sci-libs/linbox: backport commit to fix gcc 14 build

Closes: https://bugs.gentoo.org/930923
Signed-off-by: Kostadin Shishmanov <kocelfc@tutanota.com>
Signed-off-by: Michael Orlitzky <mjo@gentoo.org>

2 files changed, 547 insertions, 0 deletions

diff --git a/sci-libs/linbox/files/linbox-1.7.0-gcc14.patch b/sci-libs/linbox/files/linbox-1.7.0-gcc14.patch
new file mode 100644
index 000000000000..f35f1072955d
--- /dev/null
+++ b/sci-libs/linbox/files/linbox-1.7.0-gcc14.patch
@@ -0,0 +1,433 @@
+https://bugs.gentoo.org/930923
+https://github.com/linbox-team/linbox/commit/b8f2d4ccdc0af4418d14f72caf6c4d01969092a3
+https://src.fedoraproject.org/rpms/linbox/c/7389d46e81dc00dcb952b2ccbbbec3fb4fcc6c8b
+
+From c614c401386ee8db014a9be56244888f7b282a18 Mon Sep 17 00:00:00 2001
+From: Jean-Guillaume Dumas <Jean-Guillaume.Dumas@imag.fr>
+Date: Fri, 26 Jan 2024 16:31:56 +0100
+Subject: [PATCH] const_cast missing faster empty init
+
+---
+ linbox/algorithms/gauss/gauss-nullspace.inl   |  10 +-
+ .../matrix/sparsematrix/sparse-ell-matrix.h   |   8 +-
+ .../matrix/sparsematrix/sparse-ellr-matrix.h  |  18 +--
+ linbox/ring/ntl/ntl-lzz_p.h                   |  11 +-
+ linbox/ring/ntl/ntl-lzz_pe.h                  | 143 +++++++++---------
+ linbox/ring/ntl/ntl-zz_px.h                   |   6 +
+ 6 files changed, 104 insertions(+), 92 deletions(-)
+
+diff --git a/linbox/algorithms/gauss/gauss-nullspace.inl b/linbox/algorithms/gauss/gauss-nullspace.inl
+index 0b70e1d7c..2d6032563 100644
+--- a/linbox/algorithms/gauss/gauss-nullspace.inl
++++ b/linbox/algorithms/gauss/gauss-nullspace.inl
+@@ -2,7 +2,7 @@
+  * Copyright (C) LinBox 2008
+  *
+  * Written by Jean-Guillaume Dumas <Jean-Guillaume.Dumas@imag.fr>
+- * Time-stamp: <27 Aug 20 15:17:09 Jean-Guillaume.Dumas@imag.fr>
++ * Time-stamp: <26 Jan 24 16:05:55 Jean-Guillaume.Dumas@imag.fr>
+  *
+  *
+  * ========LICENCE========
+@@ -104,11 +104,11 @@ namespace LinBox
+ 
+ 		Permutation<Field> P(field(),(int)Nj);
+ 
+-		// A.write( std::cerr << "A:=", Tag::FileFormat::Maple ) << ';' << std::endl;
++// A.write( std::cerr << "A:=", Tag::FileFormat::Maple ) << ';' << std::endl;
+ 		this->InPlaceLinearPivoting(Rank, Det, A, P, Ni, Nj );
+ 
+-		// P.write( std::cerr << "P:=", Tag::FileFormat::Maple ) << ';' << std::endl;
+-		// A.write( std::cerr << "Ua:=", Tag::FileFormat::Maple ) << ';' << std::endl;
++// P.write( std::cerr << "P:=", Tag::FileFormat::Maple ) << ';' << std::endl;
++// A.write( std::cerr << "Ua:=", Tag::FileFormat::Maple ) << ';' << std::endl;
+ 
+ 		for(size_t i=0; i< Ni; ++i) {
+ 			if (A[i].size() == 0) {
+@@ -123,7 +123,7 @@ namespace LinBox
+ 			}
+ 		}
+ 
+-		// A.write( std::cerr << "Ub:=", Tag::FileFormat::Maple ) << ';' << std::endl;
++// A.write( std::cerr << "Ub:=", Tag::FileFormat::Maple ) << ';' << std::endl;
+ 
+ 		return this->nullspacebasis(x, Rank, A, P);
+ 	}
+diff --git a/linbox/matrix/sparsematrix/sparse-ell-matrix.h b/linbox/matrix/sparsematrix/sparse-ell-matrix.h
+index 59006d6c5..2604f47b8 100644
+--- a/linbox/matrix/sparsematrix/sparse-ell-matrix.h
++++ b/linbox/matrix/sparsematrix/sparse-ell-matrix.h
