gentoo resync : 25.04.2020

19 files changed, 195 insertions, 421 deletions

diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz
index 0eff5dc5b928..ef11ccf14b64 100644
--- a/sci-mathematics/Manifest.gz
+++ b/sci-mathematics/Manifest.gz
diff --git a/sci-mathematics/dunshire/Manifest b/sci-mathematics/dunshire/Manifest
index 1558f3847adb..d52424969367 100644
--- a/sci-mathematics/dunshire/Manifest
+++ b/sci-mathematics/dunshire/Manifest
@@ -1,3 +1,3 @@
 DIST dunshire-0.1.1.tar.gz 300878 BLAKE2B b0ed57e535313fbc653fdc7c8fd32fb98382db71dfe419e315f4b82fc4630e47757d74b9105e846b2eefaa7dcd93b12886eee341b11d0e8b562a52e480478e9a SHA512 5cdf8125d7fc1f76a483009392360e9e9088f9b58ca3f123d14e366421e831e4e7c8e17d367ba0430fb3cd61873cae7a004c903ff5417bfc9adecb7831681081
-EBUILD dunshire-0.1.1.ebuild 716 BLAKE2B 3299010971dd19a8e2fc82718629296221c73277b0c54a54ff9f96dd821e008e6e099e03731cf23e3e7338db506bf7ff7907871454e94c59c1f62dd4e5714169 SHA512 8c8605f04a6f5024844fd4f522c0ce9cb706768dd04ad58cdb95a0b1664fc2aedb308c7bd6f14ba581f5f42beb537dc69e928103cceeb1a15df98bc4b00b10ed
+EBUILD dunshire-0.1.1-r1.ebuild 973 BLAKE2B 8481023de71fb16fa09cd88aeb25de4f065a7e6f63c33c9850bfa8c038c84c51d826b6b372da0044d9e2ba70c09ac2a83fe9cac7c277e70e369f6721cad93067 SHA512 2a42b93acfe5d2c857de4a233cf516b3c4643c3b1bea920feddbefe31adf3268eb1454622cef7ea98b80807954b470a4fd0bea37c48d9b06fa397082612b1692
 MISC metadata.xml 328 BLAKE2B 16beb1fab1e231e2bb2c8088729c9ab6fa1d4ab06f12f1da462fdeb18738d5fed80b28456df94b2af14f97855042d356b7f69ef956524c456bae62e12b4ba499 SHA512 1ae4898a1247c78ba707aa6e38819cbc5277e46fd32d3ca1172c70c18f42247624755262e3886a2deee76d2a39a3a54750edbc2d77a339543741c2488b095e45
diff --git a/sci-mathematics/dunshire/dunshire-0.1.1.ebuild b/sci-mathematics/dunshire/dunshire-0.1.1-r1.ebuild
index 82de99fb080f..2824f031c377 100644
--- a/sci-mathematics/dunshire/dunshire-0.1.1.ebuild
+++ b/sci-mathematics/dunshire/dunshire-0.1.1-r1.ebuild
@@ -1,14 +1,14 @@
 # Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python3_6 )
+PYTHON_COMPAT=( python3_6 python3_7 python3_8 )
 
 inherit distutils-r1
 
 DESCRIPTION="Python library to solve linear games over symmetric cones"
-HOMEPAGE="http://michael.orlitzky.com/code/dunshire"
+HOMEPAGE="http://michael.orlitzky.com/code/dunshire/"
 SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz"
 
 LICENSE="AGPL-3+"
@@ -18,8 +18,15 @@ IUSE="doc test"
 RESTRICT="!test? ( test )"
 
 RDEPEND="dev-python/cvxopt[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]"
+
+# Tests run on the build host? Bug #693916. There's one doctest that
+# uses a numpy matrix, sorry. That will be fixed in the next release.
+# Otherwise numpy is not needed; the required interfaces are provided
+# through cvxopt.
