gentoo resync : 25.04.2020

7 files changed, 13 insertions, 250 deletions

diff --git a/sci-mathematics/gfan/Manifest b/sci-mathematics/gfan/Manifest
index a0e9b343e7d3..10ef992c17ad 100644
--- a/sci-mathematics/gfan/Manifest
+++ b/sci-mathematics/gfan/Manifest
@@ -1,12 +1,6 @@
-AUX gfan-0.5-double-declare-fix.patch 470 BLAKE2B e5d12f62b2efe9781f616825dce16cab9cf5181358c466945577ca2666e89d5f223572a0ef530644aaf1e1c345ce8942e7826f37134263ef2f83d0cf569dc6cd SHA512 25f340d5636c1cc719328a00561d9c4e5ab3a67633a9fb0ceb23ca0c771fe579f60678649affdf5be76d189f43a986eecd13a91d9681e847ed8b7c1c4c4ed118
-AUX gfan-0.5-fix-build-system.patch 1349 BLAKE2B bce148ee12c3fd720baeccc6a75b0b66ed76f1bb7d1b7ef92c3d67ab26a4743502169b0fbac87b24496f5319adc85dbed1c4efdc1dfb68ecaf795f2d7441d4f1 SHA512 e53e7ec77ef18fa05f14ab0aa011b524439d4c4bdad79d2e197bde1e136df1c2ca043287d17722140ea79351969d87df29eb845ac441f9703c7c786bd6ac582e
-AUX gfan-0.5-fix-gcc9.patch 3712 BLAKE2B fd8b89d8f3019db71ea9bba05a8652666ddef6d35dd75cc97510cf96267ce1cc651375cfb9e269ab765b5bc3c30c0b33cbf73d1a74eea8a564a3d5482c15af28 SHA512 6c1186c2a549191b4db31433ca006de7d916bb43b2a9176f83b0c6516ac757f693721c355aff8b1669987b6db862858b4f428cc372f6787a0f4503242bb5e035
-AUX gfan-0.5-gcc6.1-compat.patch 2000 BLAKE2B 0ba13745140bb56d3398669e453cd245ee31c351ee3899dbded117ad48a238e99306c0c08b050168ddd204f4f30840ab8f04a609b135b782a06522cf65236995 SHA512 daf9527baf68299063ccdd82b53e92a63584fd5cf432b2d889c4aad08ccff0a31c0a75a7b6defd018021df4f46831ed7727a1bd6ea1b0da1fe9a924f9b208fe9
 AUX gfan-0.6.2-Makefile.patch 6603 BLAKE2B 48f9b4280418aef41d502d770c070ec1dcef947a39c6263d991be0f6f41147d06b78a4b07ca76e0fb4bc9780cb9469c98c637473789d857925df8d546ad35e92 SHA512 e1eef6f01c9942b38780f19b774fa3e99df4dbdba738cc2c6c69e2f1858e5e6294db72d7b679c5ff1313a76143bd611077731d360479f9375d6506e33a4a620a
 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 gfan0.5.tar.gz 1134987 BLAKE2B 73ea793f5dbceb76a9f143a258ee3e38e1466e4e15ed96dbabb58f33d3a091a885479dd00f8179d3bf2c85cf275605823f63aa33272f1f9984e0fc5841ab35e9 SHA512 11a9657adcd5b39f73244450c09b132d8cd19474d0f9151c0127682bc16847537e4096d39e8a0a63b5c6aef6720e54a72bfd361a5271808d5a5595fd2df494fa
 DIST gfan0.6.2.tar.gz 1321059 BLAKE2B 1ed61e1e084a1ceb65dd21848440bc3a90486c0ce4012b3b64c8029e89636696d2b0e5446ea156d2cf050b5db179c7c2f25c97e683cecf6e9616e8553d8513bf SHA512 5961820750af2522fdc1a86c0254742c3b003607a8707df5d6cd5f0bc6461e4d3db3b1d3cb537979d57eb9dff387974a58aeb91d0b5246d7c701cadc5a2cf4cf
