academic/suitesparse: Updated for version 4.5.4 + new maintainer

Signed-off-by: Christoph Willing <chris.willing@iinet.net.au>

4 files changed, 59 insertions, 387 deletions

diff --git a/academic/suitesparse/README b/academic/suitesparse/README
index 376e0e0c99ff..d4f385acca77 100644
--- a/academic/suitesparse/README
+++ b/academic/suitesparse/README
@@ -20,8 +20,14 @@ Suitesparse is an optional dependency for the octave package.
 
 NOTES:
 
-* CHOLMOD can also be compiled to use the METIS library, but it is not
-used here because its licensing terms exclude it from Octave.
+* CHOLMOD is now compiled to use the METIS library. It was not
+used previously because the licensing terms of earlier METIS
+versions excluded it from Octave in some circumstances. Recent
+versions of METIS now use the Apache License Version 2.0 and
+should cause no problems. However if it is still desired to
+build CHOLMOD without METIS, set the USEMETIS environment
+variable to "no" when running the SlackBuild e.g.
+    USEMETIS=no sh suitesparse.SlackBuild
 
 * CXSparse is a superset of CSparse, and the two share common header
 names, so it does not make sense to build both. CXSparse is built
diff --git a/academic/suitesparse/UFconfig.mk b/academic/suitesparse/UFconfig.mk
deleted file mode 100644
index fba2a1c8758e..000000000000
--- a/academic/suitesparse/UFconfig.mk
+++ /dev/null
@@ -1,354 +0,0 @@
-#===============================================================================
-# UFconfig.mk:  common configuration file for the SuiteSparse
-#===============================================================================
-
-# This file contains all configuration settings for all packages authored or
-# co-authored by Tim Davis at the University of Florida:
-#
-# Package Version       Description
-# ------- -------       -----------
-# AMD	  1.2 or later  approximate minimum degree ordering
-# COLAMD  2.4 or later  column approximate minimum degree ordering
-# CCOLAMD 1.0 or later  constrained column approximate minimum degree ordering
-# CAMD    any		constrained approximate minimum degree ordering
-# UMFPACK 4.5 or later	sparse LU factorization, with the BLAS
-# CHOLMOD any		sparse Cholesky factorization, update/downdate
-# KLU	  0.8 or later  sparse LU factorization, BLAS-free
-# BTF	  0.8 or later  permutation to block triangular form
-# LDL	  1.2 or later	concise sparse LDL'
-# LPDASA  any		linear program solve (dual active set algorithm)
-# CXSparse any		extended version of CSparse (int/long, real/complex)
-# SuiteSparseQR	any	sparse QR factorization
-#
-# The UFconfig directory and the above packages should all appear in a single
-# directory, in order for the Makefile's within each package to find this file.
-#
-# To enable an option of the form "# OPTION = ...", edit this file and
-# delete the "#" in the first column of the option you wish to use.
-
-#------------------------------------------------------------------------------
-# Generic configuration
-#------------------------------------------------------------------------------
-
-# C compiler and compiler flags:  These will normally not give you optimal
-# performance.  You should select the optimization parameters that are best
-# for your system.  On Linux, use "CFLAGS = -O3 -fexceptions" for example.
-CC = cc
-# CFLAGS = -O   (for example; see below for details)
-
-# C++ compiler (also uses CFLAGS)
-CPLUSPLUS = g++
-
-# ranlib, and ar, for generating libraries
-RANLIB = ranlib
-AR = ar cr
-
-# delete and rename a file
-RM = rm -f
-MV = mv -f
-
-# Fortran compiler (not normally required)
-F77 = gfortran
-F77FLAGS = -O
-F77LIB =
-
-# C and Fortran libraries
