academic/csparse: BUILD bump for SuiteSparse 4.5.5.

Signed-off-by: Kyle Guinn <elyk03@gmail.com>

4 files changed, 596 insertions, 222 deletions

diff --git a/academic/csparse/csparse.SlackBuild b/academic/csparse/csparse.SlackBuild
index 64f4d270fa..d44bc46a8b 100644
--- a/academic/csparse/csparse.SlackBuild
+++ b/academic/csparse/csparse.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for CSparse
 
-# Copyright 2013-2016 Kyle Guinn <elyk03@gmail.com>, USA
+# Copyright 2013-2017 Kyle Guinn <elyk03@gmail.com>, USA
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -26,8 +26,8 @@ PRGNAM=csparse
 SRCNAM=SuiteSparse
 SUBDIR=CSparse
 VERSION=${VERSION:-3.1.9}
-SRCVER=${SRCVER:-4.5.3}
-BUILD=${BUILD:-1}
+SRCVER=${SRCVER:-4.5.5}
+BUILD=${BUILD:-2}
 TAG=${TAG:-_SBo}
 
 if [ -z "$ARCH" ]; then
@@ -40,7 +40,7 @@ fi
 
 CWD=$(pwd)
 TMP=${TMP:-/tmp/SBo}
-PKG=$TMP/package-$PRGNAM
+PKG=$TMP/package-$PRGNAM-$VERSION
 OUTPUT=${OUTPUT:-/tmp}
 
 DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt"
@@ -76,7 +76,7 @@ cd $SRCNAM/$SUBDIR
 chown -R root:root .
 chmod -R u+w,go-w,a+rX-st .
 
-patch -p1 < $CWD/patches/autotoolize.diff
+patch -p1 < $CWD/patches/autoconfiscate.diff
 autoreconf -vif
 
 ./configure \
@@ -87,8 +87,6 @@ autoreconf -vif
   --mandir=/usr/man \
   --infodir=/usr/info \
   --docdir=/usr/doc/$PRGNAM-$VERSION \
-  --enable-shared \
-  --disable-static \
   --disable-dependency-tracking \
   --build=$ARCH-slackware-linux \
   CFLAGS="$SLKCFLAGS" \
diff --git a/academic/csparse/csparse.info b/academic/csparse/csparse.info
index 3835d4eaa3..428fe3e46d 100644
--- a/academic/csparse/csparse.info
+++ b/academic/csparse/csparse.info
@@ -1,8 +1,8 @@
 PRGNAM="csparse"
 VERSION="3.1.9"
 HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html"
-DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.3.tar.gz"
-MD5SUM="8ec57324585df3c6483ad7f556afccbd"
+DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.5.tar.gz"
+MD5SUM="0a5b38af0016f009409a9606d2f1b555"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES=""
diff --git a/academic/csparse/patches/autoconfiscate.diff b/academic/csparse/patches/autoconfiscate.diff
new file mode 100644
index 0000000000..9cae925af1
--- /dev/null
+++ b/academic/csparse/patches/autoconfiscate.diff
@@ -0,0 +1,589 @@
+diff --git a/Demo/Makefile.am b/Demo/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Demo/Makefile.am
+@@ -0,0 +1,88 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include
++LDADD = $(top_builddir)/Source/libcsparse.la
++
++EXTRA_DIST = \
++	README.txt \
++	cs_demo.out
++
++# Disable the .out implicit pattern rule.  Prevents GNU make from
++# adding bogus dependencies for the .out files listed above.
++%.out: %
++
++check_PROGRAMS = \
++	cs_demo1 \
++	cs_demo2 \
++	cs_demo3
++
++check_LTLIBRARIES = \
++	libcs_demo.la
++
++cs_demo1_SOURCES = cs_demo1.c
++cs_demo2_SOURCES = cs_demo2.c
++cs_demo3_SOURCES = cs_demo3.c
++libcs_demo_la_SOURCES = cs_demo.c cs_demo.h
++cs_demo2_LDADD = libcs_demo.la $(LDADD)
++cs_demo3_LDADD = libcs_demo.la $(LDADD)
++
++if !CODE_COVERAGE_ENABLED
++MATRICES = \
++	$(top_srcdir)/Matrix/ash219 \
++	$(top_srcdir)/Matrix/bcsstk01 \
++	$(top_srcdir)/Matrix/bcsstk16 \
++	$(top_srcdir)/Matrix/fs_183_1 \
++	$(top_srcdir)/Matrix/lp_afiro \
++	$(top_srcdir)/Matrix/mbeacxc \
