libraries/CHOLMOD: Updated for version 2.1.2.

Signed-off-by: Robby Workman <rworkman@slackbuilds.org>

5 files changed, 941 insertions, 508 deletions

diff --git a/libraries/CHOLMOD/CHOLMOD.SlackBuild b/libraries/CHOLMOD/CHOLMOD.SlackBuild
index 3de7305a20553..1475bce85253c 100644
--- a/libraries/CHOLMOD/CHOLMOD.SlackBuild
+++ b/libraries/CHOLMOD/CHOLMOD.SlackBuild
@@ -1,10 +1,29 @@
 #!/bin/sh
 
 # Slackware build script for CHOLMOD
-# Written by Kyle Guinn <elyk03@gmail.com>
+
+# Copyright 2013 Kyle Guinn <elyk03@gmail.com>, USA
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
+# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=CHOLMOD
-VERSION=${VERSION:-1.7.3}
+VERSION=${VERSION:-2.1.2}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -57,10 +76,7 @@ find -L . \
  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
 patch -p1 < $CWD/autotoolize.diff
-if [ -e Include/cholmod_config.h ]; then
-  # patch can't handle git-diff renames
-  mv Include/cholmod_config.h Include/cholmod_config.h.in
-fi
+patch -p1 < $CWD/atlas-threaded-blas.diff
 autoreconf -vif
 
 CFLAGS="$SLKCFLAGS" \
@@ -75,9 +91,11 @@ FFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION \
   --enable-shared \
   --disable-static \
+  --disable-dependency-tracking \
   --build=$ARCH-slackware-linux
 
 make
+make check
 make install-strip DESTDIR=$PKG
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
diff --git a/libraries/CHOLMOD/CHOLMOD.info b/libraries/CHOLMOD/CHOLMOD.info
index 5fb7d0e8c7ed6..8551cb3ca1c4c 100644
--- a/libraries/CHOLMOD/CHOLMOD.info
+++ b/libraries/CHOLMOD/CHOLMOD.info
@@ -1,10 +1,10 @@
 PRGNAM="CHOLMOD"
-VERSION="1.7.3"
-HOMEPAGE="http://www.cise.ufl.edu/research/sparse/cholmod/"
-DOWNLOAD="http://www.cise.ufl.edu/research/sparse/cholmod/CHOLMOD-1.7.3.tar.gz"
-MD5SUM="e3bcfeefe40a2f3ef712e1bd3ec36781"
+VERSION="2.1.2"
+HOMEPAGE="https://www.cise.ufl.edu/research/sparse/cholmod/"
+DOWNLOAD="https://www.cise.ufl.edu/research/sparse/cholmod/CHOLMOD-2.1.2.tar.gz"
+MD5SUM="0c55ade78bb1b1f1e7b6a6cba024f70d"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
-REQUIRES="AMD CAMD CCOLAMD COLAMD lapack metis"
+REQUIRES="%README% blas lapack SuiteSparse_config AMD CAMD COLAMD CCOLAMD"
 MAINTAINER="Kyle Guinn"
 EMAIL="elyk03@gmail.com"
diff --git a/libraries/CHOLMOD/README b/libraries/CHOLMOD/README
index 70df366576a27..ebbb152bc38aa 100644
--- a/libraries/CHOLMOD/README
+++ b/libraries/CHOLMOD/README
@@ -2,3 +2,5 @@ CHOLMOD is a set of ANSI C routines for sparse Cholesky factorization and
 update/downdate.
 
 This package is part of SuiteSparse.
+
+metis is an optional dependency and will be used if found.
diff --git a/libraries/CHOLMOD/atlas-threaded-blas.diff b/libraries/CHOLMOD/atlas-threaded-blas.diff
new file mode 100644
index 0000000000000..e7f34ef011e3a
--- /dev/null
+++ b/libraries/CHOLMOD/atlas-threaded-blas.diff
@@ -0,0 +1,26 @@
+diff --git a/ax_blas.m4 b/ax_blas.m4
+--- a/ax_blas.m4
++++ b/ax_blas.m4
+@@ -117,12 +117,16 @@
+ # BLAS in ATLAS library? (http://math-atlas.sourceforge.net/)
+ if test $ax_blas_ok = no; then
+ 	AC_CHECK_LIB(atlas, ATL_xerbla,
+-		[AC_CHECK_LIB(f77blas, $sgemm,
+-		[AC_CHECK_LIB(cblas, cblas_dgemm,
+-			[ax_blas_ok=yes
+-			 BLAS_LIBS="-lcblas -lf77blas -latlas"],
+-			[], [-lf77blas -latlas])],
+-			[], [-latlas])])
++		[AC_CHECK_LIB(ptf77blas, $sgemm,
++			[AC_CHECK_LIB(ptcblas, cblas_dgemm,
++				[ax_blas_ok=yes; BLAS_LIBS="-lptcblas -lptf77blas -latlas"],,
++				[-lptf77blas -latlas])],
++			[AC_CHECK_LIB(f77blas, $sgemm,
++				[AC_CHECK_LIB(cblas, cblas_dgemm,
++					[ax_blas_ok=yes; BLAS_LIBS="-lcblas -lf77blas -latlas"],,
++					[-lf77blas -latlas])],,
++				[-latlas])],
++			[-latlas])])
+ fi
+ 
+ # BLAS in PhiPACK libraries? (requires generic BLAS lib, too)
diff --git a/libraries/CHOLMOD/autotoolize.diff b/libraries/CHOLMOD/autotoolize.diff
index 3bb7f6c8ebadd..5e93cf2f1cb29 100644
--- a/libraries/CHOLMOD/autotoolize.diff
+++ b/libraries/CHOLMOD/autotoolize.diff
@@ -3,7 +3,7 @@ new file mode 100644
 --- /dev/null
 +++ b/Check/Makefile.am
 @@ -0,0 +1,24 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(UFCONFIG_CFLAGS)
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
 +
 +EXTRA_DIST = \
 +	License.txt \
@@ -32,7 +32,7 @@ new file mode 100644
 --- /dev/null
 +++ b/Cholesky/Makefile.am
 @@ -0,0 +1,41 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(COLAMD_CFLAGS) $(AMD_CFLAGS) $(UFCONFIG_CFLAGS)
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(COLAMD_CFLAGS) $(AMD_CFLAGS) $(SUITESPARSECONFIG_CFLAGS)
 +
 +EXTRA_DIST = \
 +	License.txt \
@@ -77,8 +77,8 @@ diff --git a/Core/Makefile.am b/Core/Makefile.am
 new file mode 100644
 --- /dev/null
 +++ b/Core/Makefile.am
-@@ -0,0 +1,43 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(UFCONFIG_CFLAGS)