+BDEPEND="test? (
+	${RDEPEND}
+	 dev-python/numpy[${PYTHON_USEDEP}]
+)"
 
 python_install_all() {
 	use doc && local HTML_DOCS=( doc/build/html/. )
diff --git a/sci-mathematics/flintqs/Manifest b/sci-mathematics/flintqs/Manifest
index bb93b4b7d83a..dd2462a41358 100644
--- a/sci-mathematics/flintqs/Manifest
+++ b/sci-mathematics/flintqs/Manifest
@@ -1,3 +1,3 @@
 DIST flintqs-1.0.tar.gz 151535 BLAKE2B c05761767af65ed5e5c42e75640c0736a26de76126907a91914083791ce0fa3659fb6f9fcdddb0b7aaaf2200010d826a18e7fcbdad0ffc6f861d4bcd941caabb SHA512 8391bb13bcc91f4ea68c972f0f6eaf9aa37bedc4c8694d039a21fd5153b203d561364ae545478d34013001354c4e8a013b2e5a5cb947b6e7f453c6f0f392f8be
-EBUILD flintqs-1.0.ebuild 1009 BLAKE2B 07dca8c379b639415bd62e8cc675eb4634e2aefb62aac16314e1ae2a9e504387a42a18300994b43e2bd914d053d8d3de30cafde8bb226fdc1157df6756f90334 SHA512 254919e66b3e2ceda923e90958a478fd97ece56d3a711da7ecc1f120b8ee8ef0a033cf78b0d941566d9700debd3220ed318f3c51a592074039fdab02c4db6c1a
+EBUILD flintqs-1.0.ebuild 1018 BLAKE2B f7bb64f4cb2c7d7b1fb763800a2504b2d71e1f38346b31ceb1cf28c43b20f673a05b7165f0c40994fc79ee0ad3b9dcb60fdb91dfbdbbc74577e9dfb2ee57ead8 SHA512 c87ffe7635d41e962029bd8e6e4f11db13db9a1571565882b1c751c29d22932d893896c65338cc2d919ee57ee4653bef3fac3333b6c474883aaccc73593428ef
 MISC metadata.xml 736 BLAKE2B 553a7c524f86f30ba868d5e0db2fe5d1b4c501a5be3041fd7cccdb50e5945ecf794dde68c058ff88a1ed918d9466636d723e117e1c073665c20d5330a3e2ad4c SHA512 5ca499866911f12338a1303be4d037b60a62e257e77856349accff7d002c5fef5f6b1f74e6558392e1ed265413440f237a6775a57ec9a57429ce480fea6f838d
diff --git a/sci-mathematics/flintqs/flintqs-1.0.ebuild b/sci-mathematics/flintqs/flintqs-1.0.ebuild
index 676e751c8bd8..5914bbbd5025 100644
--- a/sci-mathematics/flintqs/flintqs-1.0.ebuild
+++ b/sci-mathematics/flintqs/flintqs-1.0.ebuild
@@ -10,7 +10,7 @@ SRC_URI="http://files.sagemath.org/spkg/upstream/${PN}/${P}.tar.gz"
 
 LICENSE="GPL-2+"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 IUSE=""
 
 DEPEND="dev-libs/gmp:="
@@ -28,7 +28,7 @@ src_test() {
 	# The sed command deletes all lines up to the pattern match.
 	#
 	ACTUAL=$(echo 1000000000000000005490000000000000001989 | \
-				 QuadraticSieve | \
+				 "${S}"/src/QuadraticSieve | \
 				 sed '0,/FACTORS:/d' | \
 				 sort --numeric | \
 				 uniq |
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"
diff --git a/sci-mathematics/glpk/Manifest b/sci-mathematics/glpk/Manifest
index e8337e380151..8adb05e22424 100644
--- a/sci-mathematics/glpk/Manifest
+++ b/sci-mathematics/glpk/Manifest
@@ -1,9 +1,6 @@
