gentoo auto-resync : 30:08:2024 - 12:00:55

5 files changed, 177 insertions, 0 deletions

diff --git a/sci-mathematics/gfan/Manifest b/sci-mathematics/gfan/Manifest
index c97d5be4f7e3..eb4c57d1c9bf 100644
--- a/sci-mathematics/gfan/Manifest
+++ b/sci-mathematics/gfan/Manifest
@@ -1,6 +1,10 @@
 AUX gfan-0.6.2-Makefile.patch 6603 BLAKE2B 48f9b4280418aef41d502d770c070ec1dcef947a39c6263d991be0f6f41147d06b78a4b07ca76e0fb4bc9780cb9469c98c637473789d857925df8d546ad35e92 SHA512 e1eef6f01c9942b38780f19b774fa3e99df4dbdba738cc2c6c69e2f1858e5e6294db72d7b679c5ff1313a76143bd611077731d360479f9375d6506e33a4a620a
+AUX gfan-0.6.2-find-name.patch 433 BLAKE2B 452e286223f4607f42e0895bba443c1534e491dc5e182f6f14c1d5d0d63c5992684b36ad0d028b68c286644e7ccc84786b0e49c311fcbe0fa6151a60ee3001d9 SHA512 f561189e887af930fa09ffa8870e9fbc4e5d5ed1b1a1b81c2001ea3d2a404b025a640eb7a4d504e448a60be4c58af3a3d00421abb48762bb2b32357e862252fc
+AUX gfan-0.6.2-fix-0602ResultantFanProjection.patch 689 BLAKE2B 4531bd59dc7a356b2907b043dc71a5e34e647dd15822d3e3846785bb27162ba607eea8492b972574c1f64a227d428b1db0b385a7a54624f5d33b3f4522bd7fe6 SHA512 0de03e0f40f7cde6ae8709a8c6f26cd39458752d1480c49635e58ce57c0b0ff1c03382bd41097af7609ee6320f98d83f600e7dde842fe545b758982e704e52eb
+AUX gfan-0.6.2-fix-spelling-errors.patch 2826 BLAKE2B 1a5b662dafd42834c9254d79cad84717d5b407c0fd14bf3f58320203b847953284597aa2add8dcb7eaa40700fa2a5c6e1c0ba99c2715d7fb0c6deedc45c44c8e SHA512 a30947bda62723f0d5a916d1a05de52fd67a2a3d4303b5774e7517407f531df67eb2968be255aab91634d46fdb61243e8b38ac355eef02c01c4ee95576e10159
 AUX gfan-0.6.2-testsuite.patch 3223 BLAKE2B ddb94775a13bd503df5c9563750a6b4b68c9e72e1a19aaa0415c5484e07765dfd28ba02b3a0fab65a0b9cd5c61afafbc6a3d862a1de68ece57ef9d8bb2835c16 SHA512 d62e765a39ee1a8cb149fcae8afb538b19a91206dd0b8cf0ac2b681b28569e44f492b770b9e61d7573f2d52f265ad4cf25671197c204238a89075709753a83e6
 AUX gfan-0.6.2-xcode9.3_compat.patch 367 BLAKE2B fb7c685a4dd811fed83e2734a16507b1792e3a97c666d0e7de1d2ed53a7b9b43c5319517f9eef829f47147dc725f2c4ead38968fa3868baa1d16630a8b844636 SHA512 129d2c35777f82bf2a1581450ecb12dd6811fb72b583748b30665c0f9b20d39646233d9b40fb64a3c7790360514a51b30e49c53d83c34d259f664bf820ae1ce2
 DIST gfan0.6.2.tar.gz 1321059 BLAKE2B 1ed61e1e084a1ceb65dd21848440bc3a90486c0ce4012b3b64c8029e89636696d2b0e5446ea156d2cf050b5db179c7c2f25c97e683cecf6e9616e8553d8513bf SHA512 5961820750af2522fdc1a86c0254742c3b003607a8707df5d6cd5f0bc6461e4d3db3b1d3cb537979d57eb9dff387974a58aeb91d0b5246d7c701cadc5a2cf4cf
 EBUILD gfan-0.6.2-r4.ebuild 2007 BLAKE2B 21d014cbabb76f661135ffc1c1ce72b016448511e0ec7cb71cffc6f68fec9328c140f268ae3dce2a7ed58ee5559f56c274fb9ce1f7edcc000a9f0606f013bd3d SHA512 76b1e4b63458d5992b5036a7fff2f0e9be5ec0269fcd8a3d2854db21a89f8efd54b9d043049e9e9ac969852f975a8774735c6c426ac03068078c75c1517d0f2a
+EBUILD gfan-0.6.2-r5.ebuild 1971 BLAKE2B b50e2c1bbcbd4269850575bd4f36bb42dcad534d3a55e4257bf3281e907dfe0730deb81fbb66373356ec474e9273b4c9b40ae227842edce682e68530be0de2f6 SHA512 5eed708f34f910390a024e45b9a613ab424729122f58bae8573832f4f217c3f6424309c7f068f162d797a0c19f8d56926b97054c4ece1d9d62094a8848a913e3
 MISC metadata.xml 1344 BLAKE2B 1a1d24099e2338877b068dee2b9e17feb4063de3a681a3b8d6a707c863708d6f380bb4864eb2fd5fef8ed49d6b1a770a8d1b4c12ce722b4f7fe113876de0b792 SHA512 8d5c93337a82b132c66c8d7e64c97deedcfdc724e9874bf308e6d817f71e663bc2b281ea133ae15e30096f5c801f88116b11e4d36dd8dd8eec526b5bc16d5f54
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 <jensen@math.au.dk>
+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 <dtorrance@piedmont.edu>
+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 <boutil@debian.org>
+Author: Doug Torrance <dtorrance@piedmont.edu>
+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
+}