-LIB = -lm
-
-# For compiling MATLAB mexFunctions (MATLAB 7.5 or later)
-MEX = mex -O -largeArrayDims -lmwlapack -lmwblas
-
-# For compiling MATLAB mexFunctions (MATLAB 7.3 and 7.4)
-# MEX = mex -O -largeArrayDims -lmwlapack
-
-# For MATLAB 7.2 or earlier, you must use one of these options:
-# MEX = mex -O -lmwlapack
-# MEX = mex -O
-
-# Which version of MAKE you are using (default is "make")
-# MAKE = make
-# MAKE = gmake
-
-#------------------------------------------------------------------------------
-# BLAS and LAPACK configuration:
-#------------------------------------------------------------------------------
-
-# UMFPACK and CHOLMOD both require the BLAS.  CHOLMOD also requires LAPACK.
-# See Kazushige Goto's BLAS at http://www.cs.utexas.edu/users/flame/goto/ or
-# http://www.tacc.utexas.edu/~kgoto/ for the best BLAS to use with CHOLMOD.
-# LAPACK is at http://www.netlib.org/lapack/ .  You can use the standard
-# Fortran LAPACK along with Goto's BLAS to obtain very good performance.
-# CHOLMOD gets a peak numeric factorization rate of 3.6 Gflops on a 3.2 GHz
-# Pentium 4 (512K cache, 4GB main memory) with the Goto BLAS, and 6 Gflops
-# on a 2.5Ghz dual-core AMD Opteron.
-
-# These settings will probably not work, since there is no fixed convention for
-# naming the BLAS and LAPACK library (*.a or *.so) files.
-
-# Using the Goto BLAS:
-# BLAS = -lgoto -lgfortran -lgfortranbegin -lg2c
-
-# This is probably slow ... it might connect to the Standard Reference BLAS:
-BLAS = -lblas -lgfortran -lgfortranbegin 
-LAPACK = -llapack
-
-# Using non-optimized versions:
-# BLAS = -lblas_plain -lgfortran -lgfortranbegin -lg2c
-# LAPACK = -llapack_plain
-
-# The BLAS might not contain xerbla, an error-handling routine for LAPACK and
-# the BLAS.  Also, the standard xerbla requires the Fortran I/O library, and
-# stops the application program if an error occurs.  A C version of xerbla
-# distributed with this software (UFconfig/xerbla/libcerbla.a) includes a
-# Fortran-callable xerbla routine that prints nothing and does not stop the
-# application program.  This is optional.
-# XERBLA = ../../UFconfig/xerbla/libcerbla.a 
-
-# If you wish to use the XERBLA in LAPACK and/or the BLAS instead,
-# use this option:
-XERBLA = 
-
-# If you wish to use the Fortran UFconfig/xerbla/xerbla.f instead, use this:
-# XERBLA = ../../UFconfig/xerbla/libxerbla.a 
-
-#------------------------------------------------------------------------------
-# METIS, optionally used by CHOLMOD
-#------------------------------------------------------------------------------
-
-# If you do not have METIS, or do not wish to use it in CHOLMOD, you must
-# compile CHOLMOD with the -DNPARTITION flag.  You must also use the
-# "METIS =" option, below.
-
-# The path is relative to where it is used, in CHOLMOD/Lib, CHOLMOD/MATLAB, etc.
-# You may wish to use an absolute path.  METIS is optional.  Compile
-# CHOLMOD with -DNPARTITION if you do not wish to use METIS.
-#METIS_PATH = ../../metis-4.0
-#METIS = ../../metis-4.0/libmetis.a
-
-# If you use CHOLMOD_CONFIG = -DNPARTITION then you must use the following
-# options:
-METIS_PATH =
-METIS =
-
-#------------------------------------------------------------------------------
-# UMFPACK configuration:
-#------------------------------------------------------------------------------
-
-# Configuration flags for UMFPACK.  See UMFPACK/Source/umf_config.h for details.
-#
-# -DNBLAS	do not use the BLAS.  UMFPACK will be very slow.
-# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
-#  		LAPACK and the BLAS (defaults to 'int')
-# -DNSUNPERF	do not use the Sun Perf. Library (default is use it on Solaris)