++	$(top_srcdir)/Matrix/t1 \
++	$(top_srcdir)/Matrix/west0067
++
++check-local: $(check_PROGRAMS) $(MATRICES)
++	-./cs_demo1 < $(top_srcdir)/Matrix/t1
++	-./cs_demo2 < $(top_srcdir)/Matrix/t1
++	-./cs_demo2 < $(top_srcdir)/Matrix/ash219
++	-./cs_demo2 < $(top_srcdir)/Matrix/bcsstk01
++	-./cs_demo2 < $(top_srcdir)/Matrix/fs_183_1
++	-./cs_demo2 < $(top_srcdir)/Matrix/mbeacxc
++	-./cs_demo2 < $(top_srcdir)/Matrix/west0067
++	-./cs_demo2 < $(top_srcdir)/Matrix/lp_afiro
++	-./cs_demo2 < $(top_srcdir)/Matrix/bcsstk16
++	-./cs_demo3 < $(top_srcdir)/Matrix/bcsstk01
++	-./cs_demo3 < $(top_srcdir)/Matrix/bcsstk16
++
++else
++MATRICES = \
++	$(top_srcdir)/Tcov/nil \
++	$(top_srcdir)/Tcov/zero \
++	$(top_srcdir)/Matrix/ash219 \
++	$(top_srcdir)/Matrix/bcsstk01 \
++	$(top_srcdir)/Matrix/bcsstk16 \
++	$(top_srcdir)/Matrix/fs_183_1 \
++	$(top_srcdir)/Matrix/ibm32a \
++	$(top_srcdir)/Matrix/ibm32b \
++	$(top_srcdir)/Matrix/lp_afiro \
++	$(top_srcdir)/Matrix/mbeacxc \
++	$(top_srcdir)/Matrix/t1 \
++	$(top_srcdir)/Matrix/west0067
++
++check-local: $(check_PROGRAMS) $(MATRICES)
++# tiny tests
++	-./cs_demo1 < $(top_srcdir)/Tcov/nil
++	-./cs_demo1 < $(top_srcdir)/Tcov/zero
++	-./cs_demo2 < $(top_srcdir)/Tcov/nil
++	-./cs_demo2 < $(top_srcdir)/Tcov/zero
++	-./cs_demo3 < $(top_srcdir)/Tcov/nil
++# test coverage for book:
++	-./cs_demo1 < $(top_srcdir)/Matrix/t1
++	-./cs_demo2 < $(top_srcdir)/Matrix/bcsstk01
++	-./cs_demo2 < $(top_srcdir)/Matrix/fs_183_1
++	-./cs_demo2 < $(top_srcdir)/Matrix/mbeacxc
++	-./cs_demo2 < $(top_srcdir)/Matrix/west0067
++	-./cs_demo2 < $(top_srcdir)/Matrix/lp_afiro
++	-./cs_demo3 < $(top_srcdir)/Matrix/bcsstk16
++# other tests
++	-./cs_demo2 < $(top_srcdir)/Matrix/t1
++	-./cs_demo2 < $(top_srcdir)/Matrix/ash219
++	-./cs_demo3 < $(top_srcdir)/Matrix/bcsstk01
++	-./cs_demo2 < $(top_srcdir)/Matrix/bcsstk16
++	-./cs_demo2 < $(top_srcdir)/Matrix/ibm32a
++	-./cs_demo2 < $(top_srcdir)/Matrix/ibm32b
++endif
+diff --git a/Include/Makefile.am b/Include/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Include/Makefile.am
+@@ -0,0 +1 @@
++pkginclude_HEADERS = cs.h
+diff --git a/Makefile.am b/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Makefile.am
+@@ -0,0 +1,9 @@
++ACLOCAL_AMFLAGS = -I m4
++
++SUBDIRS = Include Source Matrix Demo Tcov
++EXTRA_DIST = README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt
++
++pkgconfig_DATA = csparse.pc
++
++CODE_COVERAGE_BRANCH_COVERAGE = 1
++@CODE_COVERAGE_RULES@
+diff --git a/Matrix/Makefile.am b/Matrix/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Matrix/Makefile.am
+@@ -0,0 +1,11 @@
++dist_noinst_DATA = \
++	ash219 \
++	bcsstk01 \
++	bcsstk16 \
++	fs_183_1 \
++	ibm32a \
++	ibm32b \
++	lp_afiro \
++	mbeacxc \
++	t1 \
++	west0067
+diff --git a/Source/Makefile.am b/Source/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Source/Makefile.am
+@@ -0,0 +1,72 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include
++
++EXTRA_DIST = \
++	README.txt
++
++CSPARSESRC = \
++	cs_add.c \
++	cs_amd.c \
++	cs_chol.c \
++	cs_cholsol.c \
++	cs_compress.c \
++	cs_counts.c \
++	cs_cumsum.c \
++	cs_dfs.c \
++	cs_dmperm.c \
++	cs_droptol.c \
++	cs_dropzeros.c \
++	cs_dupl.c \
++	cs_entry.c \
++	cs_ereach.c \
++	cs_etree.c \
++	cs_fkeep.c \
++	cs_gaxpy.c \
++	cs_happly.c \
++	cs_house.c \
++	cs_ipvec.c \
++	cs_leaf.c \