+@@ -0,0 +1,44 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
 +
 +EXTRA_DIST = \
 +	License.txt \
@@ -98,7 +98,8 @@ new file mode 100644
 +	cholmod_memory.c \
 +	cholmod_sparse.c \
 +	cholmod_transpose.c \
-+	cholmod_triplet.c
++	cholmod_triplet.c \
++	cholmod_version.c
 +
 +noinst_HEADERS = \
 +	t_cholmod_change_factor.c \
@@ -125,13 +126,12 @@ diff --git a/Demo/Makefile.am b/Demo/Makefile.am
 new file mode 100644
 --- /dev/null
 +++ b/Demo/Makefile.am
-@@ -0,0 +1,51 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(UFCONFIG_CFLAGS)
+@@ -0,0 +1,60 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
 +
 +EXTRA_DIST = \
 +	License.txt \
-+	gpl.txt \
-+	make.out
++	gpl.txt
 +
 +dist_noinst_HEADERS = \
 +	cholmod_demo.h
@@ -142,46 +142,56 @@ new file mode 100644
 +	Matrix/can___24.mtx \
 +	Matrix/c.tri
 +
-+check_PROGRAMS = \
-+	cholmod_demo \
-+	cholmod_l_demo \
-+	cholmod_simple
-+
 +noinst_PROGRAMS = \
 +	reade \
 +	readhb \
 +	readhb2
 +
++reade_SOURCES = reade.f
++readhb_SOURCES = readhb.f
++readhb2_SOURCES = readhb2.f
++
++if MOD_CHOLESKY
++if MOD_CHECK
++if MOD_MATRIXOPS
++
++check_PROGRAMS = \
++	cholmod_demo \
++	cholmod_l_demo \
++	cholmod_simple
++
 +cholmod_demo_SOURCES = cholmod_demo.c
-+cholmod_demo_LDADD = $(top_builddir)/libcholmod.la
++cholmod_demo_LDADD = $(top_builddir)/libcholmod.la $(SUITESPARSECONFIG_LIBS)
 +
 +cholmod_l_demo_SOURCES = cholmod_l_demo.c
-+cholmod_l_demo_LDADD = $(top_builddir)/libcholmod.la
++cholmod_l_demo_LDADD = $(top_builddir)/libcholmod.la $(SUITESPARSECONFIG_LIBS)
 +
 +cholmod_simple_SOURCES = cholmod_simple.c
 +cholmod_simple_LDADD = $(top_builddir)/libcholmod.la
 +
-+reade_SOURCES = reade.f
-+readhb_SOURCES = readhb.f
-+readhb2_SOURCES = readhb2.f
-+
 +check-local: $(check_PROGRAMS) $(dist_noinst_DATA)
-+	./cholmod_demo < Matrix/bcsstk01.tri
-+	./cholmod_l_demo < Matrix/bcsstk01.tri
-+	./cholmod_demo < Matrix/lp_afiro.tri
-+	./cholmod_l_demo < Matrix/lp_afiro.tri
-+	./cholmod_demo < Matrix/can___24.mtx
-+	./cholmod_l_demo < Matrix/can___24.mtx
-+	./cholmod_demo < Matrix/c.tri
-+	./cholmod_l_demo < Matrix/c.tri
-+	./cholmod_simple < Matrix/c.tri
-+	./cholmod_simple < Matrix/can___24.mtx
-+	./cholmod_simple < Matrix/bcsstk01.tri
++	./cholmod_demo < $(srcdir)/Matrix/bcsstk01.tri
++	./cholmod_l_demo < $(srcdir)/Matrix/bcsstk01.tri
++	./cholmod_demo < $(srcdir)/Matrix/lp_afiro.tri
++	./cholmod_l_demo < $(srcdir)/Matrix/lp_afiro.tri
++	./cholmod_demo < $(srcdir)/Matrix/can___24.mtx
++	./cholmod_l_demo < $(srcdir)/Matrix/can___24.mtx
++	./cholmod_demo < $(srcdir)/Matrix/c.tri
++	./cholmod_l_demo < $(srcdir)/Matrix/c.tri
++	./cholmod_simple < $(srcdir)/Matrix/c.tri
++	./cholmod_simple < $(srcdir)/Matrix/can___24.mtx
++	./cholmod_simple < $(srcdir)/Matrix/bcsstk01.tri
++
++endif
++endif
++endif
++
++CLEANFILES = timelog.m
 diff --git a/Doc/Makefile.am b/Doc/Makefile.am
 new file mode 100644
 --- /dev/null
 +++ b/Doc/Makefile.am
-@@ -0,0 +1,235 @@
+@@ -0,0 +1,436 @@
 +EXTRA_DIST = \
 +	ChangeLog
 +
@@ -195,228 +205,429 @@ new file mode 100644
 +	mfile.awk \
 +	rule.awk
 +
-+pdf_DATA = \
++dist_pdf_DATA = \
 +	UserGuide.pdf
 +
 +dist_noinst_SCRIPTS = \
 +	getmproto \
 +	getproto
 +
-+PROTO_C = \
-+	../Demo/cholmod_simple.c
-+
-+PROTO_H = \
-+	../Include/cholmod.h \
-+	../Include/cholmod_blas.h \
-+	../Include/cholmod_check.h \
-+	../Include/cholmod_cholesky.h \
-+	../Include/cholmod_complexity.h \
-+	../Include/cholmod_config.h \
-+	../Include/cholmod_core.h \
-+	../Include/cholmod_internal.h \
-+	../Include/cholmod_matrixops.h \
-+	../Include/cholmod_modify.h \
-+	../Include/cholmod_partition.h \
-+	../Include/cholmod_supernodal.h \
-+	../Include/cholmod_template.h
++# ./getmproto file.m > _file_m.tex
++define getmproto =
++( \
++cat $(srcdir)/mheader.tex; \
++expand -8 $< | awk -f $(srcdir)/mfile.awk; \
++cat $(srcdir)/mfooter.tex; \
++) > $@
++endef
++
++# ./getproto 'proto' header.h > _file.tex
++define getproto =
++( \
++echo -n $(PATTERN); \
++cat $(srcdir)/rule.awk; \
++) > $(basename $@).awk
++( \
++cat $(srcdir)/header.tex; \
++expand -8 $< | awk -f $(basename $@).awk; \
++cat $(srcdir)/footer.tex; \
++) > $@
++$(RM) $(basename $@).awk
++endef
 +
 +PROTO_M = \
-+	../MATLAB/analyze.m \
-+	../MATLAB/bisect.m \
-+	../MATLAB/chol2.m \
-+	../MATLAB/cholmod2.m \
-+	../MATLAB/cholmod_demo.m \
-+	../MATLAB/cholmod_make.m \
-+	../MATLAB/etree2.m \
-+	../MATLAB/graph_demo.m \
-+	../MATLAB/lchol.m \
-+	../MATLAB/ldl_normest.m \
-+	../MATLAB/ldlchol.m \
-+	../MATLAB/ldlsolve.m \
-+	../MATLAB/ldlsplit.m \
-+	../MATLAB/ldlupdate.m \
-+	../MATLAB/metis.m \
-+	../MATLAB/mread.m \
-+	../MATLAB/mwrite.m \
-+	../MATLAB/nesdis.m \
-+	../MATLAB/resymbol.m \
-+	../MATLAB/sdmult.m \
-+	../MATLAB/sparse2.m \
-+	../MATLAB/spsym.m \
