academic/cholmod: Updated for version 3.0.13.

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

3 files changed, 88 insertions, 81 deletions

diff --git a/academic/cholmod/cholmod.SlackBuild b/academic/cholmod/cholmod.SlackBuild
index 042346c4711e0..2116fba3e4c6b 100644
--- a/academic/cholmod/cholmod.SlackBuild
+++ b/academic/cholmod/cholmod.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for CHOLMOD
 
-# Copyright 2013-2018 Kyle Guinn <elyk03@gmail.com>, USA
+# Copyright 2013-2019 Kyle Guinn <elyk03@gmail.com>
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -25,8 +25,8 @@
 PRGNAM=cholmod
 SRCNAM=SuiteSparse
 SUBDIR=CHOLMOD
-VERSION=${VERSION:-3.0.12}
-SRCVER=${SRCVER:-5.2.0}
+VERSION=${VERSION:-3.0.13}
+SRCVER=${SRCVER:-5.4.0}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
diff --git a/academic/cholmod/cholmod.info b/academic/cholmod/cholmod.info
index 585dddc05417f..954e244269117 100644
--- a/academic/cholmod/cholmod.info
+++ b/academic/cholmod/cholmod.info
@@ -1,8 +1,8 @@
 PRGNAM="cholmod"
-VERSION="3.0.12"
+VERSION="3.0.13"
 HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html"
-DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.2.0.tar.gz"
-MD5SUM="8e625539dbeed061cc62fbdfed9be7cf"
+DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz"
+MD5SUM="4a6d4e74fc44c503f52996ae95cad03a"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="blas lapack suitesparseconfig amd camd colamd ccolamd"
diff --git a/academic/cholmod/patches/autoconfiscate.diff b/academic/cholmod/patches/autoconfiscate.diff
index dd9746043caac..66a831b846c03 100644
--- a/academic/cholmod/patches/autoconfiscate.diff
+++ b/academic/cholmod/patches/autoconfiscate.diff
@@ -1469,7 +1469,7 @@ new file mode 100644
 +# Process this file with autoconf to produce a configure script.
 +
 +AC_PREREQ([2.69])
-+AC_INIT([CHOLMOD],[3.0.12],[DrTimothyAldenDavis@gmail.com],[cholmod],[http://www.suitesparse.com/])
++AC_INIT([CHOLMOD],[3.0.13],[DrTimothyAldenDavis@gmail.com],[cholmod],[http://www.suitesparse.com/])
 +AC_CONFIG_SRCDIR([Core/cholmod_common.c])
 +AC_CONFIG_AUX_DIR([build-aux])
 +AC_CONFIG_MACRO_DIR([m4])
@@ -1666,7 +1666,7 @@ new file mode 100644
 +
 +AC_SUBST([CHOLMOD_REQUIRES])
 +
-+PKG_INSTALLDIR
++m4_ifdef([PKG_INSTALLDIR], [PKG_INSTALLDIR], [AC_SUBST([pkgconfigdir], [${libdir}/pkgconfig])])
 +AC_CONFIG_FILES([
 +	cholmod.pc
 +	Makefile
@@ -1756,11 +1756,11 @@ new file mode 100644
 +#   modified version of the Autoconf Macro, you may extend this special
 +#   exception to the GPL to apply to your modified version as well.