++	cs_load.c \
++	cs_lsolve.c \
++	cs_ltsolve.c \
++	cs_lu.c \
++	cs_lusol.c \
++	cs_maxtrans.c \
++	cs_multiply.c \
++	cs_norm.c \
++	cs_permute.c \
++	cs_pinv.c \
++	cs_post.c \
++	cs_print.c \
++	cs_pvec.c \
++	cs_qr.c \
++	cs_qrsol.c \
++	cs_randperm.c \
++	cs_reach.c \
++	cs_scatter.c \
++	cs_scc.c \
++	cs_schol.c \
++	cs_spsolve.c \
++	cs_sqr.c \
++	cs_symperm.c \
++	cs_tdfs.c \
++	cs_transpose.c \
++	cs_updown.c \
++	cs_usolve.c \
++	cs_util.c \
++	cs_utsolve.c
++
++if !CODE_COVERAGE_ENABLED
++CSPARSESRC += \
++	cs_malloc.c
++else
++CSPARSESRC += \
++	$(top_srcdir)/Tcov/cstcov_malloc_test.c \
++	$(top_srcdir)/Tcov/cstcov_malloc_test.h
++endif
++
++lib_LTLIBRARIES = libcsparse.la
++libcsparse_la_SOURCES = $(CSPARSESRC)
++libcsparse_la_LIBADD = -lm $(CODE_COVERAGE_LIBS)
++libcsparse_la_CPPFLAGS = $(AM_CPPFLAGS) $(CODE_COVERAGE_CPPFLAGS)
++libcsparse_la_CFLAGS = $(AM_CFLAGS) $(CODE_COVERAGE_CFLAGS)
++libcsparse_la_LDFLAGS = -no-undefined -release $(PACKAGE_VERSION)
+diff --git a/Tcov/Makefile.am b/Tcov/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Tcov/Makefile.am
+@@ -0,0 +1,40 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include -I$(top_srcdir)/Demo
++LDADD = $(top_builddir)/Source/libcsparse.la
++
++EXTRA_DIST = \
++	README.txt
++
++dist_noinst_DATA = \
++	nil \
++	zero
++
++if CODE_COVERAGE_ENABLED
++check_PROGRAMS = \
++	cstcov_test
++
++cstcov_test_SOURCES = cstcov_test.c
++cstcov_test_LDADD = $(top_builddir)/Demo/libcs_demo.la $(LDADD)
++
++MATRICES = \
++	$(top_srcdir)/Tcov/nil \
++	$(top_srcdir)/Tcov/zero \
++	$(top_srcdir)/Matrix/ash219 \
++	$(top_srcdir)/Matrix/bcsstk01 \
++	$(top_srcdir)/Matrix/fs_183_1 \
++	$(top_srcdir)/Matrix/lp_afiro \
++	$(top_srcdir)/Matrix/t1 \
++	$(top_srcdir)/Matrix/west0067
++
++check-local: $(check_PROGRAMS) $(MATRICES)
++# exhaustive memory tests
++	-./cstcov_test $(top_srcdir)/Tcov/nil > test_nil.out
++	-./cstcov_test $(top_srcdir)/Tcov/zero > test_zero.out
++	-./cstcov_test $(top_srcdir)/Matrix/t1 > test_t1.out
++	-./cstcov_test $(top_srcdir)/Matrix/bcsstk01 > test_k1.out
++	-./cstcov_test $(top_srcdir)/Matrix/fs_183_1 > test_fs.out
++	-./cstcov_test $(top_srcdir)/Matrix/west0067 > test_we.out
++	-./cstcov_test $(top_srcdir)/Matrix/ash219 > test_ash.out
++	-./cstcov_test $(top_srcdir)/Matrix/lp_afiro > test_afiro.out
++endif
++
++CLEANFILES = *.out
+diff --git a/configure.ac b/configure.ac
+new file mode 100644
+--- /dev/null
++++ b/configure.ac
+@@ -0,0 +1,47 @@
++#                                               -*- Autoconf -*-
++# Process this file with autoconf to produce a configure script.
++
++AC_PREREQ([2.69])
++AC_INIT([CSparse],[3.1.9],[DrTimothyAldenDavis@gmail.com],[csparse],[http://www.suitesparse.com/])
++AC_CONFIG_SRCDIR([Source/cs_print.c])
++AC_CONFIG_AUX_DIR([build-aux])
++AC_CONFIG_MACRO_DIR([m4])
++AC_CONFIG_HEADERS([config.h])
++AM_INIT_AUTOMAKE([foreign])
++AM_SILENT_RULES([yes])
++LT_INIT([disable-static])
++
++# Checks for programs.
++AC_PROG_INSTALL
++AC_PROG_CC
++AX_CODE_COVERAGE
++
++AS_VAR_SET([LIBS_SAVED], [$LIBS])
++
++# Checks for libraries.
++AC_CHECK_LIB([m], [sqrt])
++
++# Checks for header files.
++AC_CHECK_HEADERS([limits.h stddef.h stdlib.h])
++
++# Checks for typedefs, structures, and compiler characteristics.
++AC_TYPE_SIZE_T
++
++# Checks for library functions.