-+	../MATLAB/symbfact2.m
-+
-+UserGuide.pdf: $(dist_noinst_DATA) $(dist_noinst_SCRIPTS) $(PROTO_C) $(PROTO_H) $(PROTO_M)
-+	./getmproto ../MATLAB/analyze.m > _analyze_m.tex
-+	./getmproto ../MATLAB/bisect.m > _bisect_m.tex
-+	./getmproto ../MATLAB/chol2.m > _chol2_m.tex
-+	./getmproto ../MATLAB/cholmod2.m > _cholmod2_m.tex
-+	./getmproto ../MATLAB/cholmod_demo.m > _cholmod_demo_m.tex
-+	./getmproto ../MATLAB/cholmod_make.m > _cholmod_make_m.tex
-+	./getmproto ../MATLAB/etree2.m > _etree2_m.tex
-+	./getmproto ../MATLAB/graph_demo.m > _graph_demo_m.tex
-+	./getmproto ../MATLAB/lchol.m > _lchol_m.tex
-+	./getmproto ../MATLAB/ldl_normest.m > _ldl_normest_m.tex
-+	./getmproto ../MATLAB/ldlchol.m > _ldlchol_m.tex
-+	./getmproto ../MATLAB/ldlsolve.m > _ldlsolve_m.tex
-+	./getmproto ../MATLAB/ldlsplit.m > _ldlsplit_m.tex
-+	./getmproto ../MATLAB/ldlupdate.m > _ldlupdate_m.tex
-+	./getmproto ../MATLAB/metis.m > _metis_m.tex
-+	./getmproto ../MATLAB/mread.m > _mread_m.tex
-+	./getmproto ../MATLAB/mwrite.m > _mwrite_m.tex
-+	./getmproto ../MATLAB/nesdis.m > _nesdis_m.tex
-+	./getmproto ../MATLAB/resymbol.m > _resymbol_m.tex
-+	./getmproto ../MATLAB/sdmult.m > _sdmult_m.tex
-+	./getmproto ../MATLAB/sparse2.m > _sparse2_m.tex
-+	./getmproto ../MATLAB/spsym.m > _spsym_m.tex
-+	./getmproto ../MATLAB/symbfact2.m > _symbfact2_m.tex
-+	./getproto '/include/, /^}/' ../Demo/cholmod_simple.c > _simple.tex
-+	./getproto '/typedef struct cholmod_common/, /^}/' ../Include/cholmod_core.h > _common.tex
-+	./getproto '/int cholmod_start/, /\*\) ;/' ../Include/cholmod_core.h > _start.tex
-+	./getproto '/int cholmod_finish/, /\*\) ;/' ../Include/cholmod_core.h > _finish.tex
-+	./getproto '/int cholmod_defaults/, /\*\) ;/' ../Include/cholmod_core.h > _defaults.tex
-+	./getproto '/size_t cholmod_maxrank/, /\*\) ;/' ../Include/cholmod_core.h > _maxrank.tex
-+	./getproto '/int cholmod_allocate_work/, /\*\) ;/' ../Include/cholmod_core.h > _allocate_work.tex
-+	./getproto '/int cholmod_free_work/, /\*\) ;/' ../Include/cholmod_core.h > _free_work.tex
-+	./getproto '/long cholmod_clear_flag/, /\*\) ;/' ../Include/cholmod_core.h > _clear_flag.tex
-+	./getproto '/int cholmod_error/, /\*\) ;/' ../Include/cholmod_core.h > _error.tex
-+	./getproto '/double cholmod_dbound/, /\*\) ;/' ../Include/cholmod_core.h > _dbound.tex
-+	./getproto '/double cholmod_hypot/, /double\) ;/' ../Include/cholmod_core.h > _hypot.tex
-+	./getproto '/int cholmod_divcomplex/, /\*\) ;/' ../Include/cholmod_core.h > _divcomplex.tex
-+	./getproto '/typedef struct cholmod_sparse/, /^}/' ../Include/cholmod_core.h > _sparse.tex
-+	./getproto '/cholmod_sparse \*cholmod_allocate_sparse/, /\*\) ;/' ../Include/cholmod_core.h > _allocate_sparse.tex
-+	./getproto '/int cholmod_free_sparse/, /\*\) ;/' ../Include/cholmod_core.h > _free_sparse.tex
-+	./getproto '/int cholmod_reallocate_sparse/, /\*\) ;/' ../Include/cholmod_core.h > _reallocate_sparse.tex
-+	./getproto '/long cholmod_nnz/, /\*\) ;/' ../Include/cholmod_core.h > _nnz.tex
-+	./getproto '/cholmod_sparse \*cholmod_speye/, /\*\) ;/' ../Include/cholmod_core.h > _speye.tex
-+	./getproto '/cholmod_sparse \*cholmod_spzeros/, /\*\) ;/' ../Include/cholmod_core.h > _spzeros.tex
-+	./getproto '/cholmod_sparse \*cholmod_transpose/, /\*\) ;/' ../Include/cholmod_core.h > _transpose.tex
-+	./getproto '/int cholmod_transpose_unsym/, /\*\) ;/' ../Include/cholmod_core.h > _transpose_unsym.tex
-+	./getproto '/int cholmod_transpose_sym/, /\*\) ;/' ../Include/cholmod_core.h > _transpose_sym.tex
-+	./getproto '/cholmod_sparse \*cholmod_ptranspose/, /\*\) ;/' ../Include/cholmod_core.h > _ptranspose.tex
-+	./getproto '/int cholmod_sort/, /\*\) ;/' ../Include/cholmod_core.h > _sort.tex
-+	./getproto '/cholmod_sparse \*cholmod_band/, /\*\) ;/' ../Include/cholmod_core.h > _band.tex
-+	./getproto '/int cholmod_band_inplace/, /\*\) ;/' ../Include/cholmod_core.h > _band_inplace.tex
-+	./getproto '/cholmod_sparse \*cholmod_aat/, /\*\) ;/' ../Include/cholmod_core.h > _aat.tex
-+	./getproto '/cholmod_sparse \*cholmod_copy_sparse/, /\*\) ;/' ../Include/cholmod_core.h > _copy_sparse.tex
-+	./getproto '/cholmod_sparse \*cholmod_copy /, /\*\) ;/' ../Include/cholmod_core.h > _copy.tex
-+	./getproto '/cholmod_sparse \*cholmod_add/, /\*\) ;/' ../Include/cholmod_core.h > _add.tex
-+	./getproto '/int cholmod_sparse_xtype/, /\*\) ;/' ../Include/cholmod_core.h > _sparse_xtype.tex
-+	./getproto '/typedef struct cholmod_factor/, /^}/' ../Include/cholmod_core.h > _factor.tex
-+	./getproto '/cholmod_factor \*cholmod_allocate_factor/, /\*\) ;/' ../Include/cholmod_core.h > _allocate_factor.tex
-+	./getproto '/int cholmod_free_factor/, /\*\) ;/' ../Include/cholmod_core.h > _free_factor.tex
-+	./getproto '/int cholmod_reallocate_factor/, /\*\) ;/' ../Include/cholmod_core.h > _reallocate_factor.tex
