math/suitesparse: Update 4.0.2 -> 5.2.0

Port changes:
* Change to DISTVERSION
* Update MASTER_SITES
* Change to LICENSE_COMB=dual
* Add LIB_DEPENDS
* Unbundle metis, made it a dependency
* Update do-build and do-install
* Update WWW

Bump 11 ports.
games/naev is marked broken because it depends on the no longer installed library.

PR:		210579
Submitted by:	yuri
Submitted by:	pfg
Approved by:	maintainer timeout (maho@FreeBSD.org, 21 months)
Approved by:	maintainer timeout (fortran@FreeBSD.org, 45 days)

16 files changed, 81 insertions, 89 deletions

diff --git a/games/naev/Makefile b/games/naev/Makefile
index c794b4c1656c..098430c62b27 100644
--- a/games/naev/Makefile
+++ b/games/naev/Makefile
@@ -13,6 +13,8 @@ COMMENT=	2D action/RPG space game
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
+BROKEN=		Depends on the library that isn't installed by SuiteSparse any more: https://github.com/naev/naev/issues/774
+
 LIB_DEPENDS=	libpng.so:graphics/png \
 		libfreetype.so:print/freetype2 \
 		libvorbisfile.so:audio/libvorbis \
diff --git a/math/arpack++/Makefile b/math/arpack++/Makefile
index 85017c825d14..49645508f503 100644
--- a/math/arpack++/Makefile
+++ b/math/arpack++/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	arpack++
 PORTVERSION=	1.2
-PORTREVISION=	8
+PORTREVISION=	9
 CATEGORIES=	math
 MASTER_SITES=	http://www.ime.unicamp.br/%7echico/arpack++/
 DISTNAME=	${PORTNAME}
diff --git a/math/ceres-solver/Makefile b/math/ceres-solver/Makefile
index 55056cfd9a35..436a3cdf9522 100644
--- a/math/ceres-solver/Makefile
+++ b/math/ceres-solver/Makefile
@@ -2,6 +2,7 @@
 
 PORTNAME=	ceres-solver
 DISTVERSION=	1.14.0
+PORTREVISION=	1
 CATEGORIES=	math
 
 MAINTAINER=	jbeich@FreeBSD.org
diff --git a/math/dynare/Makefile b/math/dynare/Makefile
index a8bc739e4263..0ecb25f8a2f3 100644
--- a/math/dynare/Makefile
+++ b/math/dynare/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=	dynare
 DISTVERSION=	4.5.4
-PORTREVISION=	3
+PORTREVISION=	4
 CATEGORIES=	math
 MASTER_SITES=	http://www.dynare.org/release/source/
 
diff --git a/math/freemat/Makefile b/math/freemat/Makefile
index ae3f05c77d56..1649d425f243 100644
--- a/math/freemat/Makefile
+++ b/math/freemat/Makefile
@@ -4,7 +4,7 @@
 PORTNAME=	FreeMat
 PORTVERSION=	4.2
 DISTVERSIONSUFFIX=	-Source
-PORTREVISION=	17
+PORTREVISION=	18
 CATEGORIES=	math science
 MASTER_SITES=	SF/freemat/FreeMat4
 
diff --git a/math/g2o/Makefile b/math/g2o/Makefile
index 4e1b8097eefa..5c77ffd89c79 100644
--- a/math/g2o/Makefile
+++ b/math/g2o/Makefile
@@ -3,6 +3,7 @@
 PORTNAME=	g2o
 DISTVERSION=	20170730_git-87
 DISTVERSIONSUFFIX=	-gbbe3c2b
+PORTREVISION=	1
 CATEGORIES=	math
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/math/octave/Makefile b/math/octave/Makefile
index b57420adabb7..edc0d22f6f4d 100644
--- a/math/octave/Makefile
+++ b/math/octave/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	octave
 PORTVERSION=	${OCTAVE_VERSION}
+PORTREVISION=	1
 CATEGORIES=	math java
 MASTER_SITES=	GNU
 
diff --git a/math/py-cvxopt/Makefile b/math/py-cvxopt/Makefile
index 15025fa9655c..0fe626b81740 100644
--- a/math/py-cvxopt/Makefile
+++ b/math/py-cvxopt/Makefile
@@ -2,6 +2,7 @@
 
