academic/amd: BUILD bump for SuiteSparse 4.5.5.

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

4 files changed, 498 insertions, 219 deletions

diff --git a/academic/amd/amd.SlackBuild b/academic/amd/amd.SlackBuild
index 18dedf926b..c0a208f859 100644
--- a/academic/amd/amd.SlackBuild
+++ b/academic/amd/amd.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for AMD
 
-# 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=amd
 SRCNAM=SuiteSparse
 SUBDIR=AMD
 VERSION=${VERSION:-2.4.6}
-SRCVER=${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
 
 # Avoid rebuilding the docs.
@@ -90,8 +90,6 @@ touch Doc/AMD_UserGuide.pdf
   --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/amd/amd.info b/academic/amd/amd.info
index 7e00843fb8..6f006e064b 100644
--- a/academic/amd/amd.info
+++ b/academic/amd/amd.info
@@ -1,8 +1,8 @@
 PRGNAM="amd"
 VERSION="2.4.6"
 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="suitesparseconfig"
diff --git a/academic/amd/patches/autoconfiscate.diff b/academic/amd/patches/autoconfiscate.diff
new file mode 100644
index 0000000000..6cfcf4bf06
--- /dev/null
+++ b/academic/amd/patches/autoconfiscate.diff
@@ -0,0 +1,491 @@
+diff --git a/Demo/Makefile.am b/Demo/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Demo/Makefile.am
+@@ -0,0 +1,54 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
++LDADD = $(top_builddir)/Source/libamd.la
++
++EXTRA_DIST = \
++	amd_demo.out \
++	amd_demo2.out \
++	amd_l_demo.out \
++	amd_simple.out \
++	amd_f77cross.out \
++	amd_f77demo.out \
++	amd_f77simple.out
++
++# Disable the .out implicit pattern rule.  Prevents GNU make from
++# adding bogus dependencies for the .out files listed above.
++%.out: %
++
++check_PROGRAMS = \
++	amd_demo \
++	amd_demo2 \
++	amd_l_demo \
++	amd_simple \
++	amd_f77cross \
++	amd_f77demo \
++	amd_f77simple
++
++amd_demo_SOURCES = amd_demo.c
++amd_demo2_SOURCES = amd_demo2.c
++amd_l_demo_SOURCES = amd_l_demo.c
++amd_simple_SOURCES = amd_simple.c
++
++check_LTLIBRARIES = libamd_f77wrapper.la
++libamd_f77wrapper_la_SOURCES = amd_f77wrapper.c
++libamd_f77wrapper_la_LIBADD = $(top_builddir)/Source/libamd.la
++libamd_f77wrapper_la_CPPFLAGS = $(AM_CPPFLAGS) -DDINT
++
++amd_f77cross_SOURCES = amd_f77cross.f
++amd_f77cross_LDADD = libamd_f77wrapper.la
++amd_f77demo_SOURCES = amd_f77demo.f
++amd_f77demo_LDADD = $(top_builddir)/Source/libamdf77.la
++amd_f77simple_SOURCES = amd_f77simple.f
++amd_f77simple_LDADD = $(top_builddir)/Source/libamdf77.la
++
++check-local: $(check_PROGRAMS) $(check_PROGRAMS:=.out)
++	@for i in $(check_PROGRAMS); do \
++		echo "Testing $$i"; \
++		./$$i$(EXEEXT) > my_$$i.out; \
++		if diff -u $(srcdir)/$$i.out my_$$i.out; then \
++			echo "Test $$i PASSED."; \
++		else \
++			echo "Test $$i FAILED."; \
++		fi; \
++	done
++
++CLEANFILES = my_*.out
+diff --git a/Doc/Makefile.am b/Doc/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Doc/Makefile.am
+@@ -0,0 +1,27 @@
++EXTRA_DIST = ChangeLog License.txt lesser.txt
++
++dist_noinst_DATA = AMD_UserGuide.tex AMD_UserGuide.bib
++dist_pdf_DATA = AMD_UserGuide.pdf
++
++AMD_UserGuide.pdf AMD_UserGuide.aux: amd_h.tex
++.INTERMEDIATE: AMD_UserGuide.aux amd_h.tex
++
++%_h.tex: $(top_srcdir)/Include/%.h
++	echo '\begin{verbatim}' > $@
++	expand -8 $< >> $@
++	echo '\end{verbatim}' >> $@
