academic/rbio: BUILD bump for SuiteSparse 4.5.5.

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

2 files changed, 551 insertions, 245 deletions

diff --git a/academic/rbio/patches/autoconfiscate.diff b/academic/rbio/patches/autoconfiscate.diff
new file mode 100644
index 0000000000..93b2e1bff9
--- /dev/null
+++ b/academic/rbio/patches/autoconfiscate.diff
@@ -0,0 +1,551 @@
+diff --git a/Demo/Makefile.am b/Demo/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Demo/Makefile.am
+@@ -0,0 +1,94 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
++LDADD = $(top_builddir)/Source/librbio.la $(SUITESPARSECONFIG_LIBS)
++
++EXTRA_DIST = \
++	RBdemo.out
++
++# Disable the .out implicit pattern rule.  Prevents GNU make from
++# adding bogus dependencies for the .out files listed above.
++%.out: %
++
++check_PROGRAMS = \
++	RBdemo
++
++RBdemo_SOURCES = \
++	RBdemo.c
++
++if !CODE_COVERAGE_ENABLED
++RB = \
++	$(top_srcdir)/RBio/private/west0479.rua
++
++check-local: $(check_PROGRAMS) $(RB)
++	./RBdemo < $(top_srcdir)/RBio/private/west0479.rua
++
++else
++TAR = tar -O -xvvzf
++
++RB = \
++	$(top_srcdir)/RBio/private/bcsstk01.rb \
++	$(top_srcdir)/RBio/private/farm.rb \
++	$(top_srcdir)/RBio/private/lap_25.pse \
++	$(top_srcdir)/RBio/private/lap_25.rb \
++	$(top_srcdir)/RBio/private/west0479.rb \
++	$(top_srcdir)/RBio/private/west0479.rua \
++	$(top_srcdir)/Tcov/matrices/dwg961a.tar.gz \
++	$(top_srcdir)/Tcov/matrices/mhd1280a.tar.gz \
++	$(top_srcdir)/Tcov/matrices/mhd1280b.tar.gz \
++	$(top_srcdir)/Tcov/matrices/qc324.tar.gz \
++	$(top_srcdir)/Tcov/matrices/plskz362.tar.gz \
++	$(top_srcdir)/Tcov/matrices/west0067.tar.gz \
++	$(top_srcdir)/Tcov/matrices/Tina_DisCog.tar.gz \
++	$(top_srcdir)/Tcov/matrices/m4.rb \
++	$(top_srcdir)/Tcov/matrices/s4.rb \
++	$(top_srcdir)/Tcov/matrices/m4b.rb \
++	$(top_srcdir)/Tcov/mangled/1.rb \
++	$(top_srcdir)/Tcov/mangled/2.rb \
++	$(top_srcdir)/Tcov/mangled/3.rb \
++	$(top_srcdir)/Tcov/mangled/4.rb \
++	$(top_srcdir)/Tcov/mangled/5.rb \
++	$(top_srcdir)/Tcov/mangled/6.rb \
++	$(top_srcdir)/Tcov/mangled/7.rb \
++	$(top_srcdir)/Tcov/mangled/8.rb \
++	$(top_srcdir)/Tcov/mangled/9.rb \
++	$(top_srcdir)/Tcov/mangled/10.rb \
++	$(top_srcdir)/Tcov/mangled/11.rb \
++	$(top_srcdir)/Tcov/mangled/12.rb \
++	$(top_srcdir)/Tcov/mangled/13.rb \
++	$(top_srcdir)/Tcov/mangled/14.rb \
++	$(top_srcdir)/Tcov/mangled/15.rb
++
++check-local: $(check_PROGRAMS) $(RB)
++	-./RBdemo $(top_srcdir)/RBio/private/bcsstk01.rb
++	-./RBdemo $(top_srcdir)/RBio/private/farm.rb
++	-./RBdemo $(top_srcdir)/RBio/private/lap_25.pse
++	-./RBdemo $(top_srcdir)/RBio/private/lap_25.rb
++	-./RBdemo $(top_srcdir)/RBio/private/west0479.rb
++	-./RBdemo $(top_srcdir)/RBio/private/west0479.rua