++AC_FUNC_MALLOC
++AC_FUNC_REALLOC
++AC_CHECK_FUNCS([sqrt])
++
++AS_VAR_SET([LIBS], [$LIBS_SAVED])
++
++PKG_INSTALLDIR
++AC_CONFIG_FILES([
++	csparse.pc
++	Makefile
++	Demo/Makefile
++	Include/Makefile
++	Matrix/Makefile
++	Source/Makefile
++	Tcov/Makefile
++])
++AC_OUTPUT
+diff --git a/csparse.pc.in b/csparse.pc.in
+new file mode 100644
+--- /dev/null
++++ b/csparse.pc.in
+@@ -0,0 +1,12 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: @PACKAGE_NAME@
++Description: A concise sparse matrix package
++Version: @PACKAGE_VERSION@
++URL: @PACKAGE_URL@
++Libs: -L${libdir} -lcsparse
++Libs.private: -lm
++Cflags: -I${includedir}/csparse
+diff --git a/m4/ax_code_coverage.m4 b/m4/ax_code_coverage.m4
+new file mode 100644
+--- /dev/null
++++ b/m4/ax_code_coverage.m4
+@@ -0,0 +1,264 @@
++# ===========================================================================
++#     https://www.gnu.org/software/autoconf-archive/ax_code_coverage.html
++# ===========================================================================
++#
++# SYNOPSIS
++#
++#   AX_CODE_COVERAGE()
++#
++# DESCRIPTION
++#
++#   Defines CODE_COVERAGE_CPPFLAGS, CODE_COVERAGE_CFLAGS,
++#   CODE_COVERAGE_CXXFLAGS and CODE_COVERAGE_LIBS which should be included
++#   in the CPPFLAGS, CFLAGS CXXFLAGS and LIBS/LIBADD variables of every
++#   build target (program or library) which should be built with code
++#   coverage support. Also defines CODE_COVERAGE_RULES which should be
++#   substituted in your Makefile; and $enable_code_coverage which can be
++#   used in subsequent configure output. CODE_COVERAGE_ENABLED is defined
++#   and substituted, and corresponds to the value of the
++#   --enable-code-coverage option, which defaults to being disabled.
++#
++#   Test also for gcov program and create GCOV variable that could be
++#   substituted.
++#
++#   Note that all optimization flags in CFLAGS must be disabled when code
++#   coverage is enabled.
++#
++#   Usage example:
++#
++#   configure.ac:
++#
++#     AX_CODE_COVERAGE
++#
++#   Makefile.am:
++#
++#     @CODE_COVERAGE_RULES@
++#     my_program_LIBS = ... $(CODE_COVERAGE_LIBS) ...
++#     my_program_CPPFLAGS = ... $(CODE_COVERAGE_CPPFLAGS) ...
++#     my_program_CFLAGS = ... $(CODE_COVERAGE_CFLAGS) ...
++#     my_program_CXXFLAGS = ... $(CODE_COVERAGE_CXXFLAGS) ...
++#
++#   This results in a "check-code-coverage" rule being added to any
++#   Makefile.am which includes "@CODE_COVERAGE_RULES@" (assuming the module
++#   has been configured with --enable-code-coverage). Running `make
++#   check-code-coverage` in that directory will run the module's test suite
++#   (`make check`) and build a code coverage report detailing the code which
++#   was touched, then print the URI for the report.
++#
++#   In earlier versions of this macro, CODE_COVERAGE_LDFLAGS was defined
++#   instead of CODE_COVERAGE_LIBS. They are both still defined, but use of
++#   CODE_COVERAGE_LIBS is preferred for clarity; CODE_COVERAGE_LDFLAGS is
++#   deprecated. They have the same value.
++#
++#   This code was derived from Makefile.decl in GLib, originally licenced
++#   under LGPLv2.1+.
++#
++# LICENSE
++#
++#   Copyright (c) 2012, 2016 Philip Withnall
++#   Copyright (c) 2012 Xan Lopez
++#   Copyright (c) 2012 Christian Persch
++#   Copyright (c) 2012 Paolo Borelli
++#   Copyright (c) 2012 Dan Winship
++#   Copyright (c) 2015 Bastien ROUCARIES
++#
++#   This library is free software; you can redistribute it and/or modify it
++#   under the terms of the GNU Lesser General Public License as published by
++#   the Free Software Foundation; either version 2.1 of the License, or (at
++#   your option) any later version.
++#
++#   This library is distributed in the hope that it will be useful, but
++#   WITHOUT ANY WARRANTY; without even the implied warranty of
++#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser
++#   General Public License for more details.
++#
++#   You should have received a copy of the GNU Lesser General Public License
++#   along with this program. If not, see <https://www.gnu.org/licenses/>.