+@@ -1210,10 +1210,10 @@ namespace LinBox
+ 				_colid_beg = iter._colid_beg ;
+ 				_colid_it  = iter._colid_it ;
+ 				_data_it   = iter._data_it  ;
+-				_data_beg  = iter._data_beg ;
+-				_data_end  = iter._data_end  ;
+-				_field     = iter._field ;
+-				_ld        = iter._ld ;
++				const_cast<data_it>(_data_beg)  = iter._data_beg ;
++				const_cast<data_it>(_data_end)  = iter._data_end  ;
++				const_cast<Field &>(_field)     = iter._field ;
++				const_cast<size_t&>(ld)         = iter._ld ;
+ 				_row       = iter._row ;
+ 
+ 				return *this;
+diff --git a/linbox/matrix/sparsematrix/sparse-ellr-matrix.h b/linbox/matrix/sparsematrix/sparse-ellr-matrix.h
+index 498a5525d..a60943868 100644
+--- a/linbox/matrix/sparsematrix/sparse-ellr-matrix.h
++++ b/linbox/matrix/sparsematrix/sparse-ellr-matrix.h
+@@ -1102,11 +1102,11 @@ namespace LinBox
+ 			_Iterator &operator = (const _Iterator &iter)
+ 			{
+ 				_data_it  = iter._data_it  ;
+-				_data_beg  = iter._data_beg  ;
+-				_data_end  = iter._data_end  ;
+-				_field  = iter._field  ;
+-				_rowid = iter._rowid;
+-				_ld = iter._ld ;
++				const_cast<element_iterator>(_data_beg) = iter._data_beg  ;
++				const_cast<element_iterator>(_data_end)= iter._data_end  ;
++				const_cast<Field &>(_field) = iter._field  ;
++				const_cast<std::vector<size_t>&>(_rowid) = iter._rowid;
++				const_cast<size_t&>(ld) = iter._ld ;
+ 				_row = iter._row ;
+ 
+ 				return *this;
+@@ -1252,10 +1252,10 @@ namespace LinBox
+ 				_colid_beg = iter._colid_beg ;
+ 				_colid_it  = iter._colid_it ;
+ 				_data_it   = iter._data_it  ;
+-				_data_beg  = iter._data_beg ;
+-				_data_end  = iter._data_end  ;
+-				_field     = iter._field ;
+-				_ld        = iter._ld ;
++				const_cast<data_it>(_data_beg) = iter._data_beg ;
++				const_cast<data_it>(_data_end) = iter._data_end  ;
++				const_cast<Field &>(_field)    = iter._field ;
++				const_cast<size_t&>(ld)= iter._ld ;
+ 				_row       = iter._row ;
+ 
+ 				return *this;
+diff --git a/linbox/ring/ntl/ntl-lzz_p.h b/linbox/ring/ntl/ntl-lzz_p.h
+index 201baaa35..def3a23f7 100644
+--- a/linbox/ring/ntl/ntl-lzz_p.h
++++ b/linbox/ring/ntl/ntl-lzz_p.h
+@@ -85,7 +85,7 @@ namespace Givaro
+          * @param x reference to Integer to contain output (reference returned).
+          * @param y constant reference to field element.
+          */
+- 	template <>
++    template <>
+ 	Integer& Caster(Integer& x, const NTL::zz_p& y)
+ 	{
+ 		return x = int64_t(rep(y));
+@@ -130,7 +130,7 @@ namespace LinBox
+ 		typedef NTL::zz_p Element ;
+ 		typedef Givaro::UnparametricOperations<Element> Father_t ;
+ 		typedef UnparametricRandIter<NTL::zz_p> RandIter;
+-		
++
+ 		const Element zero,one,mOne ;
+ 
+ 
+@@ -145,6 +145,11 @@ namespace LinBox
+ 			,zero( NTL::to_zz_p(0)),one( NTL::to_zz_p(1)),mOne(-one)
+             {}
+ 
++		Element &init (Element &x) const
++            {
++                return x = NTL::to_zz_p(0);
++            }
++
+ 		Element& init(Element& x, const double& y) const
+             {
+                 double z = fmod(y,(double)Element::modulus());
+@@ -153,7 +158,7 @@ namespace LinBox
