sci-mathematics/gfan: new version 0.6.2.

Update our version of gfan to the latest upstream v0.6.2, from
September 28th 2017. The new ebuild is based off of the version that
François Bissey maintains in the sage-on-gentoo overlay, with a few
additional changes:

  * Merged the EAPI=7 and slot dependency updates from ::gentoo.

  * Change the LICENSE to "GPL-2+", to match the upstream LICENSE file.

  * Stripped some more CFLAGS mangling out of the upstream Makefile.
    Corresponding to this we now replace "-O3" by "-O2" in the ebuild.

  * Added USE="doc", to build and install the LaTeX manual.

Closes: https://bugs.gentoo.org/711492
Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Michael Orlitzky <mjo@gentoo.org>

3 files changed, 390 insertions, 0 deletions

diff --git a/sci-mathematics/gfan/files/gfan-0.6.2-Makefile.patch b/sci-mathematics/gfan/files/gfan-0.6.2-Makefile.patch
new file mode 100644
index 000000000000..8e8db53bc911
--- /dev/null
+++ b/sci-mathematics/gfan/files/gfan-0.6.2-Makefile.patch
@@ -0,0 +1,155 @@
+diff --git a/Makefile b/Makefile
+index 2c9f949..a49a590 100644
+--- a/Makefile
++++ b/Makefile
+@@ -2,8 +2,8 @@ ALL: default
+ 
+ # When -g is used, it seems that stackdump does not work.
+ # GPROFFLAG = -pg
+-GPROFFLAG = -g
+-#GPROFFLAG = 
++#GPROFFLAG = -g
++GPROFFLAG =
+ 
+ PREFIX?=/usr/local
+ 
+@@ -22,20 +22,8 @@ STACTDUMP_OPTIONS = -DSTACKDUMP_ENABLED -D__assert_fail=__assert_fail2
+ endif
+ 
+ 
+-ifeq ($(sagepath),)
+-SAGE_LINKOPTIONS = 
+-SAGE_INCLUDEOPTIONS =
+-else
+-SAGE_LINKOPTIONS = -L$(sagepath)/ -lpython2.6 -lcsage -lsingular
+-SAGE_INCLUDEOPTIONS = -I $(sagepath)/
+-SAGE_OBJECTS = sage.o sage_link.so
+-
+-sage_link.so: sage_link.pyx setup.py
+-	python setup.py build_ext --inplace --pyrex-include-dirs=$(SAGE_ROOT)/devel/sage/
+-endif
+-
+ ifeq ($(gmppath),)
+-GMP_LINKOPTIONS = -lgmp
++GMP_LINKOPTIONS = -lgmp -lm
+ GMP_INCLUDEOPTIONS =
+ else
+ GMP_LINKOPTIONS = $(gmppath)/lib/libgmp.a
+@@ -49,7 +37,7 @@ CDDDEFINE_PREFIX = -DNOCDDPREFIX
+ endif
+ 
+ ifeq ($(cddpath),)
+-CDD_LINKOPTIONS = -L/usr/local -lcddgmp
++CDD_LINKOPTIONS = -lcddgmp
+ CDD_INCLUDEOPTIONS =
+ else
+ CDD_LINKOPTIONS = $(cddpath)/lib/libcddgmp.a
+@@ -71,37 +59,8 @@ SOPLEX_OBJECTS = lp_soplexcdd.o
+ endif
+ 
+ 
+-# rememember to adjust USEFACTORY in field_rationalfunctions2
+-ifeq ($(singular),)
+-ifeq ($(factory),)
+-SINGULAR_PATH =
+-SINGULAR_LINKOPTIONS =