++	-$(TAR) $(top_srcdir)/Tcov/matrices/dwg961a.tar.gz     dwg961a/dwg961a.rb         | ./RBdemo
++	-$(TAR) $(top_srcdir)/Tcov/matrices/mhd1280a.tar.gz    mhd1280a/mhd1280a.rb       | ./RBdemo
++	-$(TAR) $(top_srcdir)/Tcov/matrices/mhd1280b.tar.gz    mhd1280b/mhd1280b.rb       | ./RBdemo
++	-$(TAR) $(top_srcdir)/Tcov/matrices/qc324.tar.gz       qc324/qc324.rb             | ./RBdemo
++	-$(TAR) $(top_srcdir)/Tcov/matrices/plskz362.tar.gz    plskz362/plskz362.rb       | ./RBdemo
++	-$(TAR) $(top_srcdir)/Tcov/matrices/west0067.tar.gz    west0067/west0067.rb       | ./RBdemo
++	-$(TAR) $(top_srcdir)/Tcov/matrices/Tina_DisCog.tar.gz Tina_DisCog/Tina_DisCog.rb | ./RBdemo
++	-./RBdemo $(top_srcdir)/Tcov/matrices/m4.rb
++	-./RBdemo $(top_srcdir)/Tcov/matrices/s4.rb
++	-./RBdemo $(top_srcdir)/Tcov/matrices/m4b.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/1.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/2.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/3.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/4.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/5.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/6.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/7.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/8.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/9.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/10.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/11.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/12.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/13.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/14.rb
++	-./RBdemo $(top_srcdir)/Tcov/mangled/15.rb
++endif
++
++CLEANFILES = temp.rb
+diff --git a/Include/Makefile.am b/Include/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Include/Makefile.am
+@@ -0,0 +1 @@
++pkginclude_HEADERS = RBio.h
+diff --git a/Makefile.am b/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Makefile.am
+@@ -0,0 +1,9 @@
++ACLOCAL_AMFLAGS = -I m4
++
++SUBDIRS = Include Source RBio Demo Tcov
++EXTRA_DIST = README.txt Doc/ChangeLog Doc/License.txt Doc/gpl.txt
++
++pkgconfig_DATA = rbio.pc
++
++CODE_COVERAGE_BRANCH_COVERAGE = 1
++@CODE_COVERAGE_RULES@
+diff --git a/RBio/Makefile.am b/RBio/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/RBio/Makefile.am
+@@ -0,0 +1,3 @@
++SUBDIRS = private
++dist_noinst_DATA = \
++	mywest
+diff --git a/RBio/private/Makefile.am b/RBio/private/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/RBio/private/Makefile.am
+@@ -0,0 +1,7 @@
++dist_noinst_DATA = \
++	bcsstk01.rb \
++	farm.rb \
++	lap_25.pse \
++	lap_25.rb \
++	west0479.rb \
++	west0479.rua
+diff --git a/Source/Makefile.am b/Source/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Source/Makefile.am