-# -DNPOSIX	do not use POSIX routines sysconf and times.
-# -DGETRUSAGE	use getrusage
-# -DNO_TIMER	do not use any timing routines
-# -DNRECIPROCAL	do not multiply by the reciprocal
-# -DNO_DIVIDE_BY_ZERO	do not divide by zero
-
-UMFPACK_CONFIG = 
-
-#------------------------------------------------------------------------------
-# CHOLMOD configuration
-#------------------------------------------------------------------------------
-
-# CHOLMOD Library Modules, which appear in libcholmod.a:
-# Core		requires: none
-# Check		requires: Core
-# Cholesky	requires: Core, AMD, COLAMD.  optional: Partition, Supernodal
-# MatrixOps	requires: Core
-# Modify	requires: Core
-# Partition	requires: Core, CCOLAMD, METIS.  optional: Cholesky
-# Supernodal	requires: Core, BLAS, LAPACK
-#
-# CHOLMOD test/demo Modules (all are GNU GPL, do not appear in libcholmod.a):
-# Tcov		requires: Core, Check, Cholesky, MatrixOps, Modify, Supernodal
-#		optional: Partition
-# Valgrind	same as Tcov
-# Demo		requires: Core, Check, Cholesky, MatrixOps, Supernodal
-#		optional: Partition
-#
-# Configuration flags:
-# -DNCHECK	    do not include the Check module.	   License GNU LGPL
-# -DNCHOLESKY	    do not include the Cholesky module.	   License GNU LGPL
-# -DNPARTITION	    do not include the Partition module.   License GNU LGPL
-#		    also do not include METIS.
-# -DNGPL	    do not include any GNU GPL Modules in the CHOLMOD library:
-# -DNMATRIXOPS	    do not include the MatrixOps module.   License GNU GPL
-# -DNMODIFY	    do not include the Modify module.      License GNU GPL
-# -DNSUPERNODAL     do not include the Supernodal module.  License GNU GPL
-#
-# -DNPRINT	    do not print anything.
-# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
-#  		    	LAPACK and the BLAS (defaults to 'int')
-# -DNSUNPERF	    for Solaris only.  If defined, do not use the Sun
-#			Performance Library
-
-CHOLMOD_CONFIG = -DNPARTITION
-
-#------------------------------------------------------------------------------
-# SuiteSparseQR configuration:
-#------------------------------------------------------------------------------
-
-# The SuiteSparseQR library can be compiled with the following options:
-#
-# -DNPARTITION      do not include the CHOLMOD partition module
-# -DNEXPERT         do not include the functions in SuiteSparseQR_expert.cpp
-# -DTIMING          enable timing and flop counts
-# -DHAVE_TBB        enable the use of Intel's Threading Building Blocks (TBB)
-
-# default, without timing, without TBB:
-SPQR_CONFIG = -DNPARTITION
-# with timing and TBB:
-# SPQR_CONFIG = -DTIMING -DHAVE_TBB
-# with timing
-# SPQR_CONFIG = -DTIMING
-
-# with TBB, you must select this:
-# TBB = -ltbb
-# without TBB:
-TBB =
-
-# with timing, you must include the timing library:
-# RTLIB = -lrt
-# without timing
-RTLIB =
-
-#------------------------------------------------------------------------------
-# Linux
-#------------------------------------------------------------------------------
-
-# Using default compilers:
-# CC = gcc
-CFLAGS = -O3 -fexceptions
-
-# alternatives:
-# CFLAGS = -g -fexceptions \
-   	-Wall -W -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
-    	-Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi
-# CFLAGS = -O3 -fexceptions \
-   	-Wall -W -Werror -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
-    	-Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi
-# CFLAGS = -O3 -fexceptions -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
-# CFLAGS = -O3
-# CFLAGS = -O3 -g -fexceptions
-# CFLAGS = -g -fexceptions \
-   	-Wall -W -Wshadow \
-    	-Wredundant-decls -Wdisabled-optimization -ansi