+-SINGULAR_INCLUDEOPTIONS =
+-SINGULAR_OBJECTS = src/polynomialgcd.o 
+-else
+-SINGULAR_PATH =
+-SINGULAR_LINKOPTIONS = -lcf -lcfmem
+-SINGULAR_INCLUDEOPTIONS = -I /usr/local/include/factory/
+-SINGULAR_OBJECTS = src/polynomialgcd.o src/ftmpl_inst.o
+-endif
+-else
+-#SINGULAR_PATH = $(HOME)/math/software/Singular-3-1-0
+-#SINGULAR_LINKOPTIONS =  -L$(SINGULAR_PATH)/Singular -lsingular -lncurses -lreadline
+-#SINGULAR_INCLUDEOPTIONS = -I $(SINGULAR_PATH)/kernel -I $(SINGULAR_PATH)/omalloc
+-#SINGULAR_OBJECTS = src/singular.o src/singularconversion.o
+-SINGULAR_PATH = $(HOME)/math/software/Singular-svn/trunk/x86_64-Linux
+-SINGULAR_LINKOPTIONS =  -L$(SINGULAR_PATH)/lib -lsingular -lncurses -lreadline  -lcf -lcfmem
+-SINGULAR_INCLUDEOPTIONS = -I $(SINGULAR_PATH)/include -I $(SINGULAR_PATH)/include/omalloc
+-SINGULAR_OBJECTS = src/ftmpl_inst.o src/singular.o src/singularconversion.o
+-#Run the following line before running gfan
+-#export LD_LIBRARY_PATH="/home/anders/math/software/Singular-svn/trunk/x86_64-Linux/lib/:${LD_LIBRARY_PATH}"
+-endif
+-
+-# To produce factory templates:
+-#g++ -c /home/anders/math/software/factory-3-1-7/ftmpl_inst.cc  -fno-implicit-templates -I /usr/local/include/factory/ -I/home/anders/math/software/factory-3-1-7/ -O2 -fomit-frame-pointer -o ftmpl_inst.o
+-
+-ADDITIONALLINKOPTIONS = $(CDD_LINKOPTIONS) $(GMP_LINKOPTIONS) $(SOPLEX_LINKOPTIONS) $(SINGULAR_LINKOPTIONS) $(SAGE_LINKOPTIONS) 
+-ADDITIONALINCLUDEOPTIONS = $(CDD_INCLUDEOPTIONS) $(GMP_INCLUDEOPTIONS) $(SOPLEX_INCLUDEOPTIONS) $(SINGULAR_INCLUDEOPTIONS) $(SAGE_INCLUDEOPTIONS)
++ADDITIONALLINKOPTIONS = $(CDD_LINKOPTIONS) $(GMP_LINKOPTIONS) $(SOPLEX_LINKOPTIONS) 
++ADDITIONALINCLUDEOPTIONS = $(CDD_INCLUDEOPTIONS) $(GMP_INCLUDEOPTIONS) $(SOPLEX_INCLUDEOPTIONS)
+ 
+ 
+ MKDIR=mkdir -p
+@@ -110,13 +69,11 @@ MKDIR=mkdir -p
+ PREFIX =
+ SHELL       = /bin/sh
+ #ARCH        = LINUX
+-CC          = $(PREFIX)gcc
+-CLINKER     = $(CC)
+-CXX         = $(PREFIX)g++
+-CCLINKER    = $(CXX)
++CC          ?= $(PREFIX)gcc
++CXX         ?= $(PREFIX)g++
+ #OPTFLAGS    = -O2 -DGMPRATIONAL -DNDEBUG
+ # Note that gcc produces wrong code with -O3
+-OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2	 #-O3 -fno-guess-branch-probability #-DNDEBUG
++OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized
+ #OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O3 -mavx -msse2  -finline-limit=1000 -ffast-math -Wuninitialized # -fno-guess-branch-probability #-DNDEBUG -ftree-vectorizer-verbose=2