++
++#serial 24
++
++AC_DEFUN([AX_CODE_COVERAGE],[
++	dnl Check for --enable-code-coverage
++	AC_REQUIRE([AC_PROG_SED])
++
++	# allow to override gcov location
++	AC_ARG_WITH([gcov],
++	  [AS_HELP_STRING([--with-gcov[=GCOV]], [use given GCOV for coverage (GCOV=gcov).])],
++	  [_AX_CODE_COVERAGE_GCOV_PROG_WITH=$with_gcov],
++	  [_AX_CODE_COVERAGE_GCOV_PROG_WITH=gcov])
++
++	AC_MSG_CHECKING([whether to build with code coverage support])
++	AC_ARG_ENABLE([code-coverage],
++	  AS_HELP_STRING([--enable-code-coverage],
++	  [Whether to enable code coverage support]),,
++	  enable_code_coverage=no)
++
++	AM_CONDITIONAL([CODE_COVERAGE_ENABLED], [test x$enable_code_coverage = xyes])
++	AC_SUBST([CODE_COVERAGE_ENABLED], [$enable_code_coverage])
++	AC_MSG_RESULT($enable_code_coverage)
++
++	AS_IF([ test "$enable_code_coverage" = "yes" ], [
++		# check for gcov
++		AC_CHECK_TOOL([GCOV],
++		  [$_AX_CODE_COVERAGE_GCOV_PROG_WITH],
++		  [:])
++		AS_IF([test "X$GCOV" = "X:"],
++		  [AC_MSG_ERROR([gcov is needed to do coverage])])
++		AC_SUBST([GCOV])
++
++		dnl Check if gcc is being used
++		AS_IF([ test "$GCC" = "no" ], [
++			AC_MSG_ERROR([not compiling with gcc, which is required for gcov code coverage])
++		])
++
++		AC_CHECK_PROG([LCOV], [lcov], [lcov])
++		AC_CHECK_PROG([GENHTML], [genhtml], [genhtml])
++
++		AS_IF([ test -z "$LCOV" ], [
++			AC_MSG_ERROR([To enable code coverage reporting you must have lcov installed])
++		])
++
++		AS_IF([ test -z "$GENHTML" ], [
++			AC_MSG_ERROR([Could not find genhtml from the lcov package])
++		])
++
++		dnl Build the code coverage flags
++		dnl Define CODE_COVERAGE_LDFLAGS for backwards compatibility
++		CODE_COVERAGE_CPPFLAGS="-DNDEBUG"
++		CODE_COVERAGE_CFLAGS="-O0 -g -fprofile-arcs -ftest-coverage"
++		CODE_COVERAGE_CXXFLAGS="-O0 -g -fprofile-arcs -ftest-coverage"
++		CODE_COVERAGE_LIBS="-lgcov"
++		CODE_COVERAGE_LDFLAGS="$CODE_COVERAGE_LIBS"
++
++		AC_SUBST([CODE_COVERAGE_CPPFLAGS])
++		AC_SUBST([CODE_COVERAGE_CFLAGS])
++		AC_SUBST([CODE_COVERAGE_CXXFLAGS])
++		AC_SUBST([CODE_COVERAGE_LIBS])
++		AC_SUBST([CODE_COVERAGE_LDFLAGS])
++
++		[CODE_COVERAGE_RULES_CHECK='
++	-$(A''M_V_at)$(MAKE) $(AM_MAKEFLAGS) -k check
++	$(A''M_V_at)$(MAKE) $(AM_MAKEFLAGS) code-coverage-capture
++']
++		[CODE_COVERAGE_RULES_CAPTURE='
++	$(code_coverage_v_lcov_cap)$(LCOV) $(code_coverage_quiet) $(addprefix --directory ,$(CODE_COVERAGE_DIRECTORY)) --capture --output-file "$(CODE_COVERAGE_OUTPUT_FILE).tmp" --test-name "$(call code_coverage_sanitize,$(PACKAGE_NAME)-$(PACKAGE_VERSION))" --no-checksum --compat-libtool $(CODE_COVERAGE_LCOV_SHOPTS) $(CODE_COVERAGE_LCOV_OPTIONS)
++	$(code_coverage_v_lcov_ign)$(LCOV) $(code_coverage_quiet) $(addprefix --directory ,$(CODE_COVERAGE_DIRECTORY)) --remove "$(CODE_COVERAGE_OUTPUT_FILE).tmp" "/tmp/*" $(CODE_COVERAGE_IGNORE_PATTERN) --output-file "$(CODE_COVERAGE_OUTPUT_FILE)" $(CODE_COVERAGE_LCOV_SHOPTS) $(CODE_COVERAGE_LCOV_RMOPTS)
++	-@rm -f $(CODE_COVERAGE_OUTPUT_FILE).tmp
++	$(code_coverage_v_genhtml)LANG=C $(GENHTML) $(code_coverage_quiet) $(addprefix --prefix ,$(CODE_COVERAGE_DIRECTORY)) --output-directory "$(CODE_COVERAGE_OUTPUT_DIRECTORY)" --title "$(PACKAGE_NAME)-$(PACKAGE_VERSION) Code Coverage" --legend --show-details "$(CODE_COVERAGE_OUTPUT_FILE)" $(CODE_COVERAGE_GENHTML_OPTIONS)
++	@echo "file://$(abs_builddir)/$(CODE_COVERAGE_OUTPUT_DIRECTORY)/index.html"
++']
++		[CODE_COVERAGE_RULES_CLEAN='
++clean: code-coverage-clean
++distclean: code-coverage-clean
++code-coverage-clean:
++	-$(LCOV) --directory $(top_builddir) -z
++	-rm -rf $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_OUTPUT_FILE).tmp $(CODE_COVERAGE_OUTPUT_DIRECTORY)
++	-find . \( -name "*.gcda" -o -name "*.gcno" -o -name "*.gcov" \) -delete
++']
++	], [
++		[CODE_COVERAGE_RULES_CHECK='
++	@echo "Need to reconfigure with --enable-code-coverage"
++']
++		CODE_COVERAGE_RULES_CAPTURE="$CODE_COVERAGE_RULES_CHECK"
++		CODE_COVERAGE_RULES_CLEAN=''
++	])
++
++[CODE_COVERAGE_RULES='
++# Code coverage
++#
++# Optional:
++#  - CODE_COVERAGE_DIRECTORY: Top-level directory for code coverage reporting.