+@@ -0,0 +1,21 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
++
++RBIOSRC = \
++	RBio.c
++
++lib_LTLIBRARIES = librbio.la
++noinst_LTLIBRARIES = librbioi.la librbiol.la
++
++librbioi_la_SOURCES = $(RBIOSRC)
++librbioi_la_LIBADD = $(SUITESPARSECONFIG_LIBS)
++librbioi_la_CPPFLAGS = $(AM_CPPFLAGS) -DINT
++librbioi_la_CFLAGS = $(AM_CFLAGS)
++
++librbiol_la_SOURCES = $(RBIOSRC)
++librbiol_la_LIBADD = $(SUITESPARSECONFIG_LIBS) $(CODE_COVERAGE_LIBS)
++librbiol_la_CPPFLAGS = $(AM_CPPFLAGS) $(CODE_COVERAGE_CPPFLAGS)
++librbiol_la_CFLAGS = $(AM_CFLAGS) $(CODE_COVERAGE_CFLAGS)
++
++librbio_la_SOURCES =
++librbio_la_LIBADD = librbioi.la librbiol.la
++librbio_la_LDFLAGS = -no-undefined -release $(PACKAGE_VERSION)
+diff --git a/Tcov/Makefile.am b/Tcov/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Tcov/Makefile.am
+@@ -0,0 +1,45 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
++LDADD = $(top_builddir)/Source/librbio.la $(SUITESPARSECONFIG_LIBS)
++
++EXTRA_DIST = \
++	README.txt
++
++dist_noinst_DATA = \
++	matrices/Tina_DisCog.tar.gz \
++	matrices/dwg961a.tar.gz \
++	matrices/m4.rb \
++	matrices/m4b.rb \
++	matrices/mhd1280a.tar.gz \
++	matrices/mhd1280b.tar.gz \
++	matrices/plskz362.tar.gz \
++	matrices/qc324.tar.gz \
++	matrices/s4.rb \
++	matrices/west0067.tar.gz \
++	mangled/1.rb \
++	mangled/2.rb \
++	mangled/3.rb \
++	mangled/4.rb \
++	mangled/5.rb \
++	mangled/6.rb \
++	mangled/7.rb \
++	mangled/8.rb \
++	mangled/9.rb \
++	mangled/10.rb \
++	mangled/11.rb \
++	mangled/12.rb \
++	mangled/13.rb \
++	mangled/14.rb \
++	mangled/15.rb
++
++if CODE_COVERAGE_ENABLED
++check_PROGRAMS = \
++	RBtest
++
++RBtest_SOURCES = \
++	RBtest.c
++
++check-local: $(check_PROGRAMS)
++	-./RBtest
++endif
++
++CLEANFILES = temp*.rb
+diff --git a/configure.ac b/configure.ac
+new file mode 100644
+--- /dev/null
++++ b/configure.ac
+@@ -0,0 +1,45 @@
++#                                               -*- Autoconf -*-
++# Process this file with autoconf to produce a configure script.
++
++AC_PREREQ([2.69])
++AC_INIT([RBio],[2.2.6],[DrTimothyAldenDavis@gmail.com],[rbio],[http://www.suitesparse.com/])
++AC_CONFIG_SRCDIR([Source/RBio.c])
++AC_CONFIG_AUX_DIR([build-aux])
++AC_CONFIG_MACRO_DIR([m4])
++AC_CONFIG_HEADERS([config.h])
++AM_INIT_AUTOMAKE([foreign])
++AM_SILENT_RULES([yes])
++LT_INIT([disable-static])
++
++# Checks for programs.
++PKG_PROG_PKG_CONFIG
++AC_PROG_INSTALL
++AC_PROG_CC
++AX_CODE_COVERAGE
++
++AS_VAR_SET([LIBS_SAVED], [$LIBS])
++
++# Checks for libraries.
++PKG_CHECK_MODULES([SUITESPARSECONFIG], [suitesparseconfig])
++
++# Checks for header files.
++AC_CHECK_HEADERS([stddef.h stdlib.h string.h])
++
++# Checks for typedefs, structures, and compiler characteristics.
++
++# Checks for library functions.