-+	./getproto '/int cholmod_change_factor/, /\*\) ;/' ../Include/cholmod_core.h > _change_factor.tex
-+	./getproto '/int cholmod_pack_factor/, /\*\) ;/' ../Include/cholmod_core.h > _pack_factor.tex
-+	./getproto '/int cholmod_reallocate_column/, /\*\) ;/' ../Include/cholmod_core.h > _reallocate_column.tex
-+	./getproto '/cholmod_sparse \*cholmod_factor_to_sparse/, /\*\) ;/' ../Include/cholmod_core.h > _factor_to_sparse.tex
-+	./getproto '/cholmod_factor \*cholmod_copy_factor/, /\*\) ;/' ../Include/cholmod_core.h > _copy_factor.tex
-+	./getproto '/int cholmod_factor_xtype/, /\*\) ;/' ../Include/cholmod_core.h > _factor_xtype.tex
-+	./getproto '/typedef struct cholmod_dense/, /^}/' ../Include/cholmod_core.h > _dense.tex
-+	./getproto '/cholmod_dense \*cholmod_allocate_dense/, /\*\) ;/' ../Include/cholmod_core.h > _allocate_dense.tex
-+	./getproto '/cholmod_dense \*cholmod_zeros/, /\*\) ;/' ../Include/cholmod_core.h > _zeros.tex
-+	./getproto '/cholmod_dense \*cholmod_ones/, /\*\) ;/' ../Include/cholmod_core.h > _ones.tex
-+	./getproto '/cholmod_dense \*cholmod_eye/, /\*\) ;/' ../Include/cholmod_core.h > _eye.tex
-+	./getproto '/int cholmod_free_dense/, /\*\) ;/' ../Include/cholmod_core.h > _free_dense.tex
-+	./getproto '/cholmod_dense \*cholmod_sparse_to_dense/, /\*\) ;/' ../Include/cholmod_core.h > _sparse_to_dense.tex
-+	./getproto '/cholmod_sparse \*cholmod_dense_to_sparse/, /\*\) ;/' ../Include/cholmod_core.h > _dense_to_sparse.tex
-+	./getproto '/cholmod_dense \*cholmod_copy_dense/, /\*\) ;/' ../Include/cholmod_core.h > _copy_dense.tex
-+	./getproto '/int cholmod_copy_dense2/, /\*\) ;/' ../Include/cholmod_core.h > _copy_dense2.tex
-+	./getproto '/int cholmod_dense_xtype/, /\*\) ;/' ../Include/cholmod_core.h > _dense_xtype.tex
-+	./getproto '/typedef struct cholmod_triplet/, /^}/' ../Include/cholmod_core.h > _triplet.tex
-+	./getproto '/cholmod_triplet \*cholmod_allocate_triplet/, /\*\) ;/' ../Include/cholmod_core.h > _allocate_triplet.tex
-+	./getproto '/int cholmod_free_triplet/, /\*\) ;/' ../Include/cholmod_core.h > _free_triplet.tex
-+	./getproto '/int cholmod_reallocate_triplet/, /\*\) ;/' ../Include/cholmod_core.h > _reallocate_triplet.tex
-+	./getproto '/cholmod_triplet \*cholmod_sparse_to_triplet/, /\*\) ;/' ../Include/cholmod_core.h > _sparse_to_triplet.tex
-+	./getproto '/cholmod_sparse \*cholmod_triplet_to_sparse/, /\*\) ;/' ../Include/cholmod_core.h > _triplet_to_sparse.tex
-+	./getproto '/cholmod_triplet \*cholmod_copy_triplet/, /\*\) ;/' ../Include/cholmod_core.h > _copy_triplet.tex
-+	./getproto '/int cholmod_triplet_xtype/, /\*\) ;/' ../Include/cholmod_core.h > _triplet_xtype.tex
-+	./getproto '/void \*cholmod_malloc/, /\*\) ;/' ../Include/cholmod_core.h > _malloc.tex
-+	./getproto '/void \*cholmod_calloc/, /\*\) ;/' ../Include/cholmod_core.h > _calloc.tex
-+	./getproto '/void \*cholmod_free/, /\*\) ;/' ../Include/cholmod_core.h > _free.tex
-+	./getproto '/void \*cholmod_realloc/, /\*\) ;/' ../Include/cholmod_core.h > _realloc.tex
-+	./getproto '/int cholmod_realloc_multiple/, /\*\) ;/' ../Include/cholmod_core.h > _realloc_multiple.tex
-+	./getproto '/itype defines the/, /define CHOLMOD_SUPERNODAL/' ../Include/cholmod_core.h > _defn.tex
-+	./getproto '/int cholmod_check_common/, /\*\) ;/' ../Include/cholmod_check.h > _check_common.tex
-+	./getproto '/int cholmod_print_common/, /\*\) ;/' ../Include/cholmod_check.h > _print_common.tex
-+	./getproto '/int cholmod_check_sparse/, /\*\) ;/' ../Include/cholmod_check.h > _check_sparse.tex
-+	./getproto '/int cholmod_print_sparse/, /\*\) ;/' ../Include/cholmod_check.h > _print_sparse.tex
-+	./getproto '/int cholmod_check_dense/, /\*\) ;/' ../Include/cholmod_check.h > _check_dense.tex
-+	./getproto '/int cholmod_print_dense/, /\*\) ;/' ../Include/cholmod_check.h > _print_dense.tex
-+	./getproto '/int cholmod_check_factor/, /\*\) ;/' ../Include/cholmod_check.h > _check_factor.tex
-+	./getproto '/int cholmod_print_factor/, /\*\) ;/' ../Include/cholmod_check.h > _print_factor.tex
-+	./getproto '/int cholmod_check_triplet/, /\*\) ;/' ../Include/cholmod_check.h > _check_triplet.tex
-+	./getproto '/int cholmod_print_triplet/, /\*\) ;/' ../Include/cholmod_check.h > _print_triplet.tex
-+	./getproto '/int cholmod_check_subset/, /\*\) ;/' ../Include/cholmod_check.h > _check_subset.tex
-+	./getproto '/int cholmod_print_subset/, /\*\) ;/' ../Include/cholmod_check.h > _print_subset.tex
-+	./getproto '/int cholmod_check_perm/, /\*\) ;/' ../Include/cholmod_check.h > _check_perm.tex
-+	./getproto '/int cholmod_print_perm/, /\*\) ;/' ../Include/cholmod_check.h > _print_perm.tex
-+	./getproto '/int cholmod_check_parent/, /\*\) ;/' ../Include/cholmod_check.h > _check_parent.tex