++#    Multiple directories may be specified, separated by whitespace.
++#    (Default: $(top_builddir))
++#  - CODE_COVERAGE_OUTPUT_FILE: Filename and path for the .info file generated
++#    by lcov for code coverage. (Default:
++#    $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage.info)
++#  - CODE_COVERAGE_OUTPUT_DIRECTORY: Directory for generated code coverage
++#    reports to be created. (Default:
++#    $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage)
++#  - CODE_COVERAGE_BRANCH_COVERAGE: Set to 1 to enforce branch coverage,
++#    set to 0 to disable it and leave empty to stay with the default.
++#    (Default: empty)
++#  - CODE_COVERAGE_LCOV_SHOPTS_DEFAULT: Extra options shared between both lcov
++#    instances. (Default: based on $CODE_COVERAGE_BRANCH_COVERAGE)
++#  - CODE_COVERAGE_LCOV_SHOPTS: Extra options to shared between both lcov
++#    instances. (Default: $CODE_COVERAGE_LCOV_SHOPTS_DEFAULT)
++#  - CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH: --gcov-tool pathtogcov
++#  - CODE_COVERAGE_LCOV_OPTIONS_DEFAULT: Extra options to pass to the
++#    collecting lcov instance. (Default: $CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH)
++#  - CODE_COVERAGE_LCOV_OPTIONS: Extra options to pass to the collecting lcov
++#    instance. (Default: $CODE_COVERAGE_LCOV_OPTIONS_DEFAULT)
++#  - CODE_COVERAGE_LCOV_RMOPTS_DEFAULT: Extra options to pass to the filtering
++#    lcov instance. (Default: empty)
++#  - CODE_COVERAGE_LCOV_RMOPTS: Extra options to pass to the filtering lcov
++#    instance. (Default: $CODE_COVERAGE_LCOV_RMOPTS_DEFAULT)
++#  - CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT: Extra options to pass to the
++#    genhtml instance. (Default: based on $CODE_COVERAGE_BRANCH_COVERAGE)
++#  - CODE_COVERAGE_GENHTML_OPTIONS: Extra options to pass to the genhtml
++#    instance. (Default: $CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT)
++#  - CODE_COVERAGE_IGNORE_PATTERN: Extra glob pattern of files to ignore
++#
++# The generated report will be titled using the $(PACKAGE_NAME) and
++# $(PACKAGE_VERSION). In order to add the current git hash to the title,
++# use the git-version-gen script, available online.
++
++# Optional variables
++CODE_COVERAGE_DIRECTORY ?= $(top_builddir)
++CODE_COVERAGE_OUTPUT_FILE ?= $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage.info
++CODE_COVERAGE_OUTPUT_DIRECTORY ?= $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage
++CODE_COVERAGE_BRANCH_COVERAGE ?=
++CODE_COVERAGE_LCOV_SHOPTS_DEFAULT ?= $(if $(CODE_COVERAGE_BRANCH_COVERAGE),\
++--rc lcov_branch_coverage=$(CODE_COVERAGE_BRANCH_COVERAGE))
++CODE_COVERAGE_LCOV_SHOPTS ?= $(CODE_COVERAGE_LCOV_SHOPTS_DEFAULT)
++CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH ?= --gcov-tool "$(GCOV)"
++CODE_COVERAGE_LCOV_OPTIONS_DEFAULT ?= $(CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH)
++CODE_COVERAGE_LCOV_OPTIONS ?= $(CODE_COVERAGE_LCOV_OPTIONS_DEFAULT)
++CODE_COVERAGE_LCOV_RMOPTS_DEFAULT ?=
++CODE_COVERAGE_LCOV_RMOPTS ?= $(CODE_COVERAGE_LCOV_RMOPTS_DEFAULT)
++CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT ?=\
++$(if $(CODE_COVERAGE_BRANCH_COVERAGE),\
++--rc genhtml_branch_coverage=$(CODE_COVERAGE_BRANCH_COVERAGE))
++CODE_COVERAGE_GENHTML_OPTIONS ?= $(CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT)
++CODE_COVERAGE_IGNORE_PATTERN ?=
++
++code_coverage_v_lcov_cap = $(code_coverage_v_lcov_cap_$(V))