++
++AS_VAR_SET([LIBS], [$LIBS_SAVED])
++
++PKG_INSTALLDIR
++AC_CONFIG_FILES([
++	rbio.pc
++	Makefile
++	Demo/Makefile
++	Include/Makefile
++	RBio/Makefile
++	RBio/private/Makefile
++	Source/Makefile
++	Tcov/Makefile
++])
++AC_OUTPUT
+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) $(CODE_COVERAGE_OUTPUT_DIRECTORY)
++
++A''M_DISTCHECK_CONFIGURE_FLAGS ?=
++A''M_DISTCHECK_CONFIGURE_FLAGS += --disable-code-coverage
++
++.PHONY: check-code-coverage code-coverage-capture code-coverage-capture-hook code-coverage-clean
++']
++
++	AC_SUBST([CODE_COVERAGE_RULES])
++	m4_ifdef([_AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE([CODE_COVERAGE_RULES])])
++])
+diff --git a/rbio.pc.in b/rbio.pc.in
+new file mode 100644
+--- /dev/null
++++ b/rbio.pc.in
+@@ -0,0 +1,12 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: @PACKAGE_NAME@
++Description: Toolbox for reading/writing sparse matrices in Rutherford/Boeing format
++Version: @PACKAGE_VERSION@
++URL: @PACKAGE_URL@
++Requires.private: suitesparseconfig
++Libs: -L${libdir} -lrbio
++Cflags: -I${includedir}/rbio
diff --git a/academic/rbio/patches/autotoolize.diff b/academic/rbio/patches/autotoolize.diff
deleted file mode 100644
index b20e1a88e5..0000000000
--- a/academic/rbio/patches/autotoolize.diff
+++ /dev/null
@@ -1,245 +0,0 @@
-diff --git a/Demo/Makefile.am b/Demo/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Demo/Makefile.am
-@@ -0,0 +1,22 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
-+LDADD = $(top_builddir)/Source/librbio.la $(SUITESPARSECONFIG_LIBS)
-+
-+EXTRA_DIST = \
-+	RBdemo.out
-+
-+# Disable the .out implicit pattern rule.  Prevents GNU make from
-+# adding bogus dependencies for the .out files listed above.
-+%.out: %
-+
-+check_PROGRAMS = \
-+	RBdemo
-+
-+RBdemo_SOURCES = RBdemo.c
-+
-+RB = \
-+	$(top_srcdir)/RBio/private/west0479.rua
-+
-+check-local: $(check_PROGRAMS) $(RB)
-+	./RBdemo < $(top_srcdir)/RBio/private/west0479.rua
-+
-+CLEANFILES = temp.rb
-diff --git a/Include/Makefile.am b/Include/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Include/Makefile.am
-@@ -0,0 +1 @@
-+pkginclude_HEADERS = RBio.h
-diff --git a/Makefile.am b/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Makefile.am
-@@ -0,0 +1,4 @@
-+SUBDIRS = Include Source RBio Demo Tcov
-+EXTRA_DIST = README.txt Doc/ChangeLog Doc/License.txt Doc/gpl.txt
-+
-+pkgconfig_DATA = rbio.pc
-diff --git a/RBio/Makefile.am b/RBio/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/RBio/Makefile.am
-@@ -0,0 +1,3 @@
-+SUBDIRS = private
-+dist_noinst_DATA = \
-+	mywest
-diff --git a/RBio/private/Makefile.am b/RBio/private/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/RBio/private/Makefile.am
-@@ -0,0 +1,7 @@
-+dist_noinst_DATA = \