 PORTNAME=	cvxopt
 DISTVERSION=	1.2.0
+PORTREVISION=	1
 CATEGORIES=	math python
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
diff --git a/math/py-numpy/Makefile b/math/py-numpy/Makefile
index df666c0bafe8..48de3a221c4f 100644
--- a/math/py-numpy/Makefile
+++ b/math/py-numpy/Makefile
@@ -4,7 +4,7 @@
 PORTNAME=	numpy
 PORTVERSION=	1.13.3
 DISTVERSIONPREFIX=	v
-PORTREVISION=	2
+PORTREVISION=	3
 PORTEPOCH=	1
 CATEGORIES=	math python
 MASTER_SITES=	http://docs.scipy.org/doc/${PORTNAME}-${PORTVERSION:R}.0/:doc
diff --git a/math/scilab/Makefile b/math/scilab/Makefile
index a770e1c95c39..46126c8302a2 100644
--- a/math/scilab/Makefile
+++ b/math/scilab/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	scilab
 PORTVERSION=	5.5.2
-PORTREVISION=	10
+PORTREVISION=	11
 CATEGORIES=	math cad java
 MASTER_SITES=	http://www.scilab.org/download/${PORTVERSION}/
 DISTFILES=	${DISTNAME}-src${EXTRACT_SUFX}
diff --git a/math/suitesparse/Makefile b/math/suitesparse/Makefile
index 6bf41274436c..991794fde84d 100644
--- a/math/suitesparse/Makefile
+++ b/math/suitesparse/Makefile
@@ -2,19 +2,27 @@
 # $FreeBSD$
 
 PORTNAME=	suitesparse
-PORTVERSION=	4.0.2
-PORTREVISION=	8
+DISTVERSION=	5.2.0
 CATEGORIES=	math
-MASTER_SITES=	http://www.cise.ufl.edu/research/sparse/SuiteSparse/
+MASTER_SITES=	http://faculty.cse.tamu.edu/davis/SuiteSparse/
 DISTNAME=	SuiteSparse-${PORTVERSION}
 
 MAINTAINER=	fortran@FreeBSD.org
 COMMENT=	SuiteSparse is a set of packages for sparse matrices calculation
 
 LICENSE=	GPLv2 LGPL21
-LICENSE_COMB=	multi
+LICENSE_COMB=	dual
 
-USES=		fortran gmake
+LIB_DEPENDS=	libmetis.so:math/metis \
+		liblapack.so:math/lapack
+
+USES=		compiler:openmp fortran gmake
+USE_LDCONFIG=	yes
+
+PLIST_SUB=	SHL3=${DISTVERSION} SHL1=${DISTVERSION:R:R}
+
+WRKSRC=		${WRKDIR}/SuiteSparse
+WRKSRC_SHARED=	${WRKSRC}_shared
 
 OPTIONS_RADIO=	BLAS
 OPTIONS_RADIO_BLAS=	OPENBLAS NETLIB ATLAS
@@ -24,16 +32,6 @@ OPENBLAS_USES=	blaslapack:openblas
 NETLIB_USES=	blaslapack:netlib
 ATLAS_USES=	blaslapack:atlas
 
-.if defined (WITH_METIS)
-LIB_DEPENDS=	libmetis.so:math/metis4
-
-RESTRICTED=	GPL and METIS licenses are contradictory
-.endif
-
-CONFLICTS=	umfpack-*
-
-LDFLAGS+=	-L${LOCALBASE}/lib
-
 .include <bsd.port.options.mk>
 
 .if ${ARCH} == "sparc64"
@@ -42,22 +40,18 @@ PICFLAG?=	-fPIC
 PICFLAG?=	-fpic
 .endif
 