++code_coverage_v_lcov_cap_ = $(code_coverage_v_lcov_cap_$(AM_DEFAULT_VERBOSITY))
++code_coverage_v_lcov_cap_0 = @echo "  LCOV   --capture"\
++ $(CODE_COVERAGE_OUTPUT_FILE);
++code_coverage_v_lcov_ign = $(code_coverage_v_lcov_ign_$(V))
++code_coverage_v_lcov_ign_ = $(code_coverage_v_lcov_ign_$(AM_DEFAULT_VERBOSITY))
++code_coverage_v_lcov_ign_0 = @echo "  LCOV   --remove /tmp/*"\
++ $(CODE_COVERAGE_IGNORE_PATTERN);
++code_coverage_v_genhtml = $(code_coverage_v_genhtml_$(V))
++code_coverage_v_genhtml_ = $(code_coverage_v_genhtml_$(AM_DEFAULT_VERBOSITY))
++code_coverage_v_genhtml_0 = @echo "  GEN   " $(CODE_COVERAGE_OUTPUT_DIRECTORY);
++code_coverage_quiet = $(code_coverage_quiet_$(V))
++code_coverage_quiet_ = $(code_coverage_quiet_$(AM_DEFAULT_VERBOSITY))
++code_coverage_quiet_0 = --quiet
++
++# sanitizes the test-name: replaces with underscores: dashes and dots
++code_coverage_sanitize = $(subst -,_,$(subst .,_,$(1)))
++
++# Use recursive makes in order to ignore errors during check
++check-code-coverage:'"$CODE_COVERAGE_RULES_CHECK"'
++
++# Capture code coverage data
++code-coverage-capture: code-coverage-capture-hook'"$CODE_COVERAGE_RULES_CAPTURE"'
++
++# Hook rule executed before code-coverage-capture, overridable by the user
++code-coverage-capture-hook:
++
++'"$CODE_COVERAGE_RULES_CLEAN"'
++
++GITIGNOREFILES ?=
++GITIGNOREFILES += $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_OUTPUT_DIRECTORY)
++
++A''M_DISTCHECK_CONFIGURE_FLAGS ?=
++A''M_DISTCHECK_CONFIGURE_FLAGS += --disable-code-coverage
++
++.PHONY: check-code-coverage code-coverage-capture code-coverage-capture-hook code-coverage-clean
++']
++
++	AC_SUBST([CODE_COVERAGE_RULES])
++	m4_ifdef([_AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE([CODE_COVERAGE_RULES])])
++])
diff --git a/academic/csparse/patches/autotoolize.diff b/academic/csparse/patches/autotoolize.diff
deleted file mode 100644
index 0fe8f18458..0000000000
--- a/academic/csparse/patches/autotoolize.diff
+++ /dev/null
@@ -1,213 +0,0 @@
-diff --git a/Demo/Makefile.am b/Demo/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Demo/Makefile.am
-@@ -0,0 +1,46 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include
-+LDADD = $(top_builddir)/Source/libcsparse.la
-+
-+EXTRA_DIST = \
-+	README.txt \
-+	cs_demo.out
-+
-+# Disable the .out implicit pattern rule.  Prevents GNU make from
-+# adding bogus dependencies for the .out files listed above.
-+%.out: %
-+
-+noinst_HEADERS = \
-+	cs_demo.h
-+
-+check_PROGRAMS = \
-+	cs_demo1 \
-+	cs_demo2 \
-+	cs_demo3
-+
-+cs_demo1_SOURCES = cs_demo1.c
-+cs_demo2_SOURCES = cs_demo2.c cs_demo.c
-+cs_demo3_SOURCES = cs_demo3.c cs_demo.c
-+
-+MATRICES = \
-+	$(top_srcdir)/Matrix/ash219 \
-+	$(top_srcdir)/Matrix/bcsstk01 \
-+	$(top_srcdir)/Matrix/bcsstk01 \
-+	$(top_srcdir)/Matrix/bcsstk16 \
-+	$(top_srcdir)/Matrix/fs_183_1 \
-+	$(top_srcdir)/Matrix/lp_afiro \
-+	$(top_srcdir)/Matrix/mbeacxc \
-+	$(top_srcdir)/Matrix/t1 \
-+	$(top_srcdir)/Matrix/west0067
-+
-+check-local: $(check_PROGRAMS) $(MATRICES)
-+	-./cs_demo1 < $(top_srcdir)/Matrix/t1
-+	-./cs_demo2 < $(top_srcdir)/Matrix/t1
-+	-./cs_demo2 < $(top_srcdir)/Matrix/ash219
-+	-./cs_demo2 < $(top_srcdir)/Matrix/bcsstk01
-+	-./cs_demo2 < $(top_srcdir)/Matrix/fs_183_1
-+	-./cs_demo2 < $(top_srcdir)/Matrix/mbeacxc
-+	-./cs_demo2 < $(top_srcdir)/Matrix/west0067
-+	-./cs_demo2 < $(top_srcdir)/Matrix/lp_afiro
-+	-./cs_demo2 < $(top_srcdir)/Matrix/bcsstk16
-+	-./cs_demo3 < $(top_srcdir)/Matrix/bcsstk01
-+	-./cs_demo3 < $(top_srcdir)/Matrix/bcsstk16