-EBUILD gfan-0.5-r1.ebuild 803 BLAKE2B efaa6db36e8f2c593ef82779cbbd9806197198d4150d785e7df5d5605e167fe11f172703723a89357fc23697f00c5ffd642be1a3dbac412b8b67f175cb524427 SHA512 c47d99455abbd85d48909d59a23408271015a3a1b9f6a79b2b26aa390769c41e32ae6ab2f89e29f9cddc0b5db217c619f2eee0cddfe5a9bab670196ac3ac10fa
-EBUILD gfan-0.6.2.ebuild 1355 BLAKE2B 1b1429fa29232e3bde6892547fcff912595bef83ab2a5c44e6ef763da65f678fde3bee193ed7efaad74bfd75389512367c69688d4e54918e08542571c6ae1ea0 SHA512 502b4c7a5619a09d3897b975cdf24834e5592ead0c61f9775ca5627e7bd1fd0eb558b18c25a7721aa5294dd3fa826f4c87ea841c55fb424a47bb2dfd25c87c9a
+EBUILD gfan-0.6.2.ebuild 1628 BLAKE2B 272e77ecdf1e7132bb3a703ed3871cea502d621d596ec47c3529459c120a44921028aa0c064936a49c6b727b6bf44f78971679ff3bf3f9450d3ae945a02193e0 SHA512 c4eaf7e2debfcca9d3a92e6f9abfc1e568c09747db8ebf7caa3ad34c3208de47b8841819d1c5ddd6866b127f9d9496e61616f2bda1cbeb1588c58b682cc0550c
 MISC metadata.xml 1343 BLAKE2B 1e3385eaf888fa6a69e1e3f761bd5a1037e5a5308878664e604ba5efd096747f84a0a3343d8de7f6eb5dd3ce726d94bdb933e17b9eaf8e345b02fd071fbf821b SHA512 ca914de593af1279439f35fdcc812924b831c30bfa86366443f16cb720acd3e38267f25057f59e76a6b8ff1aa48a33ecfa72c093419aab95c92ed82c3308cd94
diff --git a/sci-mathematics/gfan/files/gfan-0.5-double-declare-fix.patch b/sci-mathematics/gfan/files/gfan-0.5-double-declare-fix.patch
deleted file mode 100644
index 239540884011..000000000000
--- a/sci-mathematics/gfan/files/gfan-0.5-double-declare-fix.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -U 3 -dHrN gfan0.5/app_minkowski.cpp gfan0.5-new/app_minkowski.cpp
---- gfan0.5/app_minkowski.cpp	2011-01-23 12:21:47.000000000 -0500
-+++ gfan0.5-new/app_minkowski.cpp	2012-06-29 15:23:48.604280985 -0400
-@@ -160,7 +160,7 @@
- 	    //log0 fprintf(Stderr,"4");
- 	    f.insert(c);
- 	    //log0 fprintf(Stderr,"5\n");
--	    static int i;
-+	    //	    static int i;
- 	    //log0 fprintf(Stderr,"inserted:%i\n",++i);
- 	  }
- 	log1 fprintf(Stderr,"Resolving symmetries.\n");
diff --git a/sci-mathematics/gfan/files/gfan-0.5-fix-build-system.patch b/sci-mathematics/gfan/files/gfan-0.5-fix-build-system.patch
deleted file mode 100644
index 3bf96ed088ce..000000000000
--- a/sci-mathematics/gfan/files/gfan-0.5-fix-build-system.patch
+++ /dev/null
@@ -1,55 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -1,7 +1,5 @@
- ALL: default
- 
--# GPROFFLAG = -pg
-- GPROFFLAG = -g
- 
- PREFIX?=/usr/local
- 
-@@ -77,16 +75,13 @@