-USE_LDCONFIG=	yes
-WRKSRC=${WRKDIR}/SuiteSparse
-WRKSRC_SHARED=${WRKSRC}_shared
-SVERSION=1
-
-.if defined (WITH_METIS)
-METIS=${LOCALBASE}/lib/libmetis.a
-METIS_PATH=${LOCALBASE}/include/metis
+METIS=		${LOCALBASE}/lib/libmetis.a
+METIS_PATH=	${LOCALBASE}/include/metis
 CHOLMOD_CONFIG=
-.else
-CHOLMOD_CONFIG=		-DNPARTITION
-.endif
+CFLAGS+=	-I${LOCALBASE}/include
+CXXFLAGS+=	-I${LOCALBASE}/include
+MAKE_ARGS+=	MY_METIS_LIB="-L${LOCALBASE}/lib -lmetis $(LDFLAGS)"
 
 post-patch:
+	@${RM} -r ${WRKSRC}/metis-5.1.0
 	@${FIND} -X ${WRKSRC} -type f -name 'Makefile' -or -name '*.mk' | ${XARGS} \
-	${REINPLACE_CMD} -e '\|^AR =|s|ar|${AR}|' \
+	${REINPLACE_CMD} -i '' \
+			-e '\|^AR =|s|ar|${AR}|' \
 			-e '\|^BLAS =|s|=.*|= ${LDFLAGS} ${BLASLIB}|' \
 			-e '\|^CC =|d' \
 			-e '\|^CFLAGS =|{s|-O[1-9]\{0,1\}||g;s|=|= ${CFLAGS} $${PICFLAG} |;}' \
@@ -78,30 +72,21 @@ post-patch:
 	${REINPLACE_CMD} -e 's|$$(CFLAGS)|$$(CFLAGS) $$(PICFLAG)|g'
 
 do-build:
-	@cd ${WRKSRC} ; ${SETENV} ${MAKE_ENV} PICFLAG= \
-		${MAKE_CMD} ${_MAKE_JOBS} ${MAKE_ARGS}
-	@cd ${WRKSRC_SHARED} ; ${SETENV} ${MAKE_ENV} PICFLAG=${PICFLAG} \
-		${MAKE_CMD} ${_MAKE_JOBS} ${MAKE_ARGS}
-
-post-build:
-	@for i in `find ${WRKSRC_SHARED} -type f -name '*.a'` ; do \
-		j=$${i##*/} ; ${LD} -Bshareable -o $${i%.a}.so.${SVERSION} -x \
-		-soname $${j%.a}.so.${SVERSION} --whole-archive $${i} ; \
-	done
+	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} PICFLAG= \
+		LD_LIBRARY_PATH=${WRKDIR}/SuiteSparse/lib ${MAKE_CMD} ${_MAKE_JOBS} ${MAKE_ARGS}
+	@cd ${WRKSRC_SHARED} && ${SETENV} ${MAKE_ENV} PICFLAG=${PICFLAG} \
+		LD_LIBRARY_PATH=${WRKDIR}/SuiteSparse/lib ${MAKE_CMD} ${_MAKE_JOBS} ${MAKE_ARGS}
 