-
-# consider:
-# -fforce-addr -fmove-all-movables -freduce-all-givs -ftsp-ordering
-# -frename-registers -ffast-math -funroll-loops
-
-# Using the Goto BLAS:
-# BLAS = -lgoto -lfrtbegin -lg2c $(XERBLA) -lpthread
-
-# Using Intel's icc and ifort compilers:
-#   (does not work for mexFunctions unless you add a mexopts.sh file)
-# F77 = ifort
-# CC = icc
-# CFLAGS = -O3 -xN -vec_report=0
-# CFLAGS = -g
-# old (broken): CFLAGS = -ansi -O3 -ip -tpp7 -xW -vec_report0
-
-# 64bit:
-# F77FLAGS = -O -m64
-# CFLAGS = -O3 -fexceptions -m64
-# BLAS = -lgoto64 -lfrtbegin -lg2c -lpthread $(XERBLA)
-# LAPACK = -llapack64
-
-
-# SUSE Linux 10.1, AMD Opteron, with GOTO Blas
-# F77 = gfortran
-# BLAS = -lgoto_opteron64 -lgfortran
-
-# SUSE Linux 10.1, Intel Pentium, with GOTO Blas
-# F77 = gfortran
-# BLAS = -lgoto -lgfortran
-
-#------------------------------------------------------------------------------
-# Solaris
-#------------------------------------------------------------------------------
-
-# 32-bit
-# CFLAGS = -KPIC -dalign -xc99=%none -Xc -xlibmieee -xO5 -xlibmil -m32
-
-# 64-bit
-# CFLAGS = -fast -KPIC -xc99=%none -xlibmieee -xlibmil -m64 -Xc
-
-# FFLAGS = -fast -KPIC -dalign -xlibmil -m64
-
-# The Sun Performance Library includes both LAPACK and the BLAS:
-# BLAS = -xlic_lib=sunperf
-# LAPACK =
-
-
-#------------------------------------------------------------------------------
-# Compaq Alpha
-#------------------------------------------------------------------------------
-
-# 64-bit mode only
-# CFLAGS = -O2 -std1
-# BLAS = -ldxml
-# LAPACK =
-
-#------------------------------------------------------------------------------
-# Macintosh
-#------------------------------------------------------------------------------
-
-# CC = gcc
-# CFLAGS = -O3 -fno-common -no-cpp-precomp -fexceptions
-# LIB = -lstdc++
-# BLAS = -framework Accelerate
-# LAPACK = -framework Accelerate
-
-#------------------------------------------------------------------------------
-# IBM RS 6000
-#------------------------------------------------------------------------------
-
-# BLAS = -lessl
-# LAPACK =
-
-# 32-bit mode:
-# CFLAGS   = -O4 -qipa -qmaxmem=16384 -qproto
-# F77FLAGS = -O4 -qipa -qmaxmem=16384
-
-# 64-bit mode:
-# CFLAGS   = -O4 -qipa -qmaxmem=16384 -q64 -qproto
-# F77FLAGS = -O4 -qipa -qmaxmem=16384 -q64
-# AR = ar -X64
-
-#------------------------------------------------------------------------------
-# SGI IRIX
-#------------------------------------------------------------------------------
-
-# BLAS = -lscsl
-# LAPACK =
-
-# 32-bit mode
-# CFLAGS = -O
-
-# 64-bit mode (32 bit int's and 64-bit long's):
-# CFLAGS = -64
-# F77FLAGS = -64
-
-# SGI doesn't have ranlib
-# RANLIB = echo
-
-#------------------------------------------------------------------------------
-# AMD Opteron (64 bit)
-#------------------------------------------------------------------------------
-
-# BLAS = -lgoto_opteron64 -lg2c
-# LAPACK = -llapack_opteron64
-
-# SUSE Linux 10.1, AMD Opteron
-# F77 = gfortran
-# BLAS = -lgoto_opteron64 -lgfortran
-# LAPACK = -llapack_opteron64
-
-#------------------------------------------------------------------------------
-# remove object files and profile output
-#------------------------------------------------------------------------------
-
-CLEAN = *.o *.obj *.ln *.bb *.bbg *.da *.tcov *.gcov gmon.out *.bak *.d *.gcda *.gcno
diff --git a/academic/suitesparse/suitesparse.SlackBuild b/academic/suitesparse/suitesparse.SlackBuild
index dacae9e7093e..372a0be953f0 100644
--- a/academic/suitesparse/suitesparse.SlackBuild
+++ b/academic/suitesparse/suitesparse.SlackBuild
@@ -2,17 +2,38 @@
 