+ #OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O1             -fno-guess-branch-probability
+  #-DNDEBUG
+@@ -125,10 +82,10 @@ OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2	 #-O3 -
+ #OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O3 -msse2 -ftree-vectorizer-verbose=2 -ffast-math #-DNDEBUG
+ #OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O3 -mavx -msse2 -ftree-vectorizer-verbose=2 -ffast-math #-DNDEBUG
+ 
+-CFLAGS	  = $(OPTFLAGS) $(GPROFFLAG) $(STACTDUMP_OPTIONS) $(ADDITIONALINCLUDEOPTIONS) -std=c++0x -g $(CDDDEFINE_PREFIX) #-pedantic
+-#CFLAGS	  = $(OPTFLAGS) $(GPROFFLAG) $(STACTDUMP_OPTIONS) $(ADDITIONALINCLUDEOPTIONS) -D_GLIBCXX_DEBUG -std=c++0x -g $(CDDDEFINE_PREFIX) #-pedantic
+-CCFLAGS	  = $(CFLAGS)
+-FFLAGS	  = $(OPTFLAGS)
++CFLAGS	  := $(CFLAGS) $(OPTFLAGS) $(GPROFFLAG) $(ADDITIONALINCLUDEOPTIONS) #-pedantic
++CXXFLAGS  := $(CXXFLAGS) $(OPTFLAGS) $(GPROFFLAG) $(ADDITIONALINCLUDEOPTIONS) #-pedantic
++
++SINGULAR_OBJECTS = src/polynomialgcd.o
+ 
+ CATSOBJECTS =	lp_cdd.o \
+ 		parser.o \
+@@ -394,16 +351,15 @@ EXECS	  = $(MAIN)
+ # (compiling with gcc version 4.7.2 and running gfan _tropicaltraverse on a starting cone for Grassmann3_7)
+ # Either this is a bug in the code or in the compiler. The bug disappears by compiling with -fno-guess-branch-probability
+ src/symmetrictraversal.o: src/symmetrictraversal.cpp
+-	$(CXX) $(CFLAGS) -fno-guess-branch-probability  -c src/symmetrictraversal.cpp -o src/symmetrictraversal.o
++	$(CXX) $(CXXFLAGS) -c src/symmetrictraversal.cpp -o src/symmetrictraversal.o
+ # If compiling with clang, use the line below instead:
+-#	$(CXX) $(CFLAGS) -c src/symmetrictraversal.cpp -o src/symmetrictraversal.o
++#	$(CXX) $(CXXFLAGS) -c src/symmetrictraversal.cpp -o src/symmetrictraversal.o
+ 
+ # Define suffixes to make the program compile on legolas.imf.au.dk :
+ .SUFFIXES: .o .cpp .c
+ 
+ OBJECTS = 	$(addprefix src/,$(SOPLEX_OBJECTS)) \
+ 		$(SINGULAR_OBJECTS) \
+-		$(SAGE_OBJECTS) \
+ 		$(addprefix src/,$(CATSOBJECTS)) \
+ 		$(addprefix src/,$(APPOBJECTS)) \
+ 		src/symmetrictraversal.o
+@@ -420,7 +376,7 @@ default: $(OBJECTS) $(ADDITIONALOBJECTS) $(EXECS)
+ 
+ $(MAIN): $(OBJECTS)
+ #	$(CCLINKER) $(OBJECTS) $(ADDITIONALLINKOPTIONS) $(GPROFFLAG) -lpthread  -o $(MAIN)
+-	$(CCLINKER) $(OBJECTS) $(ADDITIONALLINKOPTIONS) $(GPROFFLAG) -lpthread -rdynamic -o $(MAIN)