 do-install:
 	@${MKDIR} ${STAGEDIR}${PREFIX}/include/suitesparse
-	@${LN} -sf ${PREFIX}/include/suitesparse ${STAGEDIR}${PREFIX}/include/ufsparse
-.for d in AMD BTF CAMD CCOLAMD CHOLMOD COLAMD CXSparse KLU SPQR UMFPACK
-	@${INSTALL_DATA} ${WRKSRC}/${d}/Include/*.h ${STAGEDIR}${PREFIX}/include/suitesparse
+	@cd ${STAGEDIR}${PREFIX}/include && ${LN} -s suitesparse ufsparse
+.for d in AMD BTF CAMD CCOLAMD CHOLMOD COLAMD CSparse CXSparse KLU SPQR UMFPACK # CSparse: shared lib bot built
+	${INSTALL_DATA} ${WRKSRC}/${d}/Include/*.h ${STAGEDIR}${PREFIX}/include/suitesparse
 .endfor
-	@${INSTALL_DATA} ${WRKSRC}/SuiteSparse_config/SuiteSparse_config.h ${STAGEDIR}${PREFIX}/include/suitesparse
-	@${INSTALL_DATA} ${WRKSRC}/UMFPACK/Source/umf_config.h ${STAGEDIR}${PREFIX}/include/suitesparse
-	@${INSTALL_DATA} ${WRKSRC}/SPQR/Include/*.hpp ${STAGEDIR}${PREFIX}/include/suitesparse
-	@for i in `find ${WRKSRC_SHARED} -type f -name '*.a'` ; do \
-		${INSTALL_DATA} ${WRKSRC}/$${i##${WRKSRC_SHARED}/} \
-		$${i%.a}.so.${SVERSION} ${STAGEDIR}${PREFIX}/lib ; \
-		j=$${i##*/} ;  ${LN} -sf $${j%.a}.so.${SVERSION} ${STAGEDIR}${PREFIX}/lib/$${j%.a}.so ; \
-	done
+	${INSTALL_DATA} ${WRKSRC}/SuiteSparse_config/SuiteSparse_config.h ${STAGEDIR}${PREFIX}/include/suitesparse
+	${INSTALL_DATA} ${WRKSRC}/UMFPACK/Source/umf_config.h ${STAGEDIR}${PREFIX}/include/suitesparse
+	${INSTALL_DATA} ${WRKSRC}/SPQR/Include/*.hpp ${STAGEDIR}${PREFIX}/include/suitesparse
+	${INSTALL_DATA} ${WRKSRC_SHARED}/lib/*.so* ${STAGEDIR}${PREFIX}/lib/
+	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so*
 
 .include <bsd.port.mk>
diff --git a/math/suitesparse/distinfo b/math/suitesparse/distinfo
index 45d01b22cb39..5488239bf29e 100644
--- a/math/suitesparse/distinfo
+++ b/math/suitesparse/distinfo
@@ -1,2 +1,3 @@
-SHA256 (SuiteSparse-4.0.2.tar.gz) = 93b5928987fe010808b3fdff3e7edef42fb2d8cfd65b09dd6d4c41756acb0050
-SIZE (SuiteSparse-4.0.2.tar.gz) = 22421100
+TIMESTAMP = 1524200823
+SHA256 (SuiteSparse-5.2.0.tar.gz) = 3c46c035ea8217649958a0f73360e825b0c9dcca4e32a9349d2c7678c0d48813
+SIZE (SuiteSparse-5.2.0.tar.gz) = 46053054
diff --git a/math/suitesparse/pkg-descr b/math/suitesparse/pkg-descr
index 983ac3818b9e..3fb0b29262fb 100644
--- a/math/suitesparse/pkg-descr
+++ b/math/suitesparse/pkg-descr
@@ -12,4 +12,4 @@ It contains:
     * CSparse: a concise sparse matrix package
     * CXSparse: and extended version of CSparse
 