-AUX glpk-4.63-debundle-system-libs.patch 2240 BLAKE2B 5bd0d25768682a410159e3bf0eaf83dc038da8c6bda275c6994846516bb347caf6d4ea726e8635c77b84a463cb1ec32955f573589291486067c651a88d7f276c SHA512 186c1dd2197119b376a76a2db9a73d7fc1e43adc6ae54f5d3e39ad9114a9a406d45dd7bce4bcea31cfce94e71234b70872db22378e8312026912a93077488805
 AUX glpk-4.65-debundle-system-libs.patch 1930 BLAKE2B 0c265afe9338e75bb3d6536e9e0b2f473e15b4b524b29244bd6bce44a1f77e48c122a463a3800a246435b47d240e799fd16a21ef5c66eb00643759774c47ef73 SHA512 940c2d3dc12efd8df90c17277630a60ea6682eff0323ea82eeb8b81377db612103c29fb44bbe8ff936d96a436548be3e4c772f55f8412adaad546a6381be6333
 AUX glpk-4.65-fix-mysql-include-prefix.patch 1837 BLAKE2B ecd90024e07f29e8ebb6af80b520c8f192cfea21c90d8c247001389f2ccfcf24ad487981a0cc719d1ca99e266dd2a9d66f6416d4f2d5e7c80bdf807b9bb7b74e SHA512 c74281bf3e03e136d183b562b8f682a3e1957019a36ec0c6a048049f0d5f55361107a62e36eaa9e3306a1f13df10adf55c2f54f096b6e353108856e05d9ce799
 AUX glpk-4.65-longstep_verbosity.patch 844 BLAKE2B c1d14e6dfd596694bf1da060129713eb70ceebd4b1742e8496b89c1e1bfefa5bfdf320ecb8d863aa5b5a0d9750bca8bf59b261608cc39b1d1a0b3fe3b10a7be4 SHA512 29d8e876c0d5fba14056e8f0639e3746c6f4c0eefcad284727921e0ca7184ad96b4363dfe9bfe67b74d6d9419f37d21e453e431bf53438b624c1ab0ef9fe1092
-DIST glpk-4.63.tar.gz 4131787 BLAKE2B 791fa1a1424011668019e180fc245c0319f601255f596affe87afa0df47d9d615a8accd794d51c15bff5fe4fe6409369362f6c9e82bdde67903177b8da55e891 SHA512 3ee9b9ec5322282a9c62b2ee209fc7760383a6a764ef3816445ffb66f15ed4d00309bff1b98d50c243b58aa74f83072afde45c389799e637e11e86f4db45276c
 DIST glpk-4.65.tar.gz 4167110 BLAKE2B 4ccb5cd8301bdca2ccdecfc1648642afe26ff0a1ee9a75cb5a3906838086e5c41edfb16e7c55f4ad677d192f6a66b866f2d917c5be7103da7141bfb1f74e636b SHA512 997e8e599ff1718a08c66b86eadd0e01f4644899f1e95920f8ae91d66b4d8361021766b346845f4dcbcfe667b41ab72ea3d377017a0ebf85d7ece091cfd81375
-EBUILD glpk-4.63.ebuild 1460 BLAKE2B 87059596f20960dc68de7bd7fd804bbb7774ea373601782da090fa3dad4403e28725cfed8dc31bb25c0a229ff5275b7950665c31baf2f2fdf9c88f0489f25073 SHA512 3d5c104f103f46440499181f5c0155ca1a8d4b7418fc8c93bcff7382601f4fbcd2380ea3a637ad469c0ac3a579b67b6c011ecdcfaf66fb0cd40adb33c675dff3
-EBUILD glpk-4.65.ebuild 1792 BLAKE2B f32f1e3e8d84be2e5419114abb7aee35ad0e6c5692bb01835f58d869b571832dbc2d49f1cb8ad42fbb7a2edcc632f7a0b167fbe27c59ed05ba3a5dcfb5643a2d SHA512 31041d5866fbd516cba4f7db1332de86f0d47820da51d5cc30a22dc1109df7cf7465af31e489779c94e5faab9c4c126ef13f6ad7662d397e5ffdc3aac99d7542
+EBUILD glpk-4.65.ebuild 1787 BLAKE2B cce26aa79190ce27f60a49f7325a2adc005ebfb47ccdc5f0b6252b87441c88af90c43cf7524e61e3b9377a9108ace3d97ce7bc3feaec51a8d4aa1ea66caba5ab SHA512 2fc117d1bff9cc476b19a0a63a12701bda56fc33c80d87bc8c8cddee34702f5dbff5ff4fe37239bf349db46443ea8e4167fc853fc9d4f9cb583587d57b2c5d60