++	$(CXX) $(CXXFLAGS) -pthread -o $(MAIN) $(LDFLAGS) $(OBJECTS) -lpthread $(ADDITIONALLINKOPTIONS) $(GPROFFLAG)
+ 
+ release:
+ 	rm -f -r $(RELEASEDIR)/*
+@@ -546,7 +502,7 @@ check:
+ .c.o:
+ 	$(CC) $(CFLAGS) -c $< -o $(patsubst %.c,%.o,$<)
+ .cpp.o:
+-	$(CXX) $(CFLAGS) -c $< -o $(patsubst %.cpp,%.o,$<)
++	$(CXX) $(CXXFLAGS) -c $< -o $(patsubst %.cpp,%.o,$<)
+ 
+ # wget http://ftp.sunet.se/pub/gnu/gmp/gmp-4.2.2.tar.gz
+ # tar -xzvf gmp-4.2.2.tar.gz
diff --git a/sci-mathematics/gfan/files/gfan-0.6.2-testsuite.patch b/sci-mathematics/gfan/files/gfan-0.6.2-testsuite.patch
new file mode 100644
index 000000000000..920646e486e4
--- /dev/null
+++ b/sci-mathematics/gfan/files/gfan-0.6.2-testsuite.patch
@@ -0,0 +1,222 @@
+diff --git a/src/app_test.cpp b/src/app_test.cpp
+index 755bfe6..183c735 100644
+--- a/src/app_test.cpp
++++ b/src/app_test.cpp
+@@ -562,6 +562,9 @@ int testIntegers()
+ 			  failed.push_back(i->folder);
+ 		  }
+ 	  cout<<"\n";
++	  cout<<"Number of succesful tests "<<good<<endl;
++	  cout<<"Number of failed tests "<<bad<<endl;
++
+ 	  if(!failed.empty())
+ 	  {
+ 		  cout<<"Failed tests:\n-------------\n";
+@@ -569,11 +572,9 @@ int testIntegers()
+ 		  {
+ 			  cout<<*i<<" FAILED!\n";
+ 		  }
++		  return 1;
+ 	  }
+ 
+-	  cout<<"Number of succesful tests "<<good<<endl;
+-	  cout<<"Number of failed tests "<<bad<<endl;
+-
+ 	  return 0;
+   }
+ };
+diff --git a/testsuite/0008PolynomialSetUnion/command b/testsuite/0008PolynomialSetUnion/command
+index cbb23d6..d61cb71 100644
+--- a/testsuite/0008PolynomialSetUnion/command
++++ b/testsuite/0008PolynomialSetUnion/command
+@@ -1 +1 @@
+-%s _bases | %s _polynomialsetunion |sort
++%s _bases | %s _polynomialsetunion |LC_ALL=C sort|tail -n +2 | sed -e '$ d'
+diff --git a/testsuite/0008PolynomialSetUnion/output b/testsuite/0008PolynomialSetUnion/output
+index 38dfb6f..12a65c7 100644
+--- a/testsuite/0008PolynomialSetUnion/output
++++ b/testsuite/0008PolynomialSetUnion/output
+@@ -1,62 +1,60 @@
+-{
++a*b-c^6,
++a*b^2-c^3,
++a*b^4-b,
++a*c-b^6,
++a*c^2-b,
++a*c^6-c,
++a-b^11,
++a-b^2*c,
++a-c^9,
+ a^11-c,
+ a^15-a,
++a^2*b-c,
+ a^2*b^3-a,
++a^2*c-b^3,
+ a^2-b^8,
+-a^2*b-c,
+ a^2-c^4,
+-a^2*c-b^3,
+-a^3-b^5,
+-a^3-b*c^2,
+ a^3*c^2-c}
+-a^4-b^2,
++a^3-b*c^2,
++a^3-b^5,
+ a^4*c-a,
++a^4-b^2,
+ a^5-c^3,
+ a^6*b-a,
+ a^6-b*c,
+ a^8-c^2,
+ a^9-b,
+-a-b^11,
+-a-b^2*c,
+-a*b^2-c^3,
+-a*b^4-b,
+-a*b-c^6,
+-a*c^2-b,
+-a*c^6-c,