-+	./getproto '/int cholmod_print_parent/, /\*\) ;/' ../Include/cholmod_check.h > _print_parent.tex
-+	./getproto '/cholmod_triplet \*cholmod_read_triplet/, /\*\) ;/' ../Include/cholmod_check.h > _read_triplet.tex
-+	./getproto '/cholmod_sparse \*cholmod_read_sparse/, /\*\) ;/' ../Include/cholmod_check.h > _read_sparse.tex
-+	./getproto '/cholmod_dense \*cholmod_read_dense/, /\*\) ;/' ../Include/cholmod_check.h > _read_dense.tex
-+	./getproto '/void \*cholmod_read_matrix/, /\*\) ;/' ../Include/cholmod_check.h > _read_matrix.tex
-+	./getproto '/int cholmod_write_sparse/, /\*\) ;/' ../Include/cholmod_check.h > _write_sparse.tex
-+	./getproto '/int cholmod_write_dense/, /\*\) ;/' ../Include/cholmod_check.h > _write_dense.tex
-+	./getproto '/cholmod_factor \*cholmod_analyze /, /\*\) ;/' ../Include/cholmod_cholesky.h > _analyze.tex
-+	./getproto '/cholmod_factor \*cholmod_analyze_p/, /\*\) ;/' ../Include/cholmod_cholesky.h > _analyze_p.tex
-+	./getproto '/int cholmod_factorize /, /\*\) ;/' ../Include/cholmod_cholesky.h > _factorize.tex
-+	./getproto '/int cholmod_factorize_p/, /\*\) ;/' ../Include/cholmod_cholesky.h > _factorize_p.tex
-+	./getproto '/cholmod_dense \*cholmod_solve/, /\*\) ;/' ../Include/cholmod_cholesky.h > _solve.tex
-+	./getproto '/cholmod_sparse \*cholmod_spsolve/, /\*\) ;/' ../Include/cholmod_cholesky.h > _spsolve.tex
-+	./getproto '/int cholmod_etree/, /\*\) ;/' ../Include/cholmod_cholesky.h > _etree.tex
-+	./getproto '/int cholmod_rowcolcounts/, /\*\) ;/' ../Include/cholmod_cholesky.h > _rowcolcounts.tex
-+	./getproto '/int cholmod_analyze_ordering/, /\*\) ;/' ../Include/cholmod_cholesky.h > _analyze_ordering.tex
-+	./getproto '/int cholmod_amd/, /\*\) ;/' ../Include/cholmod_cholesky.h > _amd.tex
-+	./getproto '/int cholmod_colamd/, /\*\) ;/' ../Include/cholmod_cholesky.h > _colamd.tex
-+	./getproto '/int cholmod_rowfac/, /\*\) ;/' ../Include/cholmod_cholesky.h > _rowfac.tex
-+	./getproto '/int cholmod_rowfac_mask/, /\*\) ;/' ../Include/cholmod_cholesky.h > _rowfac_mask.tex
-+	./getproto '/int cholmod_row_subtree/, /\*\) ;/' ../Include/cholmod_cholesky.h > _row_subtree.tex
-+	./getproto '/int cholmod_row_lsubtree/, /\*\) ;/' ../Include/cholmod_cholesky.h > _row_lsubtree.tex
-+	./getproto '/int cholmod_resymbol /, /\*\) ;/' ../Include/cholmod_cholesky.h > _resymbol.tex
-+	./getproto '/int cholmod_resymbol_noperm/, /\*\) ;/' ../Include/cholmod_cholesky.h > _resymbol_noperm.tex
-+	./getproto '/double cholmod_rcond/, /\*\) ;/' ../Include/cholmod_cholesky.h > _rcond.tex
-+	./getproto '/long cholmod_postorder/, /\*\) ;/' ../Include/cholmod_cholesky.h > _postorder.tex
-+	./getproto '/int cholmod_updown /, /\*\) ;/' ../Include/cholmod_modify.h > _updown.tex
-+	./getproto '/int cholmod_updown_solve/, /\*\) ;/' ../Include/cholmod_modify.h > _updown_solve.tex
-+	./getproto '/int cholmod_updown_mark/, /\*\) ;/' ../Include/cholmod_modify.h > _updown_mark.tex
-+	./getproto '/int cholmod_updown_mask/, /\*\) ;/' ../Include/cholmod_modify.h > _updown_mask.tex
-+	./getproto '/int cholmod_rowadd /, /\*\) ;/' ../Include/cholmod_modify.h > _rowadd.tex
-+	./getproto '/int cholmod_rowadd_solve/, /\*\) ;/' ../Include/cholmod_modify.h > _rowadd_solve.tex
-+	./getproto '/int cholmod_rowadd_mark/, /\*\) ;/' ../Include/cholmod_modify.h > _rowadd_mark.tex
-+	./getproto '/int cholmod_rowdel /, /\*\) ;/' ../Include/cholmod_modify.h > _rowdel.tex
-+	./getproto '/int cholmod_rowdel_solve/, /\*\) ;/' ../Include/cholmod_modify.h > _rowdel_solve.tex
-+	./getproto '/int cholmod_rowdel_mark/, /\*\) ;/' ../Include/cholmod_modify.h > _rowdel_mark.tex
-+	./getproto '/int cholmod_drop/, /\*\) ;/' ../Include/cholmod_matrixops.h > _drop.tex
-+	./getproto '/double cholmod_norm_dense/, /\*\) ;/' ../Include/cholmod_matrixops.h > _norm_dense.tex
-+	./getproto '/double cholmod_norm_sparse/, /\*\) ;/' ../Include/cholmod_matrixops.h > _norm_sparse.tex
-+	./getproto '/cholmod_sparse \*cholmod_horzcat/, /\*\) ;/' ../Include/cholmod_matrixops.h > _horzcat.tex
-+	./getproto '/define CHOLMOD_SCALAR/, /\*\) ;/' ../Include/cholmod_matrixops.h > _scale.tex
-+	./getproto '/int cholmod_sdmult/, /\*\) ;/' ../Include/cholmod_matrixops.h > _sdmult.tex
-+	./getproto '/cholmod_sparse \*cholmod_ssmult/, /\*\) ;/' ../Include/cholmod_matrixops.h > _ssmult.tex
-+	./getproto '/cholmod_sparse \*cholmod_submatrix/, /\*\) ;/' ../Include/cholmod_matrixops.h > _submatrix.tex
-+	./getproto '/cholmod_sparse \*cholmod_vertcat/, /\*\) ;/' ../Include/cholmod_matrixops.h > _vertcat.tex
-+	./getproto '/int cholmod_symmetry/, /\*\) ;/' ../Include/cholmod_matrixops.h > _symmetry.tex
-+	./getproto '/int cholmod_super_symbolic/, /\*\) ;/' ../Include/cholmod_supernodal.h > _super_symbolic.tex
-+	./getproto '/int cholmod_super_numeric/, /\*\) ;/' ../Include/cholmod_supernodal.h > _super_numeric.tex