 MISC metadata.xml 998 BLAKE2B 11afba9ccdd6a53cee9432201eee2ae03483da71212f1c7f9907a775e6c2fcce068648fdae87965dab7550c9157c86697802707b582589626cf48e4236aa56e0 SHA512 1ef83c282b3a6143a1e85a1ecdc55463cf5617409dc990806917077c30e4acd2663b2772bf47aa96c572ee78dab76467c10b4ae9a2705220aa6e8e4936c4f7b5
diff --git a/sci-mathematics/glpk/files/glpk-4.63-debundle-system-libs.patch b/sci-mathematics/glpk/files/glpk-4.63-debundle-system-libs.patch
deleted file mode 100644
index e836219d0add..000000000000
--- a/sci-mathematics/glpk/files/glpk-4.63-debundle-system-libs.patch
+++ /dev/null
@@ -1,94 +0,0 @@
-Remove suitesparse (camd,colamd) and zlib bundles
-bicatali - apr 2014
-Updated for 4.57 by soap (Jan 2016)
-Updated for 4.60 by bicatali (Dec 2016)
-Updated for 4.63 by bicatali (Jul 2017)
-
-diff -Nuar --exclude '*.orig' --exclude '*.rej' --exclude '*~' glpk-4.63.orig/configure.ac glpk-4.63/configure.ac
---- glpk-4.63.orig/configure.ac	2017-07-25 00:00:00.000000000 -0700
-+++ glpk-4.63/configure.ac	2017-07-27 14:10:47.986520907 -0700
-@@ -69,6 +69,11 @@
- dnl Check for math library
- AC_CHECK_LIB([m], [exp])
- 
-+AC_CHECK_LIB([amd], [amd_1])
-+AC_CHECK_LIB([colamd], [colamd])
-+AC_CHECK_HEADER([amd.h])
-+AC_CHECK_LIB([z], [gzopen])
-+
- dnl Check for <sys/time.h> header
- AC_CHECK_HEADER([sys/time.h],
-    AC_DEFINE([HAVE_SYS_TIME_H], [1], [N/A]))
-diff -Nuar --exclude '*.orig' --exclude '*.rej' --exclude '*~' glpk-4.63.orig/src/Makefile.am glpk-4.63/src/Makefile.am
---- glpk-4.63.orig/src/Makefile.am	2017-07-25 00:00:00.000000000 -0700
-+++ glpk-4.63/src/Makefile.am	2017-07-27 14:11:30.841536062 -0700
-@@ -6,18 +6,15 @@
- 
- libglpk_la_CPPFLAGS = \
- -I$(srcdir) \
---I$(srcdir)/amd \
- -I$(srcdir)/api \
- -I$(srcdir)/bflib \
- -I$(srcdir)/cglib \
---I$(srcdir)/colamd \
- -I$(srcdir)/env \
- -I$(srcdir)/minisat \
- -I$(srcdir)/misc \
- -I$(srcdir)/mpl \
- -I$(srcdir)/proxy \
---I$(srcdir)/simplex \
---I$(srcdir)/zlib
-+-I$(srcdir)/simplex
- 
- libglpk_la_LDFLAGS = \
- -version-info 42:2:2 \
-@@ -57,18 +54,6 @@
- glpssx01.c \
- glpssx02.c \
- lux.c \
--amd/amd_1.c \
--amd/amd_2.c \
--amd/amd_aat.c \
--amd/amd_control.c \
--amd/amd_defaults.c \
--amd/amd_dump.c \
--amd/amd_info.c \
--amd/amd_order.c \
--amd/amd_post_tree.c \
--amd/amd_postorder.c \
--amd/amd_preprocess.c \
--amd/amd_valid.c \
- api/advbas.c \
- api/asnhall.c \
- api/asnlp.c \
-@@ -142,7 +127,6 @@
- cglib/gmigen.c \
- cglib/mirgen.c \
- cglib/spv.c \
--colamd/colamd.c \
- env/alloc.c \
- env/dlsup.c \
- env/env.c \
-@@ -196,21 +180,6 @@
- simplex/spxprob.c \
- simplex/spychuzc.c \