-WWW: http://www.cise.ufl.edu/research/sparse/SuiteSparse/
+WWW: http://faculty.cse.tamu.edu/davis/suitesparse.html
diff --git a/math/suitesparse/pkg-plist b/math/suitesparse/pkg-plist
index b725b15c93ee..038795f7ef46 100644
--- a/math/suitesparse/pkg-plist
+++ b/math/suitesparse/pkg-plist
@@ -1,7 +1,7 @@
-include/suitesparse/SuiteSparse_config.h
 include/suitesparse/SuiteSparseQR.hpp
 include/suitesparse/SuiteSparseQR_C.h
 include/suitesparse/SuiteSparseQR_definitions.h
+include/suitesparse/SuiteSparse_config.h
 include/suitesparse/amd.h
 include/suitesparse/amd_internal.h
 include/suitesparse/btf.h
@@ -11,11 +11,15 @@ include/suitesparse/camd_internal.h
 include/suitesparse/ccolamd.h
 include/suitesparse/cholmod.h
 include/suitesparse/cholmod_blas.h
+include/suitesparse/cholmod_camd.h
 include/suitesparse/cholmod_check.h
 include/suitesparse/cholmod_cholesky.h
 include/suitesparse/cholmod_complexity.h
 include/suitesparse/cholmod_config.h
 include/suitesparse/cholmod_core.h
+include/suitesparse/cholmod_function.h
+include/suitesparse/cholmod_gpu.h
+include/suitesparse/cholmod_gpu_kernels.h
 include/suitesparse/cholmod_internal.h
 include/suitesparse/cholmod_io64.h
 include/suitesparse/cholmod_matrixops.h
@@ -29,6 +33,8 @@ include/suitesparse/klu.h
 include/suitesparse/klu_internal.h
 include/suitesparse/klu_version.h
 include/suitesparse/spqr.hpp
+include/suitesparse/spqrgpu.hpp
+include/suitesparse/umf_config.h
 include/suitesparse/umfpack.h
 include/suitesparse/umfpack_col_to_triplet.h
 include/suitesparse/umfpack_defaults.h
@@ -62,50 +68,43 @@ include/suitesparse/umfpack_timer.h
 include/suitesparse/umfpack_transpose.h
 include/suitesparse/umfpack_triplet_to_col.h
 include/suitesparse/umfpack_wsolve.h
-include/suitesparse/umf_config.h
 include/ufsparse
-lib/libamd.a
 lib/libamd.so
-lib/libamd.so.1
-lib/libbtf.a
+lib/libamd.so.2
+lib/libamd.so.2.4.6
 lib/libbtf.so
 lib/libbtf.so.1
-lib/libcamd.a
+lib/libbtf.so.1.2.6
 lib/libcamd.so
-lib/libcamd.so.1
-lib/libccolamd.a
+lib/libcamd.so.2
+lib/libcamd.so.2.4.6
 lib/libccolamd.so
-lib/libccolamd.so.1
-lib/libcerbla.a
-lib/libcerbla.so
-lib/libcerbla.so.1
-lib/libcholmod.a
+lib/libccolamd.so.2
+lib/libccolamd.so.2.9.6
 lib/libcholmod.so
-lib/libcholmod.so.1
-lib/libcolamd.a
+lib/libcholmod.so.3
+lib/libcholmod.so.3.0.12
 lib/libcolamd.so
-lib/libcolamd.so.1
-lib/libcsparse.a
-lib/libcsparse.so
-lib/libcsparse.so.1
-lib/libcxsparse.a
+lib/libcolamd.so.2
+lib/libcolamd.so.2.9.6
 lib/libcxsparse.so
-lib/libcxsparse.so.1
-lib/libklu.a
+lib/libcxsparse.so.3
+lib/libcxsparse.so.3.2.0
 lib/libklu.so
 lib/libklu.so.1
-lib/libldl.a
+lib/libklu.so.1.3.8
 lib/libldl.so
-lib/libldl.so.1
-lib/librbio.a
+lib/libldl.so.2
+lib/libldl.so.2.2.6
 lib/librbio.so
-lib/librbio.so.1
-lib/libspqr.a
+lib/librbio.so.2
+lib/librbio.so.2.2.6
 lib/libspqr.so
-lib/libspqr.so.1
-lib/libsuitesparseconfig.a
+lib/libspqr.so.2
+lib/libspqr.so.2.0.8
 lib/libsuitesparseconfig.so
-lib/libsuitesparseconfig.so.1
-lib/libumfpack.a
+lib/libsuitesparseconfig.so.%%SHL1%%
+lib/libsuitesparseconfig.so.%%SHL3%%
 lib/libumfpack.so
-lib/libumfpack.so.1
+lib/libumfpack.so.5
+lib/libumfpack.so.5.7.6
diff --git a/science/mbdyn/Makefile b/science/mbdyn/Makefile
index c721b8c4543f..886003333d5a 100644
--- a/science/mbdyn/Makefile
+++ b/science/mbdyn/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	mbdyn
 PORTVERSION=	1.7.2
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	science
 MASTER_SITES=	https://www.mbdyn.org/userfiles/downloads/
 
diff --git a/science/py-scikit-sparse/Makefile b/science/py-scikit-sparse/Makefile
index f0c07abd1b9f..e86f4e1b94d5 100644
--- a/science/py-scikit-sparse/Makefile
+++ b/science/py-scikit-sparse/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	scikit-sparse
 DISTVERSION=	0.4.3
+PORTREVISION=	1
 CATEGORIES=	science python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}