-+	./getproto '/int cholmod_super_lsolve/, /\*\) ;/' ../Include/cholmod_supernodal.h > _super_lsolve.tex
-+	./getproto '/int cholmod_super_ltsolve/, /\*\) ;/' ../Include/cholmod_supernodal.h > _super_ltsolve.tex
-+	./getproto '/long cholmod_nested_dissection/, /\*\) ;/' ../Include/cholmod_partition.h > _nested_dissection.tex
-+	./getproto '/int cholmod_metis/, /\*\) ;/' ../Include/cholmod_partition.h > _metis.tex
-+	./getproto '/int cholmod_ccolamd/, /\*\) ;/' ../Include/cholmod_partition.h > _ccolamd.tex
-+	./getproto '/int cholmod_camd/, /\*\) ;/' ../Include/cholmod_partition.h > _camd.tex
-+	./getproto '/int cholmod_csymamd/, /\*\) ;/' ../Include/cholmod_partition.h > _csymamd.tex
-+	./getproto '/int cholmod_csymamd/, /\*\) ;/' ../Include/cholmod_partition.h > _csymamd.tex
-+	./getproto '/long cholmod_bisect/, /\*\) ;/' ../Include/cholmod_partition.h > _bisect.tex
-+	./getproto '/long cholmod_metis_bisector/, /\*\) ;/' ../Include/cholmod_partition.h > _metis_bisector.tex
-+	./getproto '/long cholmod_collapse_septree/, /\*\) ;/' ../Include/cholmod_partition.h > _collapse_septree.tex
-+	pdflatex UserGuide
-+	bibtex UserGuide
-+	pdflatex UserGuide
-+	pdflatex UserGuide
-+
-+clean-local:
-+	-$(RM) _temp.awk _*.tex *.dvi *.aux *.log *.lof *.lot *.toc *.bak *.bbl *.blg
++	_analyze_m.tex \
++	_bisect_m.tex \
++	_chol2_m.tex \
++	_cholmod2_m.tex \
++	_cholmod_demo_m.tex \
++	_cholmod_make_m.tex \
++	_etree2_m.tex \
++	_graph_demo_m.tex \
++	_lchol_m.tex \
++	_ldl_normest_m.tex \
++	_ldlchol_m.tex \
++	_ldlsolve_m.tex \
++	_ldlsplit_m.tex \
++	_ldlupdate_m.tex \
++	_metis_m.tex \
++	_mread_m.tex \
++	_mwrite_m.tex \
++	_nesdis_m.tex \
++	_resymbol_m.tex \
++	_sdmult_m.tex \
++	_sparse2_m.tex \
++	_spsym_m.tex \
++	_symbfact2_m.tex
++
++$(PROTO_M): mheader.tex mfile.awk mfooter.tex
++_%_m.tex: $(top_srcdir)/MATLAB/%.m
++	$(getmproto)
++
++PROTO_SIMPLE = \
++	_simple.tex
++
++_simple.tex: PATTERN = '/include/, /^}/'
++
++$(PROTO_SIMPLE): $(top_srcdir)/Demo/cholmod_simple.c header.tex rule.awk footer.tex
++	$(getproto)
++
++PROTO_CORE = \
++	_common.tex \
++	_start.tex \
++	_finish.tex \
++	_defaults.tex \
++	_maxrank.tex \
++	_allocate_work.tex \
++	_free_work.tex \
++	_clear_flag.tex \
++	_error.tex \
++	_dbound.tex \
++	_hypot.tex \
++	_divcomplex.tex \
++	_sparse.tex \
++	_allocate_sparse.tex \
++	_free_sparse.tex \
++	_reallocate_sparse.tex \
++	_nnz.tex \
++	_speye.tex \
++	_spzeros.tex \
++	_transpose.tex \
++	_transpose_unsym.tex \
++	_transpose_sym.tex \
++	_ptranspose.tex \
++	_sort.tex \
++	_band.tex \
++	_band_inplace.tex \
++	_aat.tex \
++	_copy_sparse.tex \
++	_copy.tex \
++	_add.tex \
++	_sparse_xtype.tex \
++	_factor.tex \
++	_allocate_factor.tex \
++	_free_factor.tex \
++	_reallocate_factor.tex \
++	_change_factor.tex \
++	_pack_factor.tex \
++	_reallocate_column.tex \
++	_factor_to_sparse.tex \
++	_copy_factor.tex \
++	_factor_xtype.tex \
++	_dense.tex \
++	_allocate_dense.tex \
++	_ensure_dense.tex \
++	_zeros.tex \
++	_ones.tex \
++	_eye.tex \
++	_free_dense.tex \
++	_sparse_to_dense.tex \
++	_dense_to_sparse.tex \
++	_copy_dense.tex \
++	_copy_dense2.tex \
++	_dense_xtype.tex \
++	_triplet.tex \
++	_allocate_triplet.tex \
++	_free_triplet.tex \
++	_reallocate_triplet.tex \
++	_sparse_to_triplet.tex \
++	_triplet_to_sparse.tex \
++	_copy_triplet.tex \
++	_triplet_xtype.tex \
++	_malloc.tex \
++	_calloc.tex \
++	_free.tex \
++	_realloc.tex \
++	_realloc_multiple.tex \
++	_version.tex \
++	_defn.tex
++
++_common.tex: PATTERN = '/typedef struct cholmod_common/, /^}/'
++_start.tex: PATTERN = '/int cholmod_start/, /\*\) ;/'
++_finish.tex: PATTERN = '/int cholmod_finish/, /\*\) ;/'
++_defaults.tex: PATTERN = '/int cholmod_defaults/, /\*\) ;/'
++_maxrank.tex: PATTERN = '/size_t cholmod_maxrank/, /\*\) ;/'
++_allocate_work.tex: PATTERN = '/int cholmod_allocate_work/, /\*\) ;/'
++_free_work.tex: PATTERN = '/int cholmod_free_work/, /\*\) ;/'
++_clear_flag.tex: PATTERN = '/long cholmod_clear_flag/, /\*\) ;/'
++_error.tex: PATTERN = '/int cholmod_error/, /\*\) ;/'
++_dbound.tex: PATTERN = '/double cholmod_dbound/, /\*\) ;/'
++_hypot.tex: PATTERN = '/double cholmod_hypot/, /double\) ;/'
++_divcomplex.tex: PATTERN = '/int cholmod_divcomplex/, /\*\) ;/'
++_sparse.tex: PATTERN = '/typedef struct cholmod_sparse/, /^}/'
++_allocate_sparse.tex: PATTERN = '/cholmod_sparse \*cholmod_allocate_sparse/, /\*\) ;/'
++_free_sparse.tex: PATTERN = '/int cholmod_free_sparse/, /\*\) ;/'
++_reallocate_sparse.tex: PATTERN = '/int cholmod_reallocate_sparse/, /\*\) ;/'
++_nnz.tex: PATTERN = '/long cholmod_nnz/, /\*\) ;/'
++_speye.tex: PATTERN = '/cholmod_sparse \*cholmod_speye/, /\*\) ;/'
++_spzeros.tex: PATTERN = '/cholmod_sparse \*cholmod_spzeros/, /\*\) ;/'
++_transpose.tex: PATTERN = '/cholmod_sparse \*cholmod_transpose/, /\*\) ;/'