- simplex/spychuzr.c \
--simplex/spydual.c \
--zlib/adler32.c \
--zlib/compress.c \
--zlib/crc32.c \
--zlib/deflate.c \
--zlib/gzclose.c \
--zlib/gzlib.c \
--zlib/gzread.c \
--zlib/gzwrite.c \
--zlib/inffast.c \
--zlib/inflate.c \
--zlib/inftrees.c \
--zlib/trees.c \
--zlib/uncompr.c \
--zlib/zio.c \
--zlib/zutil.c
-+simplex/spydual.c
- 
- ## eof ##
diff --git a/sci-mathematics/glpk/glpk-4.63.ebuild b/sci-mathematics/glpk/glpk-4.63.ebuild
deleted file mode 100644
index e895918d23a1..000000000000
--- a/sci-mathematics/glpk/glpk-4.63.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools flag-o-matic toolchain-funcs
-
-DESCRIPTION="GNU Linear Programming Kit"
-LICENSE="GPL-3"
-HOMEPAGE="https://www.gnu.org/software/glpk/"
-SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
-
-SLOT="0/40"
-IUSE="doc examples gmp odbc mysql static-libs"
-KEYWORDS="~alpha amd64 ~arm ~arm64 ~hppa ~ia64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~x86-macos"
-
-RDEPEND="
-	sci-libs/amd:0=
-	sci-libs/colamd:=
-	sys-libs/zlib:0=
-	gmp? ( dev-libs/gmp:0= )
-	mysql? ( virtual/mysql )
-	odbc? ( || ( dev-db/libiodbc:0 dev-db/unixODBC:0 ) )"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-4.63-debundle-system-libs.patch
-)
-
-src_prepare() {
-	sed -e 's#CPPFLAGS="-I/usr/include/mysql#CPPFLAGS="-I'"${EPREFIX}"'/usr/include/mysql#' -i configure.ac || die
-	use odbc && [[ -z $(type -P odbc_config) ]] && \
-		append-cppflags $($(tc-getPKG_CONFIG) --cflags libiodbc)
-
-	default
-	eautoreconf
-}
-
-src_configure() {
-	local myconf
-	if use mysql || use odbc; then
-		myconf="--enable-dl"
-	else
-		myconf="--disable-dl"
-	fi
-
-	econf ${myconf} \
-		$(use_enable mysql) \
-		$(use_enable odbc) \
-		$(use_enable static-libs static) \
-		$(use_with gmp)
-}
-
-src_install() {
-	default
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-		docompress -x /usr/share/doc/${PF}/examples
-	fi
-	use doc && dodoc doc/*.pdf doc/notes/*.pdf doc/*.txt
-}
diff --git a/sci-mathematics/glpk/glpk-4.65.ebuild b/sci-mathematics/glpk/glpk-4.65.ebuild
index 258796fa21ae..a08a4af54c4f 100644
--- a/sci-mathematics/glpk/glpk-4.65.ebuild
+++ b/sci-mathematics/glpk/glpk-4.65.ebuild
@@ -12,7 +12,7 @@ SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
 
 SLOT="0/40"
 IUSE="doc examples gmp odbc mysql static-libs"
-KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+KEYWORDS="~alpha amd64 ~arm ~arm64 ~hppa ~ia64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~x86-macos"
 
 BDEPEND="virtual/pkgconfig"
 DEPEND="
diff --git a/sci-mathematics/pari/Manifest b/sci-mathematics/pari/Manifest
index d54b8ef3a512..744ee099437d 100644