+                 return x = NTL::to_zz_p(static_cast<long>(z)); //rounds towards 0
+             }
+ 
+-		Element &init (Element &x, const integer &y=0) const
++		Element &init (Element &x, const integer &y) const
+             {
+                 NTL::ZZ tmp= NTL::to_ZZ(std::string(y).data());
+                 return x = NTL::to_zz_p(tmp);
+diff --git a/linbox/ring/ntl/ntl-lzz_pe.h b/linbox/ring/ntl/ntl-lzz_pe.h
+index 60b132a06..d53444b69 100644
+--- a/linbox/ring/ntl/ntl-lzz_pe.h
++++ b/linbox/ring/ntl/ntl-lzz_pe.h
+@@ -96,18 +96,18 @@ namespace LinBox
+ 			NTL::zz_pE::init(irredPoly);
+ 			_f = irredPoly;
+ 		}
+-		
++
+ 		NTL_zz_pE_Initialiser( const Integer & p, const NTL::zz_pX & f) {
+ 			NTL::zz_p::init((int64_t) p);
+ 			NTL::zz_pE::init(f);
+ 			_f = f;
+ 		}
+-		
++
+ 		NTL_zz_pE_Initialiser(const NTL::zz_pX &f) {
+ 			NTL::zz_pE::init(f);
+ 			_f = f;
+ 		}
+-		
++
+ 		const NTL::zz_pX& modulus() const {
+ 			return _f;
+ 		}
+@@ -143,22 +143,22 @@ namespace LinBox
+ 		NTL_zz_pE (const integer &p, const integer &k) :
+                 NTL_zz_pE_Initialiser(p,k),Father_t ()
+         {
+-        	init(const_cast<Element &>(zero), 0);
+-		 	init(const_cast<Element &>(one), 1);
+-		 	init(const_cast<Element &>(mOne), p-1);
++            init(const_cast<Element &>(zero), 0);
++            init(const_cast<Element &>(one), 1);
++            init(const_cast<Element &>(mOne), p-1);
+ 		}
+-        
++
+ 		NTL_zz_pE (const integer &p, const NTL::zz_pX &f) :
+                 NTL_zz_pE_Initialiser(p,f), Father_t()
+         {
+             init(const_cast<Element &>(zero), 0);
+-		 	init(const_cast<Element &>(one), 1);
+-		 	init(const_cast<Element &>(mOne), p-1);
++            init(const_cast<Element &>(one), 1);
++            init(const_cast<Element &>(mOne), p-1);
+         }
+-        
++
+         NTL_zz_pE(const NTL_zz_pE &F) :
+-        	NTL_zz_pE_Initialiser(F.modulus()), Father_t(),
+-        	zero(NTL::to_zz_pE(0)), one(NTL::to_zz_pE(1)), mOne(-one)
++                NTL_zz_pE_Initialiser(F.modulus()), Father_t(),
++                zero(NTL::to_zz_pE(0)), one(NTL::to_zz_pE(1)), mOne(-one)
+ 		{
+         }
+ 
+@@ -182,15 +182,15 @@ namespace LinBox
+ 
+ 		bool isUnit (const Element& x) const
+             {
+-            	if (isZero(x)) {
+-            		return false;
+-            	} 
+-            	
+-            	NTL::zz_pX g, tmp;
+-            	tmp = NTL::conv<NTL::zz_pX>(x);
+-            	NTL::GCD(g, tmp, modulus());
+-            	
+-            	return g == 1;
++                if (isZero(x)) {
++                    return false;
++                }
++
++                NTL::zz_pX g, tmp;
++                tmp = NTL::conv<NTL::zz_pX>(x);
++                NTL::GCD(g, tmp, modulus());
++
++                return g == 1;
+             }
+ 
+ 		bool isMOne (const Element& x) const
+@@ -207,7 +207,9 @@ namespace LinBox
+ 			return f;
+             }
+ 
+-		Element & init(Element & x, integer n = 0) const
++		Element & init(Element & x) const { return x; }
++
++		Element & init(Element & x, integer n) const
+             {   // assumes n >= 0.