++
++TEX = TEXINPUTS="$(srcdir):" pdflatex -interaction nonstopmode -file-line-error
++BIB = BIBINPUTS="$(srcdir):" bibtex
++%.pdf: %.tex %.bbl
++	$(TEX) $*
++	while grep -q "Rerun to get cross-references right" $*.log; do \
++		$(TEX) $*; \
++	done
++%.bbl: %.aux %.bib
++	$(BIB) $*
++%.aux: %.tex
++	$(TEX) $*
++
++CLEANFILES = *.aux *.bbl *.blg *.log *.toc *_h.tex
++MAINTAINERCLEANFILES = $(dist_pdf_DATA)
+diff --git a/Include/Makefile.am b/Include/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Include/Makefile.am
+@@ -0,0 +1 @@
++pkginclude_HEADERS = amd.h amd_internal.h
+diff --git a/Makefile.am b/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Makefile.am
+@@ -0,0 +1,9 @@
++ACLOCAL_AMFLAGS = -I m4
++
++SUBDIRS = Include Source Demo Doc
++EXTRA_DIST = README.txt
++
++pkgconfig_DATA = amd.pc
++
++CODE_COVERAGE_BRANCH_COVERAGE = 1
++@CODE_COVERAGE_RULES@
+diff --git a/Source/Makefile.am b/Source/Makefile.am
+new file mode 100644
+--- /dev/null
++++ b/Source/Makefile.am
+@@ -0,0 +1,35 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
++
++AMDSRC = \
++	amd_1.c \
++	amd_2.c \
++	amd_aat.c \
++	amd_control.c \
++	amd_defaults.c \
++	amd_dump.c \
++	amd_info.c \
++	amd_order.c \
++	amd_postorder.c \
++	amd_post_tree.c \
++	amd_preprocess.c \
++	amd_valid.c
++
++lib_LTLIBRARIES = libamd.la libamdf77.la
++noinst_LTLIBRARIES = libamdi.la libamdl.la
++
++libamdi_la_SOURCES = $(AMDSRC)
++libamdi_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -lm $(CODE_COVERAGE_LIBS)
++libamdi_la_CPPFLAGS = $(AM_CPPFLAGS) $(CODE_COVERAGE_CPPFLAGS) -DDINT
++libamdi_la_CFLAGS = $(AM_CFLAGS) $(CODE_COVERAGE_CFLAGS)
++
++libamdl_la_SOURCES = $(AMDSRC)
++libamdl_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -lm $(CODE_COVERAGE_LIBS)
++libamdl_la_CPPFLAGS = $(AM_CPPFLAGS) $(CODE_COVERAGE_CPPFLAGS) -DDLONG
++libamdl_la_CFLAGS = $(AM_CFLAGS) $(CODE_COVERAGE_CFLAGS)
++
++libamd_la_SOURCES =
++libamd_la_LIBADD = libamdl.la libamdi.la
++libamd_la_LDFLAGS = -no-undefined -release $(PACKAGE_VERSION)
++
++libamdf77_la_SOURCES = amd.f amdbar.f
++libamdf77_la_LDFLAGS = -no-undefined -release $(PACKAGE_VERSION)
+diff --git a/amd.pc.in b/amd.pc.in
+new file mode 100644
+--- /dev/null
++++ b/amd.pc.in
+@@ -0,0 +1,13 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: @PACKAGE_NAME@
++Description: Approximate minimum degree ordering
++Version: @PACKAGE_VERSION@
++URL: @PACKAGE_URL@
++Requires.private: suitesparseconfig
++Libs: -L${libdir} -lamd
++Libs.private: -lm
++Cflags: -I${includedir}/amd
+diff --git a/configure.ac b/configure.ac
+new file mode 100644
+--- /dev/null
++++ b/configure.ac
+@@ -0,0 +1,48 @@
++#                                               -*- Autoconf -*-
++# Process this file with autoconf to produce a configure script.
++
++AC_PREREQ([2.69])
++AC_INIT([AMD],[2.4.6],[DrTimothyAldenDavis@gmail.com],[amd],[http://www.suitesparse.com/])
++AC_CONFIG_SRCDIR([Source/amd_order.c])
++AC_CONFIG_AUX_DIR([build-aux])
++AC_CONFIG_MACRO_DIR([m4])
++AC_CONFIG_HEADERS([config.h])
++AM_INIT_AUTOMAKE([foreign])
++AM_SILENT_RULES([yes])
++LT_INIT([disable-static])
++
++# Checks for programs.
++PKG_PROG_PKG_CONFIG
++AC_PROG_INSTALL
++AC_PROG_CC
++AC_PROG_F77
++AX_CODE_COVERAGE
++
++AS_VAR_SET([LIBS_SAVED], [$LIBS])
++
++# Checks for libraries.