++_transpose_unsym.tex: PATTERN = '/int cholmod_transpose_unsym/, /\*\) ;/'
++_transpose_sym.tex: PATTERN = '/int cholmod_transpose_sym/, /\*\) ;/'
++_ptranspose.tex: PATTERN = '/cholmod_sparse \*cholmod_ptranspose/, /\*\) ;/'
++_sort.tex: PATTERN = '/int cholmod_sort/, /\*\) ;/'
++_band.tex: PATTERN = '/cholmod_sparse \*cholmod_band/, /\*\) ;/'
++_band_inplace.tex: PATTERN = '/int cholmod_band_inplace/, /\*\) ;/'
++_aat.tex: PATTERN = '/cholmod_sparse \*cholmod_aat/, /\*\) ;/'
++_copy_sparse.tex: PATTERN = '/cholmod_sparse \*cholmod_copy_sparse/, /\*\) ;/'
++_copy.tex: PATTERN = '/cholmod_sparse \*cholmod_copy /, /\*\) ;/'
++_add.tex: PATTERN = '/cholmod_sparse \*cholmod_add/, /\*\) ;/'
++_sparse_xtype.tex: PATTERN = '/int cholmod_sparse_xtype/, /\*\) ;/'
++_factor.tex: PATTERN = '/typedef struct cholmod_factor/, /^}/'
++_allocate_factor.tex: PATTERN = '/cholmod_factor \*cholmod_allocate_factor/, /\*\) ;/'
++_free_factor.tex: PATTERN = '/int cholmod_free_factor/, /\*\) ;/'
++_reallocate_factor.tex: PATTERN = '/int cholmod_reallocate_factor/, /\*\) ;/'
++_change_factor.tex: PATTERN = '/int cholmod_change_factor/, /\*\) ;/'
++_pack_factor.tex: PATTERN = '/int cholmod_pack_factor/, /\*\) ;/'
++_reallocate_column.tex: PATTERN = '/int cholmod_reallocate_column/, /\*\) ;/'
++_factor_to_sparse.tex: PATTERN = '/cholmod_sparse \*cholmod_factor_to_sparse/, /\*\) ;/'
++_copy_factor.tex: PATTERN = '/cholmod_factor \*cholmod_copy_factor/, /\*\) ;/'
++_factor_xtype.tex: PATTERN = '/int cholmod_factor_xtype/, /\*\) ;/'
++_dense.tex: PATTERN = '/typedef struct cholmod_dense/, /^}/'
++_allocate_dense.tex: PATTERN = '/cholmod_dense \*cholmod_allocate_dense/, /\*\) ;/'
++_ensure_dense.tex: PATTERN = '/cholmod_dense \*cholmod_ensure_dense/, /\*\) ;/'
++_zeros.tex: PATTERN = '/cholmod_dense \*cholmod_zeros/, /\*\) ;/'
++_ones.tex: PATTERN = '/cholmod_dense \*cholmod_ones/, /\*\) ;/'
++_eye.tex: PATTERN = '/cholmod_dense \*cholmod_eye/, /\*\) ;/'
++_free_dense.tex: PATTERN = '/int cholmod_free_dense/, /\*\) ;/'
++_sparse_to_dense.tex: PATTERN = '/cholmod_dense \*cholmod_sparse_to_dense/, /\*\) ;/'
++_dense_to_sparse.tex: PATTERN = '/cholmod_sparse \*cholmod_dense_to_sparse/, /\*\) ;/'
++_copy_dense.tex: PATTERN = '/cholmod_dense \*cholmod_copy_dense/, /\*\) ;/'
++_copy_dense2.tex: PATTERN = '/int cholmod_copy_dense2/, /\*\) ;/'
++_dense_xtype.tex: PATTERN = '/int cholmod_dense_xtype/, /\*\) ;/'
++_triplet.tex: PATTERN = '/typedef struct cholmod_triplet/, /^}/'
++_allocate_triplet.tex: PATTERN = '/cholmod_triplet \*cholmod_allocate_triplet/, /\*\) ;/'
++_free_triplet.tex: PATTERN = '/int cholmod_free_triplet/, /\*\) ;/'
++_reallocate_triplet.tex: PATTERN = '/int cholmod_reallocate_triplet/, /\*\) ;/'
++_sparse_to_triplet.tex: PATTERN = '/cholmod_triplet \*cholmod_sparse_to_triplet/, /\*\) ;/'
++_triplet_to_sparse.tex: PATTERN = '/cholmod_sparse \*cholmod_triplet_to_sparse/, /\*\) ;/'
++_copy_triplet.tex: PATTERN = '/cholmod_triplet \*cholmod_copy_triplet/, /\*\) ;/'
++_triplet_xtype.tex: PATTERN = '/int cholmod_triplet_xtype/, /\*\) ;/'
++_malloc.tex: PATTERN = '/void \*cholmod_malloc/, /\*\) ;/'
++_calloc.tex: PATTERN = '/void \*cholmod_calloc/, /\*\) ;/'
++_free.tex: PATTERN = '/void \*cholmod_free/, /\*\) ;/'
++_realloc.tex: PATTERN = '/void \*cholmod_realloc/, /\*\) ;/'
++_realloc_multiple.tex: PATTERN = '/int cholmod_realloc_multiple/, /\*\) ;/'
++_version.tex: PATTERN = '/int cholmod_version/, /l_version/'
++_defn.tex: PATTERN = '/itype defines the/, /define CHOLMOD_SUPERNODAL/'
++
++$(PROTO_CORE): $(top_srcdir)/Include/cholmod_core.h header.tex rule.awk footer.tex
++	$(getproto)
++
++PROTO_CHECK = \
++	_check_common.tex \
++	_print_common.tex \
++	_check_sparse.tex \
++	_print_sparse.tex \
++	_check_dense.tex \
++	_print_dense.tex \
++	_check_factor.tex \
++	_print_factor.tex \
++	_check_triplet.tex \
++	_print_triplet.tex \
++	_check_subset.tex \
++	_print_subset.tex \
++	_check_perm.tex \
++	_print_perm.tex \
++	_check_parent.tex \
++	_print_parent.tex \
++	_read_triplet.tex \
++	_read_sparse.tex \
++	_read_dense.tex \
++	_read_matrix.tex \
++	_write_sparse.tex \
++	_write_dense.tex
++
++_check_common.tex: PATTERN = '/int cholmod_check_common/, /\*\) ;/'
++_print_common.tex: PATTERN = '/int cholmod_print_common/, /\*\) ;/'
++_check_sparse.tex: PATTERN = '/int cholmod_check_sparse/, /\*\) ;/'
++_print_sparse.tex: PATTERN = '/int cholmod_print_sparse/, /\*\) ;/'
++_check_dense.tex: PATTERN = '/int cholmod_check_dense/, /\*\) ;/'
++_print_dense.tex: PATTERN = '/int cholmod_print_dense/, /\*\) ;/'
++_check_factor.tex: PATTERN = '/int cholmod_check_factor/, /\*\) ;/'
++_print_factor.tex: PATTERN = '/int cholmod_print_factor/, /\*\) ;/'
++_check_triplet.tex: PATTERN = '/int cholmod_check_triplet/, /\*\) ;/'