+                 int e = exponent();
+                 n %= cardinality();
+@@ -215,14 +217,14 @@ namespace LinBox
+                     //write(std::cout << "init-ed ", x) << std::endl;
+                 return x;
+             }
+-        
++
+         // documentation of NTL::conv:
+         // http://www.shoup.net/ntl/doc/conversions.txt
+         // XXX = long, ZZ, ZZ_p, ZZ_pE, ZZ_pX
+         template<class XXX>
+         Element &init(Element &x, const XXX &y) const {
+-        	x = NTL::conv<NTL::zz_pE>(y);
+-        	return x;
++            x = NTL::conv<NTL::zz_pE>(y);
++            return x;
+         }
+ 
+         integer & convert(integer & x, const Element & y) const
+@@ -279,81 +281,80 @@ namespace LinBox
+                 x=one/x;
+                 return x;
+             }
+-        
++
+         Element& div(Element &x, const Element &y, const Element &z) const {
+-        	NTL::zz_pX g, zx;
+-        	conv(zx, z);
+-        	NTL::GCD(g, zx, modulus());
+-        	
+-        	NTL::zz_pE zg;
+-        	conv(zg, zx / g);
+-        	x = NTL::conv<NTL::zz_pE>(NTL::conv<NTL::zz_pX>(y) / g);
+-        	x /= zg;
+-        	
+-        	return x;
++            NTL::zz_pX g, zx;
++            conv(zx, z);
++            NTL::GCD(g, zx, modulus());
++
++            NTL::zz_pE zg;
++            conv(zg, zx / g);
++            x = NTL::conv<NTL::zz_pE>(NTL::conv<NTL::zz_pX>(y) / g);
++            x /= zg;
++
++            return x;
+         }
+-        
++
+         Element& divin(Element &x, const Element &y) const {
+-        	Element r;
+-        	div(r, x, y);
+-        	return x = r;
++            Element r;
++            div(r, x, y);
++            return x = r;
+         }
+ 
+         bool isDivisor(const Element &x, const Element &y) const {
+-        	if (isZero(y)) {
+-        		return false;
+-        	}
+-        	
+-        	if (isUnit(y)) {
+-        		return true;
+-        	}
+-        	
+-        	NTL::zz_pX a, b;
+-        	conv(a, x);
+-        	conv(b, y);
+-        	
+-        	NTL::zz_pX ga, gb;
+-        	NTL::GCD(ga, a, modulus());
+-        	NTL::GCD(gb, b, modulus());
+-        	
+-        	NTL::zz_pX r;
+-        	r = ga % gb;
+-        	return isZero(NTL::conv<Element>(r));
++            if (isZero(y)) {
++                return false;
++            }
++
++            if (isUnit(y)) {
++                return true;
++            }
++
++            NTL::zz_pX a, b;
++            conv(a, x);
++            conv(b, y);
++
++            NTL::zz_pX ga, gb;
++            NTL::GCD(ga, a, modulus());
++            NTL::GCD(gb, b, modulus());
++            NTL::zz_pX r;
++            r = ga % gb;
++            return isZero(NTL::conv<Element>(r));
+         }
+-		
++
+ 		Element& gcd(Element &g, const Element &a, const Element &b) const {
+ 			NTL::zz_pX r1, r2, x, y;
+ 			conv(x, a);
+ 			conv(y, b);
+-			
++
+ 			NTL::GCD(r1, x, modulus());
+ 			NTL::GCD(r2, y, r1);
+-			
++
+ 			return g = NTL::conv<Element>(r2);
+ 		}
+-		
++
+ 		Element& gcdin(Element &a, const Element &b) const {
+ 			NTL::zz_pE g;
+ 			gcd(g, a, b);
+ 			return a = g;
+ 		}
+-		
++
+ 		Element& dxgcd(Element &g, Element &s, Element &t, Element &u, Element &v, const Element &a, const Element &b) const {
+ 			NTL::zz_pX gx, sx, tx, ux, vx, ax, bx;
+ 			conv(ax, a);
+ 			conv(bx, b);
+-			
++
+ 			NTL::XGCD(gx, sx, tx, ax, bx);
+-			
++
+ 			ux = ax / gx;
+ 			vx = bx / gx;
+-			
++
+ 			conv(g, gx);
+ 			conv(s, sx);
+ 			conv(t, tx);
+ 			conv(u, ux);
+ 			conv(v, vx);
+-			
++
+ 			return g;
+ 		}
+ 
+@@ -364,12 +365,12 @@ namespace LinBox
+                 x=NTL::to_zz_pE(tmp);
+                 return is;
+             }
+-            
++
+ 		std::ostream& write( std::ostream& os ) const
+             {
+                 return os << "Polynomial quotient ring using NTL::zz_pE";
+             }
+-            
++
+ 		std::ostream& write( std::ostream& os, const Element& x) const {
+ 			os << x;
+ 			return os;
+@@ -429,7 +430,7 @@ namespace LinBox
+ 		uint64_t _seed;
+         const NTL_zz_pE& _ring;
+ 	}; // class UnparametricRandIters
+-	
++
+ } // LinBox
+ 