 +
-+#serial 15
++#serial 16
 +
 +AU_ALIAS([ACX_BLAS], [AX_BLAS])
 +AC_DEFUN([AX_BLAS], [
-+AC_PREREQ(2.50)
++AC_PREREQ([2.55])
 +AC_REQUIRE([AC_F77_LIBRARY_LDFLAGS])
 +AC_REQUIRE([AC_CANONICAL_HOST])
 +ax_blas_ok=no
@@ -1786,7 +1786,7 @@ new file mode 100644
 +if test "x$BLAS_LIBS" != x; then
 +	save_LIBS="$LIBS"; LIBS="$BLAS_LIBS $LIBS"
 +	AC_MSG_CHECKING([for $sgemm in $BLAS_LIBS])
-+	AC_TRY_LINK_FUNC($sgemm, [ax_blas_ok=yes], [BLAS_LIBS=""])
++	AC_LINK_IFELSE([AC_LANG_CALL([], [$sgemm])], [ax_blas_ok=yes], [BLAS_LIBS=""])
 +	AC_MSG_RESULT($ax_blas_ok)
 +	LIBS="$save_LIBS"
 +fi
@@ -1796,7 +1796,7 @@ new file mode 100644
 +if test $ax_blas_ok = no; then
 +	save_LIBS="$LIBS"; LIBS="$LIBS"
 +	AC_MSG_CHECKING([if $sgemm is being linked in already])
-+	AC_TRY_LINK_FUNC($sgemm, [ax_blas_ok=yes])
++	AC_LINK_IFELSE([AC_LANG_CALL([], [$sgemm])], [ax_blas_ok=yes])
 +	AC_MSG_RESULT($ax_blas_ok)
 +	LIBS="$save_LIBS"
 +fi
@@ -1867,7 +1867,7 @@ new file mode 100644
 +if test $ax_blas_ok = no; then
 +	save_LIBS="$LIBS"; LIBS="-framework vecLib $LIBS"
 +	AC_MSG_CHECKING([for $sgemm in -framework vecLib])
-+	AC_TRY_LINK_FUNC($sgemm, [ax_blas_ok=yes;BLAS_LIBS="-framework vecLib"])
++	AC_LINK_IFELSE([AC_LANG_CALL([], [$sgemm])], [ax_blas_ok=yes;BLAS_LIBS="-framework vecLib"])
 +	AC_MSG_RESULT($ax_blas_ok)
 +	LIBS="$save_LIBS"
 +fi
@@ -1933,7 +1933,7 @@ diff --git a/m4/ax_code_coverage.m4 b/m4/ax_code_coverage.m4
 new file mode 100644
 --- /dev/null
 +++ b/m4/ax_code_coverage.m4
-@@ -0,0 +1,264 @@
+@@ -0,0 +1,271 @@
 +# ===========================================================================
 +#     https://www.gnu.org/software/autoconf-archive/ax_code_coverage.html
 +# ===========================================================================
@@ -2011,68 +2011,48 @@ new file mode 100644
 +#   You should have received a copy of the GNU Lesser General Public License
 +#   along with this program. If not, see <https://www.gnu.org/licenses/>.
 +
-+#serial 24
++#serial 27
 +
-+AC_DEFUN([AX_CODE_COVERAGE],[
-+	dnl Check for --enable-code-coverage
-+	AC_REQUIRE([AC_PROG_SED])
++AC_DEFUN([_AX_CODE_COVERAGE_ENABLED],[
++	# check for gcov
++	AC_CHECK_TOOL([GCOV],
++		  [$_AX_CODE_COVERAGE_GCOV_PROG_WITH],
++		  [:])
++	AS_IF([test "X$GCOV" = "X:"],
++	      [AC_MSG_ERROR([gcov is needed to do coverage])])
++	AC_SUBST([GCOV])
 +
-+	# allow to override gcov location
-+	AC_ARG_WITH([gcov],
-+	  [AS_HELP_STRING([--with-gcov[=GCOV]], [use given GCOV for coverage (GCOV=gcov).])],
-+	  [_AX_CODE_COVERAGE_GCOV_PROG_WITH=$with_gcov],
-+	  [_AX_CODE_COVERAGE_GCOV_PROG_WITH=gcov])
++	dnl Check if gcc is being used
++	AS_IF([ test "$GCC" = "no" ], [
++		AC_MSG_ERROR([not compiling with gcc, which is required for gcov code coverage])
++	      ])
 +
-+	AC_MSG_CHECKING([whether to build with code coverage support])
-+	AC_ARG_ENABLE([code-coverage],
-+	  AS_HELP_STRING([--enable-code-coverage],
-+	  [Whether to enable code coverage support]),,
-+	  enable_code_coverage=no)
++	AC_CHECK_PROG([LCOV], [lcov], [lcov])
++	AC_CHECK_PROG([GENHTML], [genhtml], [genhtml])