--- a/sci-mathematics/pari/Manifest
+++ b/sci-mathematics/pari/Manifest
@@ -1,9 +1,12 @@
 AUX pari-2.11.2-Makefile-LDFLAGS.patch 394 BLAKE2B 534fcd325397a388545acbce5d96bd5417c31005512ee8f256283921fb64ec4a9ec27fb7e721648b117d3be1000816d1e9bc5ae5adc5df63afe1b0490db020c6 SHA512 de3283be39cff0bba916b314eb9e112324626513f30b5c0e0340617535d8e66ee93fdd9613839633bf7e85244caff6fa1379cc5d0c0a7f9484d028a650eb8845
 AUX pari-2.11.2-Makefile-docinstall.patch 867 BLAKE2B e8b83357ef42ebcb00abfe7bb5adc30414d1975fbde128ffe84c42898374969c608cd6f3b8b0061023681f6416e86552c80552ac51aa884e260d716f79b750c1 SHA512 089ab09532b2e888a272495606f5c0eeb6e12f764f3605c268a3e4e20e707d87c33feea2a745f7441e2cff6e7402df64f17f7b118350a8d4a0972ad8a5a82c69
 AUX pari-2.11.2-no-automagic.patch 2626 BLAKE2B 3be495852655cf47cab2ebfc544477707ab9274329a4fc7f380bd683236968e0bafd9f91b9c45289912b2a634aa9ba38f3130e0192cacfb6dc383765803eb5ad SHA512 ff8c00f028da9e782256ad9f6af87a194286cf198e8639bd737663db9b4898903993a9ef01f9084bcd658913f3d639509f89cca9b77963790ede9bb998845821
+AUX pari-2.11.3-incorrect_bnfisunit.patch 1482 BLAKE2B 198aa6e5130f5daaa3fb13e678edc82e6efb8c8ea1ae849a62b3afbe49cf3abe1da6465f9ad8e8a5aaa67dab26afb522f7843bf4c8ed3bb904c9c4b6fb65c087 SHA512 2c061adb6e71c31c7880f51175b0ca24b8d218b543d7afe894466b22db850663ef8db5535e3dd236cbb7704638af9f37a99a3d6c6d0913bc47cc0c259c6224b8
 AUX pari-2.9.4-fltk-detection.patch 572 BLAKE2B 1c2e1fa6e52521c7865c3fd011824c83fa92623903dd1e056bda29c6735eb01013e7937f66d6ffff42d0de83f7ed104c7f933d232ee37be7c4351788e76f8daa SHA512 2ec0d8035a87b693ee6a4dfa913f0b24eed20bb4db7f8cd1a47db444310d33d19e6651d475c635be747e79a02df2705e42f6f7032b60dc763583cf9fa8633b29
 AUX pari-2.9.4-ppc.patch 363 BLAKE2B 135e76972e4121362666a25e3da236c4a5b7cffa058bbc25b59ca19ea20ccb0665327f70701adca5239cb936d513976e3ba7b5cda915a3f77c7b2eb28e75eaa0 SHA512 aaf5960010e56722f11234079a20ee7a7f8819dc084e1f6567fd11ad2820e3ae47617608f312941c2f373b5312a8c09c9cd51bfa44e263ffe1e8062c9fd9877d
 AUX pari-2.9.4-strip.patch 323 BLAKE2B 85a2b56f5501b4dafc0bffe48249c1662d6f96e81f8e8260ad52ecf84f053efef2ee6d6be6a6fda47886c372eb338d8bbf4443910df79a0d4e168b2666228c37 SHA512 50624ead82da41819ccfadfbdb746fb6ff414196ae2576c5d6a86e83c67355740b0e6e901a2860cab202db15adb1b00e346aabba338ab303230bc6aee8d33076
 DIST pari-2.11.2.tar.gz 4433038 BLAKE2B 89fd8c14d6ee8c8640432bec75e10b79897f0180212dcb1b04b654478a3258fc13a7f982bcb400e28997934a21667c0c3cb08fdb2e843a80a24c6499feafb639 SHA512 22f5a6ecad6d9b8b337c2655f538a196a0460f6fe98256d0f49557ce7b843f6b27ad364f45a9472aaafee9506386c886f1f0d62697078e501ec465151d4d10a1