-+	bcsstk01.rb \
-+	farm.rb \
-+	lap_25.pse \
-+	lap_25.rb \
-+	west0479.rb \
-+	west0479.rua
-diff --git a/Source/Makefile.am b/Source/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Source/Makefile.am
-@@ -0,0 +1,18 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
-+
-+RBIOSRC = \
-+	RBio.c
-+
-+lib_LTLIBRARIES = librbio.la
-+noinst_LTLIBRARIES = librbioi.la librbiol.la
-+
-+librbioi_la_SOURCES = $(RBIOSRC)
-+librbioi_la_LIBADD = $(SUITESPARSECONFIG_LIBS)
-+librbioi_la_CPPFLAGS = $(AM_CPPFLAGS) -DINT
-+
-+librbiol_la_SOURCES = $(RBIOSRC)
-+librbiol_la_LIBADD = $(SUITESPARSECONFIG_LIBS)
-+
-+librbio_la_SOURCES =
-+librbio_la_LIBADD = librbioi.la librbiol.la
-+librbio_la_LDFLAGS = -no-undefined -release $(PACKAGE_VERSION)
-diff --git a/Tcov/Makefile.am b/Tcov/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Tcov/Makefile.am
-@@ -0,0 +1,92 @@
-+AM_CC = gcc
-+AM_CFLAGS = -O0 -g --coverage
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
-+LDADD = $(SUITESPARSECONFIG_LIBS)
-+
-+dist_noinst_DATA = \
-+	matrices/Tina_DisCog.tar.gz \
-+	matrices/dwg961a.tar.gz \
-+	matrices/m4.rb \
-+	matrices/m4b.rb \
-+	matrices/mhd1280a.tar.gz \
-+	matrices/mhd1280b.tar.gz \
-+	matrices/plskz362.tar.gz \
-+	matrices/qc324.tar.gz \
-+	matrices/s4.rb \
-+	matrices/west0067.tar.gz \
-+	mangled/1.rb \
-+	mangled/2.rb \
-+	mangled/3.rb \
-+	mangled/4.rb \
-+	mangled/5.rb \
-+	mangled/6.rb \
-+	mangled/7.rb \
-+	mangled/8.rb \
-+	mangled/9.rb \
-+	mangled/10.rb \
-+	mangled/11.rb \
-+	mangled/12.rb \
-+	mangled/13.rb \
-+	mangled/14.rb \
-+	mangled/15.rb
-+
-+check_PROGRAMS = \
-+	RBdemo \
-+	RBtest
-+
-+RBdemo_SOURCES = $(top_srcdir)/Source/RBio.c $(top_srcdir)/Demo/RBdemo.c
-+RBtest_SOURCES = $(top_srcdir)/Source/RBio.c RBtest.c
-+
-+TAR = tar -O -xvvzf
-+
-+RB = \
-+	$(top_srcdir)/RBio/private/bcsstk01.rb \
-+	$(top_srcdir)/RBio/private/farm.rb \
-+	$(top_srcdir)/RBio/private/lap_25.pse \
-+	$(top_srcdir)/RBio/private/lap_25.rb \
-+	$(top_srcdir)/RBio/private/west0479.rb \
-+	$(top_srcdir)/RBio/private/west0479.rua \
-+	$(addprefix $(srcdir)/,$(dist_noinst_DATA))
-+
-+COV = \
-+	$(top_srcdir)/Source/RBio.c \
-+	$(top_srcdir)/Demo/RBdemo.c \
-+	$(srcdir)/RBtest.c
-+
-+check-local: $(check_PROGRAMS) $(RB) $(COV)
-+	-./RBdemo $(top_srcdir)/RBio/private/bcsstk01.rb
-+	-./RBdemo $(top_srcdir)/RBio/private/farm.rb
-+	-./RBdemo $(top_srcdir)/RBio/private/lap_25.pse
-+	-./RBdemo $(top_srcdir)/RBio/private/lap_25.rb
-+	-./RBdemo $(top_srcdir)/RBio/private/west0479.rb
-+	-./RBdemo $(top_srcdir)/RBio/private/west0479.rua
-+	-$(TAR) $(srcdir)/matrices/dwg961a.tar.gz  dwg961a/dwg961a.rb     | ./RBdemo
-+	-$(TAR) $(srcdir)/matrices/mhd1280a.tar.gz mhd1280a/mhd1280a.rb   | ./RBdemo