- 
- SHELL       = /bin/sh
- #ARCH        = LINUX
--CC          = gcc
- CLINKER     = $(CC)
--CXX         = g++
- CCLINKER    = $(CXX)
--#OPTFLAGS    = -O2 -DGMPRATIONAL -DNDEBUG
--OPTFLAGS    = -O2 -DGMPRATIONAL -Wuninitialized
- 
--CFLAGS	  = $(OPTFLAGS) $(GPROFFLAG) $(ADDITIONALINCLUDEOPTIONS) #-pedantic
--CCFLAGS	  = $(CFLAGS)
--FFLAGS	  = $(OPTFLAGS)
-+
-+CFLAGS      += $(GPROFFLAG) $(ADDITIONALINCLUDEOPTIONS) -Wuninitialized
-+CXXFLAGS    += $(GPROFFLAG) $(ADDITIONALINCLUDEOPTIONS) -Wuninitialized
-+CPPFLAGS    += -DGMPRATIONAL -DNDEBUG
- 
- CATSOBJECTS =	$(GCATSPATH)lp_cdd.o \
- 		$(SOPLEX_OBJECTS) \
-@@ -317,7 +312,7 @@
- default: $(OBJECTS) $(ADDITIONALOBJECTS) $(EXECS)
- 
- $(MAIN): $(OBJECTS)
--	$(CCLINKER) $(OBJECTS) $(ADDITIONALLINKOPTIONS) $(GPROFFLAG) -o $(MAIN)
-+	$(CCLINKER) $(LDFLAGS) $(OBJECTS) $(ADDITIONALLINKOPTIONS) $(GPROFFLAG) -o $(MAIN)
- 
- release:
- 	rm -f -r $(RELEASEDIR)/*
-@@ -430,14 +425,6 @@
- 	cp gfanlib.h gfanlib/
- 	cp gfanlib_* gfanlib/
- 	tar zcf -  gfanlib > gfanlib.tar.gz
--.c.o:
--	$(CC) $(CFLAGS) -c $<
--.cc.o:
--	$(CXX) -c $<
--.cpp.o:
--	$(CXX) $(CFLAGS) -c $<
--.C.o:
--	$(CXX) -c $<
- # wget http://ftp.sunet.se/pub/gnu/gmp/gmp-4.2.2.tar.gz
- # tar -xzvf gmp-4.2.2.tar.gz
- # cd gmp-4.2.2
diff --git a/sci-mathematics/gfan/files/gfan-0.5-fix-gcc9.patch b/sci-mathematics/gfan/files/gfan-0.5-fix-gcc9.patch
deleted file mode 100644
index 930baf9edcf2..000000000000
--- a/sci-mathematics/gfan/files/gfan-0.5-fix-gcc9.patch
+++ /dev/null
@@ -1,68 +0,0 @@
-https://bugs.gentoo.org/686484
-
-polyhedralfan.h: At global scope:
-polyhedralfan.h:77:24: error: friend declaration of ‘PolyhedralFan refinement(const PolyhedralFan&, const PolyhedralFan&, int, bool)’ specifies default arguments and isn’t a definition [-fpermissive]
-   77 |   friend PolyhedralFan refinement(const PolyhedralFan &a, const PolyhedralFan &b, int cutOffDimension=-1, bool allowASingleConeOfCutOffDimension=false);
-      |                        ^~~~~~~~~~
-
---- a/gfanlib_polyhedralfan.h
-+++ b/gfanlib_polyhedralfan.h
-@@ -24,6 +24,8 @@
- typedef std::map<int,IntVectorList> IncidenceList;
- 
- 
-+class PolyhedralFan;
-+PolyhedralFan refinement(const PolyhedralFan &a, const PolyhedralFan &b, int cutOffDimension=-1, bool allowASingleConeOfCutOffDimension=false);
- 
- /** A PolyhedralFan is simply a collection of canonicalized PolyhedralCones.
-  * It contains no combinatorial information in the sense of a polyhedral complex.