 # Slackware build script for suitesparse
 
-# Written by Pablo Santamaria (pablosantamaria@gmail.com)
+# Copyright 2017 Christoph Willing,  Brisbane Australia
+# All rights reserved.
+# Thanks to Pablo Santamaria for previous versions
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
+#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=suitesparse
-VERSION=${VERSION:-4.2.1}
+SRCNAM=SuiteSparse
+VERSION=${VERSION:-4.5.4}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
-    i?86) ARCH=i486 ;;
+    i?86) ARCH=i586 ;;
     arm*) ARCH=arm ;;
+    # Unless $ARCH is already set, use uname -m for all other archs:
        *) ARCH=$( uname -m ) ;;
   esac
 fi
@@ -22,8 +43,8 @@ TMP=${TMP:-/tmp/SBo}
 PKG=$TMP/package-$PRGNAM
 OUTPUT=${OUTPUT:-/tmp}
 
-if [ "$ARCH" = "i486" ]; then
-  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
   LIBDIRSUFFIX=""
 elif [ "$ARCH" = "i686" ]; then
   SLKCFLAGS="-O2 -march=i686 -mtune=i686"
@@ -36,39 +57,38 @@ else
   LIBDIRSUFFIX=""
 fi
 
+metis="" ; [ "${USEMETIS:-yes}" != "yes" ] && metis="CHOLMOD_CONFIG=-DNPARTITION"
+
 set -e
 
 rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
-rm -rf SuiteSparse
-tar xvf $CWD/SuiteSparse-$VERSION.tar.gz
-
-cd SuiteSparse
+rm -rf $SRCNAM
+tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
+cd $SRCNAM
 chown -R root:root .
 find -L . \
  \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
   -o -perm 511 \) -exec chmod 755 {} \; -o \
  \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
- -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
-
-for lib in SuiteSparse_config AMD CAMD COLAMD BTF KLU LDL CCOLAMD UMFPACK CHOLMOD CXSparse SPQR RBio; do
-    make -C $lib library CFLAGS="$SLKCFLAGS -DNPARTITION"
-done
+  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
-mkdir -p $PKG/usr/lib$LIBDIRSUFFIX
 mkdir -p $PKG/usr/include/suitesparse
-for lib in SuiteSparse_config AMD CAMD COLAMD BTF KLU LDL CCOLAMD UMFPACK CHOLMOD CXSparse SPQR RBio; do
-  make -C $lib INSTALL_LIB="$PKG/usr/lib$LIBDIRSUFFIX" INSTALL_INCLUDE="$PKG/usr/include/suitesparse" install
-done
-
+mkdir -p $PKG/usr/lib$LIBDIRSUFFIX
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
-cp -a README.txt $PKG/usr/doc/$PRGNAM-$VERSION
-for lib in AMD CAMD COLAMD BTF KLU LDL CCOLAMD UMFPACK CHOLMOD CXSparse SPQR RBio; do
-    mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION/$lib
-    cp -a $lib/Doc/README* $lib/Doc/*.pdf $lib/Doc/ChangeLog $lib/Doc/License* \
-	$PKG/usr/doc/$PRGNAM-$VERSION/$lib || true
-done
+
+make install \
+	MY_METIS_INC=/usr/include/metis MY_METIS_LIB=/usr/lib$LIBDIRSUFFIX/libmetis.so BLAS=-lblas \
+	$metis \
+	INSTALL_INCLUDE=$PKG/usr/include/suitesparse INSTALL_LIB=$PKG/usr/lib$LIBDIRSUFFIX \
+	INSTALL_DOC=$PKG/usr/doc/$PRGNAM-$VERSION
+chrpath --replace /usr/lib$LIBDIRSUFFIX $PKG/usr/lib$LIBDIRSUFFIX/*
+
+find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
+  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
+
+cp -a LICENSE.txt $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 
 mkdir -p $PKG/install
diff --git a/academic/suitesparse/suitesparse.info b/academic/suitesparse/suitesparse.info
index e78da251b0e2..11400a0d5c11 100644
--- a/academic/suitesparse/suitesparse.info
+++ b/academic/suitesparse/suitesparse.info
@@ -1,10 +1,10 @@
 PRGNAM="suitesparse"
-VERSION="4.2.1"
+VERSION="4.5.4"
 HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html"
-DOWNLOAD="http://pkgs.fedoraproject.org/repo/pkgs/suitesparse/SuiteSparse-4.2.1.tar.gz/4628df9eeae10ae5f0c486f1ac982fce/SuiteSparse-4.2.1.tar.gz"
-MD5SUM="4628df9eeae10ae5f0c486f1ac982fce"
+DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.4.tar.gz"
+MD5SUM="f6ab689442e64a1624a47aa220072d1b"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
-REQUIRES="lapack"
-MAINTAINER="Pablo Santamaria"
-EMAIL="pablosantamaria@gmail.com"
+REQUIRES="lapack metis chrpath"
+MAINTAINER="Christoph Willing"
+EMAIL="chris.willing@linux.com"