++AC_CHECK_LIB([m], [sqrt])
++
++PKG_CHECK_MODULES([SUITESPARSECONFIG], [suitesparseconfig])
++
++# 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_CHECK_FUNCS([sqrt])
++
++AS_VAR_SET([LIBS], [$LIBS_SAVED])
++
++PKG_INSTALLDIR
++AC_CONFIG_FILES([
++	amd.pc
++	Makefile
++	Demo/Makefile
++	Doc/Makefile
++	Include/Makefile
++	Source/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) $(CODE_COVERAGE_OUTPUT_DIRECTORY)
++
++A''M_DISTCHECK_CONFIGURE_FLAGS ?=
++A''M_DISTCHECK_CONFIGURE_FLAGS += --disable-code-coverage
++
++.PHONY: check-code-coverage code-coverage-capture code-coverage-capture-hook code-coverage-clean
++']
++
++	AC_SUBST([CODE_COVERAGE_RULES])
++	m4_ifdef([_AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE([CODE_COVERAGE_RULES])])
++])
diff --git a/academic/amd/patches/autotoolize.diff b/academic/amd/patches/autotoolize.diff
deleted file mode 100644
index a197808dbe..0000000000
--- a/academic/amd/patches/autotoolize.diff
+++ /dev/null
@@ -1,210 +0,0 @@
-diff --git a/Demo/Makefile.am b/Demo/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Demo/Makefile.am
-@@ -0,0 +1,53 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
-+LDADD = $(top_builddir)/Source/libamd.la
-+
-+EXTRA_DIST = \
-+	amd_demo.out \
-+	amd_demo2.out \
-+	amd_l_demo.out \
-+	amd_simple.out \
-+	amd_f77cross.out \
-+	amd_f77demo.out \
-+	amd_f77simple.out
-+
-+# Disable the .out implicit pattern rule.  Prevents GNU make from
-+# adding bogus dependencies for the .out files listed above.
-+%.out: %
-+
-+check_PROGRAMS = \
-+	amd_demo \
-+	amd_demo2 \
-+	amd_l_demo \
-+	amd_simple \
-+	amd_f77cross \
-+	amd_f77demo \
-+	amd_f77simple
-+
-+amd_demo_SOURCES = amd_demo.c
-+amd_demo2_SOURCES = amd_demo2.c
-+amd_l_demo_SOURCES = amd_l_demo.c
-+amd_simple_SOURCES = amd_simple.c
-+
-+check_LTLIBRARIES = libamd_f77wrapper.la
-+libamd_f77wrapper_la_SOURCES = amd_f77wrapper.c
-+libamd_f77wrapper_la_CPPFLAGS = $(AM_CPPFLAGS) -DDINT
-+
-+amd_f77cross_SOURCES = amd_f77cross.f
-+amd_f77cross_LDADD = $(LDADD) $(top_builddir)/Source/libamdf77.la libamd_f77wrapper.la
-+amd_f77demo_SOURCES = amd_f77demo.f
-+amd_f77demo_LDADD = $(LDADD) $(top_builddir)/Source/libamdf77.la
-+amd_f77simple_SOURCES = amd_f77simple.f
-+amd_f77simple_LDADD = $(LDADD) $(top_builddir)/Source/libamdf77.la
-+
-+check-local: $(check_PROGRAMS) $(check_PROGRAMS:=.out)
-+	@for i in $(check_PROGRAMS); do \
-+		echo "Testing $$i"; \
-+		./$$i$(EXEEXT) > my_$$i.out; \
-+		if diff -u $(srcdir)/$$i.out my_$$i.out; then \
-+			echo "Test $$i PASSED."; \
-+		else \
-+			echo "Test $$i FAILED."; \
-+		fi; \
-+	done
-+
-+CLEANFILES = my_*.out
-diff --git a/Doc/Makefile.am b/Doc/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Doc/Makefile.am
-@@ -0,0 +1,27 @@
-+EXTRA_DIST = ChangeLog License.txt lesser.txt
-+
-+dist_noinst_DATA = AMD_UserGuide.tex AMD_UserGuide.bib
-+dist_pdf_DATA = AMD_UserGuide.pdf
-+
-+AMD_UserGuide.pdf AMD_UserGuide.aux: amd_h.tex
-+.INTERMEDIATE: AMD_UserGuide.aux amd_h.tex
-+
-+%_h.tex: $(top_srcdir)/Include/%.h
-+	echo '\begin{verbatim}' > $@
-+	expand -8 $< >> $@
-+	echo '\end{verbatim}' >> $@
-+
-+TEX = TEXINPUTS="$(srcdir):" pdflatex -interaction nonstopmode -file-line-error