-+	-$(TAR) $(srcdir)/matrices/mhd1280b.tar.gz mhd1280b/mhd1280b.rb   | ./RBdemo
-+	-$(TAR) $(srcdir)/matrices/qc324.tar.gz    qc324/qc324.rb         | ./RBdemo
-+	-$(TAR) $(srcdir)/matrices/plskz362.tar.gz plskz362/plskz362.rb   | ./RBdemo
-+	-$(TAR) $(srcdir)/matrices/west0067.tar.gz west0067/west0067.rb   | ./RBdemo
-+	-$(TAR) $(srcdir)/matrices/Tina_DisCog.tar.gz Tina_DisCog/Tina_DisCog.rb | ./RBdemo
-+	-./RBdemo $(srcdir)/matrices/m4.rb
-+	-./RBdemo $(srcdir)/matrices/s4.rb
-+	-./RBdemo $(srcdir)/matrices/m4b.rb
-+	-./RBdemo $(srcdir)/mangled/1.rb
-+	-./RBdemo $(srcdir)/mangled/2.rb
-+	-./RBdemo $(srcdir)/mangled/3.rb
-+	-./RBdemo $(srcdir)/mangled/4.rb
-+	-./RBdemo $(srcdir)/mangled/5.rb
-+	-./RBdemo $(srcdir)/mangled/6.rb
-+	-./RBdemo $(srcdir)/mangled/7.rb
-+	-./RBdemo $(srcdir)/mangled/8.rb
-+	-./RBdemo $(srcdir)/mangled/9.rb
-+	-./RBdemo $(srcdir)/mangled/10.rb
-+	-./RBdemo $(srcdir)/mangled/11.rb
-+	-./RBdemo $(srcdir)/mangled/12.rb
-+	-./RBdemo $(srcdir)/mangled/13.rb
-+	-./RBdemo $(srcdir)/mangled/14.rb
-+	-./RBdemo $(srcdir)/mangled/15.rb
-+	-./RBtest
-+	-gcov -o $(builddir) $(COV) > gcov.out
-+	-grep -c "#####" RBio.c.gcov
-+
-+CLEANFILES = gcov.out *.gcov *.gcda *.gcno temp*.rb
-diff --git a/configure.ac b/configure.ac
-new file mode 100644
---- /dev/null
-+++ b/configure.ac
-@@ -0,0 +1,41 @@
-+#                                               -*- Autoconf -*-
-+# Process this file with autoconf to produce a configure script.
-+
-+AC_PREREQ([2.69])
-+AC_INIT([RBio],[2.2.6],[DrTimothyAldenDavis@gmail.com],[rbio],[http://www.suitesparse.com/])
-+AC_CONFIG_SRCDIR([Source/RBio.c])
-+AC_CONFIG_HEADERS([config.h])
-+AM_INIT_AUTOMAKE([foreign])
-+LT_INIT
-+
-+# Checks for programs.
-+PKG_PROG_PKG_CONFIG
-+AC_PROG_INSTALL
-+AC_PROG_CC
-+
-+AS_VAR_SET([LIBS_SAVED], [$LIBS])
-+
-+# Checks for libraries.
-+PKG_CHECK_MODULES([SUITESPARSECONFIG], [suitesparseconfig])
-+
-+# Checks for header files.
-+AC_CHECK_HEADERS([stddef.h stdlib.h string.h])
-+
-+# Checks for typedefs, structures, and compiler characteristics.
-+
-+# Checks for library functions.
-+
-+AS_VAR_SET([LIBS], [$LIBS_SAVED])
-+
-+PKG_INSTALLDIR
-+AC_CONFIG_FILES([
-+	rbio.pc
-+	Makefile
-+	Demo/Makefile
-+	Include/Makefile
-+	RBio/Makefile
-+	RBio/private/Makefile
-+	Source/Makefile
-+	Tcov/Makefile
-+])
-+AC_OUTPUT
-diff --git a/rbio.pc.in b/rbio.pc.in
-new file mode 100644
---- /dev/null
-+++ b/rbio.pc.in
-@@ -0,0 +1,12 @@
-+prefix=@prefix@
-+exec_prefix=@exec_prefix@
-+libdir=@libdir@
-+includedir=@includedir@
-+
-+Name: @PACKAGE_NAME@
-+Description: Toolbox for reading/writing sparse matrices in Rutherford/Boeing format
-+Version: @PACKAGE_VERSION@
-+URL: @PACKAGE_URL@
-+Requires.private: suitesparseconfig
-+Libs: -L${libdir} -lrbio
-+Cflags: -I${includedir}/rbio