-@@ -52,7 +54,7 @@
-   int getAmbientDimension()const;
-   int getMaxDimension()const;
-   int getMinDimension()const;
--  friend PolyhedralFan refinement(const PolyhedralFan &a, const PolyhedralFan &b, int cutOffDimension=-1, bool allowASingleConeOfCutOffDimension=false);
-+  friend PolyhedralFan refinement(const PolyhedralFan &a, const PolyhedralFan &b, int cutOffDimension, bool allowASingleConeOfCutOffDimension);
-   ZMatrix getRays(int dim=1);//This can be called for other dimensions than 1. The term "Rays" still makes sense modulo the common linearity space
-   ZMatrix getRelativeInteriorPoints();
-   void insert(ZCone const &c);
---- a/halfopencone.h
-+++ b/halfopencone.h
-@@ -6,6 +6,9 @@
- 
- #include "polyhedralfan.h"
- 
-+class HalfOpenCone;
-+HalfOpenCone intersection(const HalfOpenCone &a, const HalfOpenCone &b, bool findFacets=false);
-+
- class HalfOpenCone{
-   static void appendList(IntegerVectorList &to, IntegerVectorList const &from, int appendValue);
-   int liftedDimension;//ambient
-@@ -18,7 +21,7 @@
-   HalfOpenCone(int dimension_, IntegerVectorList const &equations, IntegerVectorList const &nonstrict, IntegerVectorList const &strict, bool findFacets=false, bool canonicalize=false);
-   HalfOpenCone(int ambientDimension);//full space
-   bool isEmpty();
--  friend HalfOpenCone intersection(const HalfOpenCone &a, const HalfOpenCone &b, bool findFacets=false);
-+  friend HalfOpenCone intersection(const HalfOpenCone &a, const HalfOpenCone &b, bool findFacets);
-   friend bool haveEmptyIntersection(const HalfOpenCone &a, const HalfOpenCone &b);
-   PolyhedralCone closure();
-   void splitIntoRelativelyOpenCones(list<HalfOpenCone> &l);
---- a/polyhedralfan.h
-+++ b/polyhedralfan.h
-@@ -30,6 +30,8 @@
-   FPF_default=2+4+8
- };
- 
-+class PolyhedralFan;
-+PolyhedralFan refinement(const PolyhedralFan &a, const PolyhedralFan &b, int cutOffDimension=-1, bool allowASingleConeOfCutOffDimension=false);
- 
- /** A PolyhedralFan is simply a collection of canonicalized PolyhedralCones.
-  * It contains no combinatorial information in the sense of a polyhedral complex.
-@@ -74,7 +76,7 @@
-   int getAmbientDimension()const;
-   int getMaxDimension()const;
-   int getMinDimension()const;
--  friend PolyhedralFan refinement(const PolyhedralFan &a, const PolyhedralFan &b, int cutOffDimension=-1, bool allowASingleConeOfCutOffDimension=false);
-+  friend PolyhedralFan refinement(const PolyhedralFan &a, const PolyhedralFan &b, int cutOffDimension, bool allowASingleConeOfCutOffDimension);
-   friend PolyhedralFan product(const PolyhedralFan &a, const PolyhedralFan &b);
-   IntegerVectorList getRays(int dim=1);//This can be called for other dimensions than 1. The term "Rays" still makes sense modulo the common linearity space
-   IntegerVectorList getRelativeInteriorPoints();
diff --git a/sci-mathematics/gfan/files/gfan-0.5-gcc6.1-compat.patch b/sci-mathematics/gfan/files/gfan-0.5-gcc6.1-compat.patch
deleted file mode 100644
index 8479557b61bb..000000000000
--- a/sci-mathematics/gfan/files/gfan-0.5-gcc6.1-compat.patch
+++ /dev/null
@@ -1,70 +0,0 @@
---- a/app_fiberpolytope.cpp
-+++ b/app_fiberpolytope.cpp
-@@ -63,7 +63,7 @@
- 
- 	    /* If the vector configuration B does not have full rank then
- 	       change coordinates. */
--	    if(rank(B)!=B.getHeight())
-+	    if(rank_(B)!=B.getHeight())
- 	      {
- 	        FieldMatrix M=integerMatrixToFieldMatrix(B,Q);
- 	        M.reduce(false,true);//force integer operations - preserving volume