+-a-c^9,
+-a*c-b^6,
++b*c-a^6,
++b*c^2-a^3,
++b*c^4-c,
++b-a*c^2,
++b-a^9,
++b-c^11,
+ b^11-a,
+ b^15-b,
+-b^2-a^4,
++b^2*c-a,
+ b^2*c^3-b,
++b^2-a^4,
+ b^2-c^8,
+-b^2*c-a,
+ b^3-a^2*c,
+ b^3-c^5,
+ b^4-c^2,
+ b^5-a^3,
+-b^6-a*c,
+ b^6*c-b,
++b^6-a*c,
+ b^8-a^2,
+ b^9-c,
+-b-a^9,
+-b-a*c^2,
+-b-c^11,
+-b*c^2-a^3,
+-b*c^4-c,
+-b*c-a^6,
++c-a^11,
++c-a^2*b,
++c-b^9,
+ c^11-b,
+ c^15-c,
+ c^2-a^8,
+ c^2-b^4,
+-c^3-a^5,
+ c^3-a*b^2,
++c^3-a^5,
+ c^4-a^2,
+ c^5-b^3,
+ c^6-a*b,
+ c^8-b^2,
+ c^9-a,
+-c-a^11,
+-c-a^2*b,
+-c-b^9,
+-Q[a,b,c]
+diff --git a/testsuite/0008PolynomialSetUnion/outputNew b/testsuite/0008PolynomialSetUnion/outputNew
+index 38dfb6f..12a65c7 100644
+--- a/testsuite/0008PolynomialSetUnion/outputNew
++++ b/testsuite/0008PolynomialSetUnion/outputNew
+@@ -1,62 +1,60 @@
+-{
++a*b-c^6,
++a*b^2-c^3,
++a*b^4-b,
++a*c-b^6,
++a*c^2-b,
++a*c^6-c,
++a-b^11,
++a-b^2*c,
++a-c^9,
+ a^11-c,
+ a^15-a,
++a^2*b-c,
+ a^2*b^3-a,
++a^2*c-b^3,
+ a^2-b^8,
+-a^2*b-c,
+ a^2-c^4,
+-a^2*c-b^3,
+-a^3-b^5,
+-a^3-b*c^2,
+ a^3*c^2-c}
+-a^4-b^2,
++a^3-b*c^2,
++a^3-b^5,
+ a^4*c-a,
++a^4-b^2,
+ a^5-c^3,
+ a^6*b-a,
+ a^6-b*c,
+ a^8-c^2,
+ a^9-b,
+-a-b^11,
+-a-b^2*c,
+-a*b^2-c^3,
+-a*b^4-b,
+-a*b-c^6,
+-a*c^2-b,
+-a*c^6-c,
+-a-c^9,
+-a*c-b^6,
++b*c-a^6,
++b*c^2-a^3,
++b*c^4-c,
++b-a*c^2,
++b-a^9,
++b-c^11,
+ b^11-a,
+ b^15-b,
+-b^2-a^4,
++b^2*c-a,
+ b^2*c^3-b,
++b^2-a^4,
+ b^2-c^8,
+-b^2*c-a,
+ b^3-a^2*c,
+ b^3-c^5,
+ b^4-c^2,
+ b^5-a^3,
+-b^6-a*c,
+ b^6*c-b,
++b^6-a*c,
+ b^8-a^2,
+ b^9-c,
+-b-a^9,
+-b-a*c^2,
+-b-c^11,
+-b*c^2-a^3,
+-b*c^4-c,
+-b*c-a^6,
++c-a^11,
++c-a^2*b,
++c-b^9,
+ c^11-b,
+ c^15-c,
+ c^2-a^8,
+ c^2-b^4,
+-c^3-a^5,
+ c^3-a*b^2,
++c^3-a^5,
+ c^4-a^2,
+ c^5-b^3,
+ c^6-a*b,
+ c^8-b^2,
+ c^9-a,
+-c-a^11,
+-c-a^2*b,
+-c-b^9,
+-Q[a,b,c]
diff --git a/sci-mathematics/gfan/files/gfan-0.6.2-xcode9.3_compat.patch b/sci-mathematics/gfan/files/gfan-0.6.2-xcode9.3_compat.patch
new file mode 100644
index 000000000000..83f4b66f8239
--- /dev/null
+++ b/sci-mathematics/gfan/files/gfan-0.6.2-xcode9.3_compat.patch
@@ -0,0 +1,13 @@
+diff --git a/src/app_main.cpp b/src/app_main.cpp
+index a33c042..e7ade81 100644
+--- a/src/app_main.cpp
++++ b/src/app_main.cpp
+@@ -205,7 +205,7 @@ public:
+     }
+ 
+     ep->close();
+-    delete ep;//<--- In next release, make the class virtual
++//    delete ep;//<--- In next release, make the class virtual # this is miscompiled clang@xcode-6.3
+ 
+     printf("\n");
+