg_setup() { + tc-export CC CXX + + # This should really go in cppflags, but that doesn't work with + # gfan's hand-written Makefile. + append-cxxflags -DNOCDDPREFIX -I"${EPREFIX}"/usr/include/cddlib +} + +src_prepare() { + default + + # And this one fails (harmlessly) on x86, bug 818397. + rm -r testsuite/0009RenderStairCase || \ + die "unable to disable test 0009RenderStairCase" +} + +src_configure() { + # -Werror=odr + # https://bugs.gentoo.org/863044 + # Only contact method is email. I have sent one detailing the issue. + filter-lto + + # The upstream Makefile says that GCC produces bad code with -O3. + replace-flags "-O3" "-O2" + default +} + +src_compile() { + default + if use doc; then + pushd doc > /dev/null || die + # The LaTeX build commands need to be repeated until the + # document "stops changing," which is not as easy as it + # sounds to detect. Running it twice seems to work here. + for iteration in 1 2; do + latex manual.tex && \ + bibtex manual && \ + dvipdf manual.dvi manual.pdf || die + done + popd > /dev/null || die + fi +} + +src_install() { + emake PREFIX="${ED}/usr" install + use doc && dodoc doc/manual.pdf +}