 +
-+	AM_CONDITIONAL([CODE_COVERAGE_ENABLED], [test x$enable_code_coverage = xyes])
-+	AC_SUBST([CODE_COVERAGE_ENABLED], [$enable_code_coverage])
-+	AC_MSG_RESULT($enable_code_coverage)
++	AS_IF([ test x"$LCOV" = x ], [
++		AC_MSG_ERROR([To enable code coverage reporting you must have lcov installed])
++	      ])
 +
-+	AS_IF([ test "$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='
++	AS_IF([ test x"$GENHTML" = x ], [
++		AC_MSG_ERROR([Could not find genhtml from the lcov package])
++	])
++
++	dnl Build the code coverage flags
++	dnl Define CODE_COVERAGE_LDFLAGS for backwards compatibility
++	CODE_COVERAGE_CPPFLAGS="-DNDEBUG"
++	CODE_COVERAGE_CFLAGS="-O0 -g -fprofile-arcs -ftest-coverage"
++	CODE_COVERAGE_CXXFLAGS="-O0 -g -fprofile-arcs -ftest-coverage"
++	CODE_COVERAGE_LIBS="-lgcov"
++	CODE_COVERAGE_LDFLAGS="$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
 +']
@@ -2091,12 +2071,39 @@ new file mode 100644
 +	-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='
++])
++
++AC_DEFUN([_AX_CODE_COVERAGE_DISABLED],[
++   [CODE_COVERAGE_RULES_CHECK='
 +	@echo "Need to reconfigure with --enable-code-coverage"
-+']
-+		CODE_COVERAGE_RULES_CAPTURE="$CODE_COVERAGE_RULES_CHECK"
-+		CODE_COVERAGE_RULES_CLEAN=''
++   ']
++   CODE_COVERAGE_RULES_CAPTURE="$CODE_COVERAGE_RULES_CHECK"
++   CODE_COVERAGE_RULES_CLEAN=''
++])
++
++AC_DEFUN([AX_CODE_COVERAGE],[
++	dnl Check for --enable-code-coverage
++
++	# 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 "x$enable_code_coverage" = xyes ], [
++		_AX_CODE_COVERAGE_ENABLED
++	      ], [
++		_AX_CODE_COVERAGE_DISABLED
 +	])
 +
 +[CODE_COVERAGE_RULES='
@@ -2157,6 +2164,9 @@ new file mode 100644
 +CODE_COVERAGE_GENHTML_OPTIONS ?= $(CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT)
 +CODE_COVERAGE_IGNORE_PATTERN ?=
 +
++GITIGNOREFILES ?=
++GITIGNOREFILES += $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_OUTPUT_DIRECTORY)
++
 +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"\
@@ -2186,9 +2196,6 @@ new file mode 100644
 +
 +'"$CODE_COVERAGE_RULES_CLEAN"'
 +
-+GITIGNOREFILES ?=
-+GITIGNOREFILES += $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_OUTPUT_DIRECTORY)
-+
 +A''M_DISTCHECK_CONFIGURE_FLAGS ?=
 +A''M_DISTCHECK_CONFIGURE_FLAGS += --disable-code-coverage
 +
@@ -2269,7 +2276,7 @@ new file mode 100644
 +#   modified version of the Autoconf Macro, you may extend this special
 +#   exception to the GPL to apply to your modified version as well.
 +
-+#serial 8
++#serial 9
 +
 +AU_ALIAS([ACX_LAPACK], [AX_LAPACK])
 +AC_DEFUN([AX_LAPACK], [
@@ -2298,7 +2305,7 @@ new file mode 100644
 +if test "x$LAPACK_LIBS" != x; then
 +        save_LIBS="$LIBS"; LIBS="$LAPACK_LIBS $BLAS_LIBS $LIBS $FLIBS"
 +        AC_MSG_CHECKING([for $cheev in $LAPACK_LIBS])
-+        AC_TRY_LINK_FUNC($cheev, [ax_lapack_ok=yes], [LAPACK_LIBS=""])
++        AC_LINK_IFELSE([AC_LANG_CALL([], [$cheev])], [ax_lapack_ok=yes], [LAPACK_LIBS=""])
 +        AC_MSG_RESULT($ax_lapack_ok)
 +        LIBS="$save_LIBS"
 +        if test $ax_lapack_ok = no; then