+DIST pari-2.11.3.tar.gz 4441199 BLAKE2B 49b001f2dc27d1be7a742c165881f2b21d55cf387a91d880bd3a16cbc5d69172f931caa779c5ccbe79b6855175695b5e88ff99b420b4f2b7404dd5e4a53a135c SHA512 2624cdd0523ec02324f58af65703003c88ab596bcaa30c366a9ea01123b0ae657285b10016abaa06b6783ba34dd4980f560900b836b8df228b9dbe0ca36a5b11
 EBUILD pari-2.11.2.ebuild 3033 BLAKE2B 7e4fd3d274c34a89419ee157bfd798db51b3462444ec886ee9ac71164c30d8d1cbf59d91f78077e792fdc0e55c3ce7ff23c201df43c6ea14bb52dca97d321745 SHA512 72dc95fcf64d2ac470ec9bcb6f30c45b18394662f0f2ab481a43310c410bbedc32c71b0e7a773d859680135c4f9fee9221e5e73bfe58dc1f0094c2f22d03c349
+EBUILD pari-2.11.3.ebuild 3092 BLAKE2B 6f7c636273ec8ddaa545aed868aa9c81628e589fa78ce3042cb2d29272327be4ac5ece9adda69fec3a86b205f2d83ab13543ba255aed1bee0e38378fd10c41c4 SHA512 f8512b9d2f8d6b5f8e2aadcd5c6880540b979300f328f557f2218a6a335c3616bdda38ba3465433fef97ff7d63b4080bf062debdc3e8a5041441c903b0fff9cb
 MISC metadata.xml 1734 BLAKE2B ffb61a9e3818ed778cd30e0b41279413fec1e624aef0c490e71f501b9797703bbd24413b180b588896d6d74af988e6102f58a04fc1c645f2b876ac2731a399c1 SHA512 b5caa3c3b98405d89681fb25c97dabb3302e971c68fda94e337b10dfc14761963ea548b4689ccb4ac59661425a85a53ea0d424b6acb35a475f42ef145ce9060e
diff --git a/sci-mathematics/pari/files/pari-2.11.3-incorrect_bnfisunit.patch b/sci-mathematics/pari/files/pari-2.11.3-incorrect_bnfisunit.patch
new file mode 100644
index 000000000000..877cc6ace756
--- /dev/null
+++ b/sci-mathematics/pari/files/pari-2.11.3-incorrect_bnfisunit.patch
@@ -0,0 +1,49 @@
+From: Karim Belabas <Karim.Belabas@math.u-bordeaux1.fr>
+Date: Mon, 9 Sep 2019 15:20:21 +0000 (+0200)
+Subject: fix #2164
+X-Git-Url: https://pari.math.u-bordeaux.fr/cgi-bin/gitweb.cgi?p=pari.git;a=commitdiff_plain;h=c7a1d35f382e96ddf14694be27a0ca5746880700
+
+fix #2164
+---
+
+diff --git a/src/basemath/buch2.c b/src/basemath/buch2.c
+index a853d3c48..e31b2278b 100644
+--- a/src/basemath/buch2.c
++++ b/src/basemath/buch2.c
+@@ -2136,7 +2136,8 @@ bnfisunit(GEN bnf,GEN x)
+   for (i = 1; i < RU; i++)
+     if (gexpo(gel(emb,i)) > -1) break;
+   p1 = imag_i( row_i(logunit,i, 1,RU-1) );
+-  p1 = RgV_dotproduct(p1, ex); if (!R1) p1 = gmul2n(p1, -1);
++  p1 = RgV_dotproduct(p1, ex);
++  if (i > R1) p1 = gmul2n(p1, -1);
+   p1 = gsub(garg(gel(emb,i),prec), p1);
+   /* p1 = arg(the missing root of 1) */
+ 
+diff --git a/src/test/32/nf b/src/test/32/nf
+index 16bf83ce3..e6c41f8b5 100644
+--- a/src/test/32/nf
++++ b/src/test/32/nf
+@@ -502,6 +502,7 @@ Mod(1/2*x - 1/2, x^2 + 23)
+ [1, 1/2*x - 1/2]
+ Mod(0, x)
+ Mod(-6/5, x)
++[0, 2, Mod(0, 2)]~
+   ***   at top-level: nfinit([y^3+2,[1,x]])
+   ***                 ^---------------------
+   *** nfinit: incorrect type in nfinit_basic (t_VEC).