+ #endif //__LINBOX_ntl_lzz_pe_H
+diff --git a/linbox/ring/ntl/ntl-zz_px.h b/linbox/ring/ntl/ntl-zz_px.h
+index 6e7d5b2fd..340df9f95 100644
+--- a/linbox/ring/ntl/ntl-zz_px.h
++++ b/linbox/ring/ntl/ntl-zz_px.h
+@@ -104,6 +104,12 @@ namespace LinBox
+ 			,_CField(cf)
+ 		{}
+ 
++		/** Initialize p to 0 */
++		Element& init( Element& p ) const
++		{
++			return p = 0;
++		}
++
+ 		/** Initialize p to the constant y (p = y*x^0) */
+ 		template <class ANY>
+ 		Element& init( Element& p, const ANY& y ) const
+-- 
+2.43.0
+
diff --git a/sci-libs/linbox/linbox-1.7.0-r1.ebuild b/sci-libs/linbox/linbox-1.7.0-r1.ebuild
new file mode 100644
index 000000000000..6f5e7d7b2b55
--- /dev/null
+++ b/sci-libs/linbox/linbox-1.7.0-r1.ebuild
@@ -0,0 +1,114 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="C++ template library for integer and finite-field linear algebra"
+HOMEPAGE="https://linalg.org/"
+SRC_URI="https://github.com/linbox-team/${PN}/releases/download/v${PV}/${P}.tar.gz"
+
+# I think only macros/libtool.m4 (and COPYING) is GPL-2+; the source
+# headers all say LGPL-2.1
+LICENSE="GPL-2+ LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos"
+IUSE="doc opencl openmp"
+
+BDEPEND="doc? ( app-text/doxygen )"
+
+# The project README says that gmp, givaro, and blas/lapack are required
+# transitively via fflas-ffpack, but that's not true. The build system
+# checks for them, and `git grep` shows that they're used directly.
+DEPEND="dev-libs/gmp[cxx(+)]
+	=sci-libs/givaro-4.2*
+	=sci-libs/fflas-ffpack-2.5*
+	virtual/cblas
+	virtual/lapack
+	opencl? ( virtual/opencl )
+	dev-libs/ntl:=
+	sci-libs/iml
+	dev-libs/mpfr:=
+	sci-mathematics/flint"
+
+# Use mathjax to render inline latex rather than requiring a working latex
+# installation to generate bitmaps.
+RDEPEND="${DEPEND}
+	doc? ( >=dev-libs/mathjax-3 )
+"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.7.0-hardened-testfails.patch
+	"${FILESDIR}"/${PN}-1.7.0-gcc14.patch
+)
+
+# The --enable-openmp flag has been removed upstream, but we don't want
+# openmp support to disappear after the package has been compiled with
+# it, so we retain the USE flag and the toolchain check.
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+src_prepare() {
+	default
+
+	if use doc; then
+		# Avoid the need for a working LaTeX installation. MathJax does
+		# slow down the browser a bit but it also renders much more
+		# nicely than the latex-generated bitmaps would.
+		echo "
+			USE_MATHJAX = YES
+			MATHJAX_VERSION = MathJax_3
+			MATHJAX_RELPATH = \"${EPREFIX}/usr/share/mathjax\"
+			MATHJAX_EXTENSIONS = ams
+		" >> doc/Doxyfile.mod || die
+	fi
+
+	eautoreconf
+}
+
+src_configure() {
+	#
+	# The --with-all flag includes,
+	#
+	#   --with-givaro: used for finite fields, integer, etc. (required)
+	#   --with-fflas-ffpack:  small field dense linear algebra (required)
+	#   --with-ntl: used for finite field, polynomial arithmetic (optional)
+	#   --with-iml: used for fast integer/rational linear algebra (optional)
+	#   --with-mpfr: not sure, doesn't seem to be used? (optional)
+	#   --with-flint: used in algorithms/matrix-blas3 once (optional)
+	#   --with-fplll: an fplll interface not directly used (optional)
+	#   --with-doxygen: needed with --enable-doc to build them (optional)
+	#
+	# Some of these could be behind USE flags, but the ./configure output
+	# says that they're "not yet mandatory," which makes me think we might
+	# be overcomplicating things to make them optional right now.
+	#
+	econf \
+		--with-docdir="${EPREFIX}/usr/share/doc/${PF}" \
+		--with-all="${EPREFIX}"/usr \
+		--without-fplll \
+		--without-archnative \
+		$(use_enable doc) \
+		$(use_with opencl ocl)
+}
+
+src_install() {
+	default
+	find "${ED}" -name '*.la' -delete || die
+	if use doc; then
+		# These files are used for incremental doxygen builds but aren't
+		# part of the final output. Check on
+		#
+		#   https://github.com/linbox-team/linbox/issues/252
+		#
+		# periodically to see if this is pointless.
+		find "${ED}/usr/share/doc/${PF}" -type f -name '*.md5' -delete || die
+		find "${ED}/usr/share/doc/${PF}" -type f -name '*.map' -delete || die
+	fi
+}