-@@ -83,7 +83,7 @@
- 	    log1 debug<<"Done computing restricting cone\n";
- 
- 	    debug<<B.getRows();
--	    debug<<int(rank(B));
-+	    debug<<int(rank_(B));
- 
- 	    Triangulation2 t(B);
- log1 debug<<"Computing initial triangulation\n";
-@@ -143,7 +143,7 @@
- */
-     /* If the vector configuration A does not have full rank then
-        change coordinates. */
--/*    if(rank(A)!=A.getHeight())
-+/*    if(rank_(A)!=A.getHeight())
-       {
- 	FieldMatrix M=integerMatrixToFieldMatrix(A,Q);
- 	M.reduce(false,true);//force integer operations - preserving volume
---- a/app_secondaryfan.cpp
-+++ b/app_secondaryfan.cpp
-@@ -307,7 +307,7 @@
- 
-     if(scaleOption.getValue())
-       {
--	if(rank(A)!=A.getHeight())
-+	if(rank_(A)!=A.getHeight())
- 	  {
- 	    cerr << "The vector configuration must have full rank in order to use the scale option.\n";
- 	    assert(0);
-@@ -342,7 +342,7 @@
- 
-     /* If the vector configuration A does not have full rank then
-        change coordinates. */
--    if(rank(A)!=A.getHeight())
-+    if(rank_(A)!=A.getHeight())
-       {
- 	FieldMatrix M=integerMatrixToFieldMatrix(A,Q);
- 	M.reduce(false,true);//force integer operations - preserving volume
---- a/matrix.cpp
-+++ b/matrix.cpp
-@@ -61,7 +61,7 @@
- 
- #include "linalg.h"
- 
--int rank(IntegerMatrix const &m)
-+int rank_(IntegerMatrix const &m)
- {
-   return integerMatrixToFieldMatrix(m,Q).rank();
- }
---- a/matrix.h
-+++ b/matrix.h
-@@ -147,6 +147,6 @@
- 
- FloatMatrix integerToFloatMatrix(IntegerMatrix const &m);
- IntegerVector flattenMatrix(IntegerMatrix const &m);
--int rank(IntegerMatrix const &m);
-+int rank_(IntegerMatrix const &m);
- 
- #endif
diff --git a/sci-mathematics/gfan/gfan-0.5-r1.ebuild b/sci-mathematics/gfan/gfan-0.5-r1.ebuild
deleted file mode 100644
index 1cd8c95fbecf..000000000000
--- a/sci-mathematics/gfan/gfan-0.5-r1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Compute Groebner fans and tropical varities"
-HOMEPAGE="http://www.math.tu-berlin.de/~jensen/software/gfan/gfan.html"
-SRC_URI="http://www.math.tu-berlin.de/~jensen/software/gfan/${PN}${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux"
-
-DEPEND="
-	dev-libs/gmp:0=[cxx]
-	sci-libs/cddlib:0="
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}${PV}/"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-double-declare-fix.patch
-	"${FILESDIR}"/${P}-gcc6.1-compat.patch
-	"${FILESDIR}"/${P}-fix-build-system.patch
-	"${FILESDIR}"/${P}-fix-gcc9.patch
-)
-
-src_configure() {
-	tc-export CXX
-}
-
-src_install() {
-	emake PREFIX="${ED}/usr" install
-	einstalldocs
-}
diff --git a/sci-mathematics/gfan/gfan-0.6.2.ebuild b/sci-mathematics/gfan/gfan-0.6.2.ebuild
index a75c9f76f0f7..44e051550034 100644
--- a/sci-mathematics/gfan/gfan-0.6.2.ebuild
+++ b/sci-mathematics/gfan/gfan-0.6.2.ebuild
@@ -11,7 +11,7 @@ SRC_URI="https://users-math.au.dk/~jensen/software/${PN}/${PN}${PV}.tar.gz"
 
 LICENSE="GPL-2+"
 SLOT="0"
-KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux"
 IUSE="doc"
 
 BDEPEND="doc? ( virtual/latex-base )"
@@ -29,9 +29,20 @@ PATCHES=(
 
 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
 }
 
+src_prepare() {
+	default
+
+	# This test hangs on x86, bug 717112.
+	rm -r testsuite/0602ResultantFanProjection || \
+		die "unable to disable test 0602ResultantFanProjection"
+}
+
 src_configure() {
 	# The upstream Makefile says that GCC produces bad code with -O3.
 	replace-flags "-O3" "-O2"