+diff --git a/src/test/in/nf b/src/test/in/nf
+index 49148123b..94d5165bc 100644
+--- a/src/test/in/nf
++++ b/src/test/in/nf
+@@ -156,6 +156,10 @@ K.zk
+ nfinit(x, 3)[2]
+ nfinit(1/2*x + 3/5, 3)[2]
+ 
++\\ #2164
++bnf = bnfinit(y^4-y-1);
++bnfisunit(bnf,-y^3+2*y^2-1)
++
+ \\ ERRORS: keep at end of file
+ 
+ nfinit([y^3+2,[1,x]])
diff --git a/sci-mathematics/pari/pari-2.11.3.ebuild b/sci-mathematics/pari/pari-2.11.3.ebuild
new file mode 100644
index 000000000000..7f3a302bbe4f
--- /dev/null
+++ b/sci-mathematics/pari/pari-2.11.3.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="Computer-aided number theory C library and tools"
+HOMEPAGE="https://pari.math.u-bordeaux.fr/"
+SRC_URI="https://pari.math.u-bordeaux.fr/pub/${PN}/unix/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0/6"
+KEYWORDS="~alpha ~amd64 ~hppa ~mips ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos ~x86-solaris"
+IUSE="data doc fltk gmp test threads X"
+RESTRICT="!test? ( test )"
+
+BDEPEND="doc? ( virtual/latex-base )"
+DEPEND="
+	sys-libs/readline:0=
+	data? ( sci-mathematics/pari-data )
+	doc? ( X? ( x11-misc/xdg-utils ) )
+	fltk? ( x11-libs/fltk:1= )
+	gmp? ( dev-libs/gmp:0= )
+	X? ( x11-libs/libX11:0= )"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${PN}"-2.9.4-strip.patch
+	"${FILESDIR}/${PN}"-2.9.4-ppc.patch
+	"${FILESDIR}/${PN}"-2.11.2-no-automagic.patch
+	"${FILESDIR}/${PN}"-2.9.4-fltk-detection.patch
+	"${FILESDIR}/${PN}"-2.11.2-Makefile-LDFLAGS.patch
+	"${FILESDIR}/${PN}"-2.11.2-Makefile-docinstall.patch
+	"${FILESDIR}/${PN}"-2.11.3-incorrect_bnfisunit.patch
+)
+
+src_prepare() {
+	default
+
+	# move doc dir to a gentoo doc dir and replace acroread by xdg-open
+	sed -i \
+		-e "s:\$d = \$0:\$d = '${EPREFIX}/usr/share/doc/${PF}':" \
+		-e 's:"acroread":"xdg-open":' \
+		doc/gphelp.in || die "Failed to fix doc dir"
+}
+
+src_configure() {
+	tc-export CC CXX
+
+	# Workaraound to "asm operand has impossible constraints" as
+	# suggested in bug #499996.
+	use x86 && append-cflags $(test-flags-CC -fno-stack-check)
+
+	# need to force optimization here, as it breaks without
+	if is-flag -O0; then
+		replace-flags -O0 -O2
+	elif ! is-flag -O?; then
+		append-flags -O2
+	fi
+
+	# sysdatadir installs a pari.cfg stuff which is informative only.
+	# It is supposed to be for "architecture-dependent" data.
+	# It needs to be easily discoverable for downstream packages such as gp2c.
+	./Configure \
+		--prefix="${EPREFIX}"/usr \
+		--datadir="${EPREFIX}/usr/share/${PN}" \
+		--libdir="${EPREFIX}/usr/$(get_libdir)" \
+		--sysdatadir="${EPREFIX}"/usr/share/pari \
+		--mandir="${EPREFIX}"/usr/share/man/man1 \
+		--with-readline="${EPREFIX}"/usr \
+		--with-readline-lib="${EPREFIX}/usr/$(get_libdir)" \
+		--with-ncurses-lib="${EPREFIX}/usr/$(get_libdir)" \
+		$(use_with fltk) \
+		$(use_with gmp) \
+		--without-qt \
+		$(usex threads "--mt=pthread" "" "" "") \
+		|| die "./Configure failed"
+}
+
+src_compile() {
+	local mymake=""
+	use hppa && \
+		mymake=DLLD\="${EPREFIX}"/usr/bin/gcc\ DLLDFLAGS\=-shared\ -Wl,-soname=\$\(LIBPARI_SONAME\)\ -lm
+
+	emake ${mymake} gp
+
+	if use doc; then
+		# To prevent sandbox violations by metafont
+		VARTEXFONTS="${T}/fonts" emake docpdf
+	fi
+}
+
+src_test() {
+	# Welcome to the jungle, where the tests fail if you make your
+	# terminal bigger.
+	emake COLUMNS=80 test-all
+}
+
+src_install() {
+	DOCS=( AUTHORS CHANGES* COMPAT NEW README* )
+	default
+
+	if use doc; then
+		docompress -x "/usr/share/doc/${PF}"
+		emake \
+			DESTDIR="${D}" \
+			EXDIR="${ED}/usr/share/doc/${PF}/examples" \
+			DOCDIR="${ED}/usr/share/doc/${PF}" \
+			install-doc
+	fi
+}