-+BIB = BIBINPUTS="$(srcdir):" bibtex
-+%.pdf: %.tex %.bbl
-+	$(TEX) $*
-+	while grep -q "Rerun to get cross-references right" $*.log; do \
-+		$(TEX) $*; \
-+	done
-+%.bbl: %.aux %.bib
-+	$(BIB) $*
-+%.aux: %.tex
-+	$(TEX) $*
-+
-+CLEANFILES = *.aux *.bbl *.blg *.log *.toc *_h.tex
-+MAINTAINERCLEANFILES = $(dist_pdf_DATA)
-diff --git a/Include/Makefile.am b/Include/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Include/Makefile.am
-@@ -0,0 +1 @@
-+pkginclude_HEADERS = amd.h amd_internal.h
-diff --git a/Makefile.am b/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Makefile.am
-@@ -0,0 +1,4 @@
-+SUBDIRS = Include Source Demo Doc
-+EXTRA_DIST = README.txt
-+
-+pkgconfig_DATA = amd.pc
-diff --git a/Source/Makefile.am b/Source/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Source/Makefile.am
-@@ -0,0 +1,33 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
-+
-+AMDSRC = \
-+	amd_1.c \
-+	amd_2.c \
-+	amd_aat.c \
-+	amd_control.c \
-+	amd_defaults.c \
-+	amd_dump.c \
-+	amd_info.c \
-+	amd_order.c \
-+	amd_postorder.c \
-+	amd_post_tree.c \
-+	amd_preprocess.c \
-+	amd_valid.c
-+
-+lib_LTLIBRARIES = libamd.la libamdf77.la
-+noinst_LTLIBRARIES = libamdi.la libamdl.la
-+
-+libamdi_la_SOURCES = $(AMDSRC)
-+libamdi_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -lm
-+libamdi_la_CPPFLAGS = $(AM_CPPFLAGS) -DDINT
-+
-+libamdl_la_SOURCES = $(AMDSRC)
-+libamdl_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -lm
-+libamdl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG
-+
-+libamd_la_SOURCES =
-+libamd_la_LIBADD = libamdl.la libamdi.la
-+libamd_la_LDFLAGS = -no-undefined -release $(PACKAGE_VERSION)
-+
-+libamdf77_la_SOURCES = amd.f amdbar.f
-+libamdf77_la_LDFLAGS = -no-undefined -release $(PACKAGE_VERSION)
-diff --git a/amd.pc.in b/amd.pc.in
-new file mode 100644
---- /dev/null
-+++ b/amd.pc.in
-@@ -0,0 +1,13 @@
-+prefix=@prefix@
-+exec_prefix=@exec_prefix@
-+libdir=@libdir@
-+includedir=@includedir@
-+
-+Name: @PACKAGE_NAME@
-+Description: Approximate minimum degree ordering
-+Version: @PACKAGE_VERSION@
-+URL: @PACKAGE_URL@
-+Requires.private: suitesparseconfig
-+Libs: -L${libdir} -lamd
-+Libs.private: -lm
-+Cflags: -I${includedir}/amd
-diff --git a/configure.ac b/configure.ac
-new file mode 100644
---- /dev/null
-+++ b/configure.ac
-@@ -0,0 +1,44 @@
-+#                                               -*- Autoconf -*-
-+# Process this file with autoconf to produce a configure script.
-+
-+AC_PREREQ([2.69])
-+AC_INIT([AMD],[2.4.6],[DrTimothyAldenDavis@gmail.com],[amd],[http://www.suitesparse.com/])
-+AC_CONFIG_SRCDIR([Source/amd_order.c])
-+AC_CONFIG_HEADERS([config.h])
-+AM_INIT_AUTOMAKE([foreign])
-+LT_INIT
-+
-+# Checks for programs.
-+PKG_PROG_PKG_CONFIG
-+AC_PROG_INSTALL
-+AC_PROG_CC
-+AC_PROG_F77
-+
-+AS_VAR_SET([LIBS_SAVED], [$LIBS])
-+
-+# Checks for libraries.
-+AC_CHECK_LIB([m], [sqrt])
-+
-+PKG_CHECK_MODULES([SUITESPARSECONFIG], [suitesparseconfig])
-+
-+# 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_CHECK_FUNCS([sqrt])
-+
-+AS_VAR_SET([LIBS], [$LIBS_SAVED])
-+
-+PKG_INSTALLDIR
-+AC_CONFIG_FILES([
-+	amd.pc
-+	Makefile
-+	Demo/Makefile
-+	Doc/Makefile
-+	Include/Makefile
-+	Source/Makefile
-+])
-+AC_OUTPUT