-diff --git a/Include/Makefile.am b/Include/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Include/Makefile.am
-@@ -0,0 +1 @@
-+pkginclude_HEADERS = cs.h
-diff --git a/Makefile.am b/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Makefile.am
-@@ -0,0 +1,4 @@
-+SUBDIRS = Include Source Matrix Demo
-+EXTRA_DIST = README.txt Doc/ChangeLog Doc/License.txt Doc/lesser.txt
-+
-+pkgconfig_DATA = csparse.pc
-diff --git a/Matrix/Makefile.am b/Matrix/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Matrix/Makefile.am
-@@ -0,0 +1,11 @@
-+dist_noinst_DATA = \
-+	ash219 \
-+	bcsstk01 \
-+	bcsstk16 \
-+	fs_183_1 \
-+	ibm32a \
-+	ibm32b \
-+	lp_afiro \
-+	mbeacxc \
-+	t1 \
-+	west0067
-diff --git a/Source/Makefile.am b/Source/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Source/Makefile.am
-@@ -0,0 +1,62 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include
-+
-+EXTRA_DIST = \
-+	README.txt
-+
-+CSPARSESRC = \
-+	cs_add.c \
-+	cs_amd.c \
-+	cs_chol.c \
-+	cs_cholsol.c \
-+	cs_compress.c \
-+	cs_counts.c \
-+	cs_cumsum.c \
-+	cs_dfs.c \
-+	cs_dmperm.c \
-+	cs_droptol.c \
-+	cs_dropzeros.c \
-+	cs_dupl.c \
-+	cs_entry.c \
-+	cs_ereach.c \
-+	cs_etree.c \
-+	cs_fkeep.c \
-+	cs_gaxpy.c \
-+	cs_happly.c \
-+	cs_house.c \
-+	cs_ipvec.c \
-+	cs_leaf.c \
-+	cs_load.c \
-+	cs_lsolve.c \
-+	cs_ltsolve.c \
-+	cs_lu.c \
-+	cs_lusol.c \
-+	cs_malloc.c \
-+	cs_maxtrans.c \
-+	cs_multiply.c \
-+	cs_norm.c \
-+	cs_permute.c \
-+	cs_pinv.c \
-+	cs_post.c \
-+	cs_print.c \
-+	cs_pvec.c \
-+	cs_qr.c \
-+	cs_qrsol.c \
-+	cs_randperm.c \
-+	cs_reach.c \
-+	cs_scatter.c \
-+	cs_scc.c \
-+	cs_schol.c \
-+	cs_spsolve.c \
-+	cs_sqr.c \
-+	cs_symperm.c \
-+	cs_tdfs.c \
-+	cs_transpose.c \
-+	cs_updown.c \
-+	cs_usolve.c \
-+	cs_util.c \
-+	cs_utsolve.c
-+
-+lib_LTLIBRARIES = libcsparse.la
-+libcsparse_la_SOURCES = $(CSPARSESRC)
-+libcsparse_la_LIBADD = -lm
-+libcsparse_la_LDFLAGS = -no-undefined -release $(PACKAGE_VERSION)
-diff --git a/configure.ac b/configure.ac
-new file mode 100644
---- /dev/null
-+++ b/configure.ac
-@@ -0,0 +1,42 @@
-+#                                               -*- Autoconf -*-
-+# Process this file with autoconf to produce a configure script.
-+
-+AC_PREREQ([2.69])
-+AC_INIT([CSparse],[3.1.9],[DrTimothyAldenDavis@gmail.com],[csparse],[http://www.suitesparse.com/])
-+AC_CONFIG_SRCDIR([Source/cs_print.c])
-+AC_CONFIG_HEADERS([config.h])
-+AM_INIT_AUTOMAKE([foreign])
-+LT_INIT
-+
-+# Checks for programs.
-+AC_PROG_INSTALL
-+AC_PROG_CC
-+
-+AS_VAR_SET([LIBS_SAVED], [$LIBS])
-+
-+# Checks for libraries.
-+AC_CHECK_LIB([m], [sqrt])
-+
-+# Checks for header files.
-+AC_CHECK_HEADERS([limits.h stddef.h stdlib.h])
-+
-+# Checks for typedefs, structures, and compiler characteristics.
-+AC_TYPE_SIZE_T
-+
-+# Checks for library functions.
-+AC_FUNC_MALLOC
-+AC_FUNC_REALLOC
-+AC_CHECK_FUNCS([sqrt])
-+
-+AS_VAR_SET([LIBS], [$LIBS_SAVED])
-+
-+PKG_INSTALLDIR
-+AC_CONFIG_FILES([
-+	csparse.pc
-+	Makefile
-+	Demo/Makefile
-+	Include/Makefile
-+	Matrix/Makefile
-+	Source/Makefile
-+])
-+AC_OUTPUT
-diff --git a/csparse.pc.in b/csparse.pc.in
-new file mode 100644
---- /dev/null
-+++ b/csparse.pc.in
-@@ -0,0 +1,12 @@
-+prefix=@prefix@
-+exec_prefix=@exec_prefix@
-+libdir=@libdir@
-+includedir=@includedir@
-+
-+Name: @PACKAGE_NAME@
-+Description: A concise sparse matrix package
-+Version: @PACKAGE_VERSION@
-+URL: @PACKAGE_URL@
-+Libs: -L${libdir} -lcsparse
-+Libs.private: -lm
-+Cflags: -I${includedir}/csparse