++_print_triplet.tex: PATTERN = '/int cholmod_print_triplet/, /\*\) ;/'
++_check_subset.tex: PATTERN = '/int cholmod_check_subset/, /\*\) ;/'
++_print_subset.tex: PATTERN = '/int cholmod_print_subset/, /\*\) ;/'
++_check_perm.tex: PATTERN = '/int cholmod_check_perm/, /\*\) ;/'
++_print_perm.tex: PATTERN = '/int cholmod_print_perm/, /\*\) ;/'
++_check_parent.tex: PATTERN = '/int cholmod_check_parent/, /\*\) ;/'
++_print_parent.tex: PATTERN = '/int cholmod_print_parent/, /\*\) ;/'
++_read_triplet.tex: PATTERN = '/cholmod_triplet \*cholmod_read_triplet/, /\*\) ;/'
++_read_sparse.tex: PATTERN = '/cholmod_sparse \*cholmod_read_sparse/, /\*\) ;/'
++_read_dense.tex: PATTERN = '/cholmod_dense \*cholmod_read_dense/, /\*\) ;/'
++_read_matrix.tex: PATTERN = '/void \*cholmod_read_matrix/, /\*\) ;/'
++_write_sparse.tex: PATTERN = '/int cholmod_write_sparse/, /\*\) ;/'
++_write_dense.tex: PATTERN = '/int cholmod_write_dense/, /\*\) ;/'
++
++$(PROTO_CHECK): $(top_srcdir)/Include/cholmod_check.h header.tex rule.awk footer.tex
++	$(getproto)
++
++PROTO_CHOLESKY = \
++	_analyze.tex \
++	_analyze_p.tex \
++	_factorize.tex \
++	_factorize_p.tex \
++	_solve.tex \
++	_solve2.tex \
++	_spsolve.tex \
++	_etree.tex \
++	_rowcolcounts.tex \
++	_analyze_ordering.tex \
++	_amd.tex \
++	_colamd.tex \
++	_rowfac.tex \
++	_rowfac_mask.tex \
++	_row_subtree.tex \
++	_row_lsubtree.tex \
++	_lsolve_pattern.tex \
++	_resymbol.tex \
++	_resymbol_noperm.tex \
++	_rcond.tex \
++	_postorder.tex
++
++_analyze.tex: PATTERN = '/cholmod_factor \*cholmod_analyze /, /\*\) ;/'
++_analyze_p.tex: PATTERN = '/cholmod_factor \*cholmod_analyze_p/, /\*\) ;/'
++_factorize.tex: PATTERN = '/int cholmod_factorize /, /\*\) ;/'
++_factorize_p.tex: PATTERN = '/int cholmod_factorize_p/, /\*\) ;/'
++_solve.tex: PATTERN = '/cholmod_dense \*cholmod_solve/, /\*\) ;/'
++_solve2.tex: PATTERN = '/int cholmod_solve2/, /\*\) ;/'
++_spsolve.tex: PATTERN = '/cholmod_sparse \*cholmod_spsolve/, /\*\) ;/'
++_etree.tex: PATTERN = '/int cholmod_etree/, /\*\) ;/'
++_rowcolcounts.tex: PATTERN = '/int cholmod_rowcolcounts/, /\*\) ;/'
++_analyze_ordering.tex: PATTERN = '/int cholmod_analyze_ordering/, /\*\) ;/'
++_amd.tex: PATTERN = '/int cholmod_amd/, /\*\) ;/'
++_colamd.tex: PATTERN = '/int cholmod_colamd/, /\*\) ;/'
++_rowfac.tex: PATTERN = '/int cholmod_rowfac/, /\*\) ;/'
++_rowfac_mask.tex: PATTERN = '/int cholmod_rowfac_mask/, /\*\) ;/'
++_row_subtree.tex: PATTERN = '/int cholmod_row_subtree/, /\*\) ;/'
++_row_lsubtree.tex: PATTERN = '/int cholmod_row_lsubtree/, /\*\) ;/'
++_lsolve_pattern.tex: PATTERN = '/int cholmod_lsolve_pattern/, /\*\) ;/'
++_resymbol.tex: PATTERN = '/int cholmod_resymbol /, /\*\) ;/'
++_resymbol_noperm.tex: PATTERN = '/int cholmod_resymbol_noperm/, /\*\) ;/'
++_rcond.tex: PATTERN = '/double cholmod_rcond/, /\*\) ;/'
++_postorder.tex: PATTERN = '/long cholmod_postorder/, /\*\) ;/'
++
++$(PROTO_CHOLESKY): $(top_srcdir)/Include/cholmod_cholesky.h header.tex rule.awk footer.tex
++	$(getproto)
++
++PROTO_MODIFY = \
++	_updown.tex \
++	_updown_solve.tex \
++	_updown_mark.tex \
++	_updown_mask.tex \
++	_rowadd.tex \
++	_rowadd_solve.tex \
++	_rowadd_mark.tex \
++	_rowdel.tex \
++	_rowdel_solve.tex \
++	_rowdel_mark.tex
++
++_updown.tex: PATTERN = '/int cholmod_updown /, /\*\) ;/'
++_updown_solve.tex: PATTERN = '/int cholmod_updown_solve/, /\*\) ;/'
++_updown_mark.tex: PATTERN = '/int cholmod_updown_mark/, /\*\) ;/'
++_updown_mask.tex: PATTERN = '/int cholmod_updown_mask/, /\*\) ;/'
++_rowadd.tex: PATTERN = '/int cholmod_rowadd /, /\*\) ;/'
++_rowadd_solve.tex: PATTERN = '/int cholmod_rowadd_solve/, /\*\) ;/'
++_rowadd_mark.tex: PATTERN = '/int cholmod_rowadd_mark/, /\*\) ;/'
++_rowdel.tex: PATTERN = '/int cholmod_rowdel /, /\*\) ;/'
++_rowdel_solve.tex: PATTERN = '/int cholmod_rowdel_solve/, /\*\) ;/'
++_rowdel_mark.tex: PATTERN = '/int cholmod_rowdel_mark/, /\*\) ;/'
++
++$(PROTO_MODIFY): $(top_srcdir)/Include/cholmod_modify.h header.tex rule.awk footer.tex
++	$(getproto)
++
++PROTO_MATRIXOPS = \
++	_drop.tex \
++	_norm_dense.tex \
++	_norm_sparse.tex \
++	_horzcat.tex \
++	_scale.tex \
++	_sdmult.tex \
++	_ssmult.tex \
++	_submatrix.tex \
++	_vertcat.tex \
++	_symmetry.tex
++
++_drop.tex: PATTERN = '/int cholmod_drop/, /\*\) ;/'
++_norm_dense.tex: PATTERN = '/double cholmod_norm_dense/, /\*\) ;/'
++_norm_sparse.tex: PATTERN = '/double cholmod_norm_sparse/, /\*\) ;/'
++_horzcat.tex: PATTERN = '/cholmod_sparse \*cholmod_horzcat/, /\*\) ;/'
++_scale.tex: PATTERN = '/define CHOLMOD_SCALAR/, /\*\) ;/'
++_sdmult.tex: PATTERN = '/int cholmod_sdmult/, /\*\) ;/'
++_ssmult.tex: PATTERN = '/cholmod_sparse \*cholmod_ssmult/, /\*\) ;/'
++_submatrix.tex: PATTERN = '/cholmod_sparse \*cholmod_submatrix/, /\*\) ;/'
++_vertcat.tex: PATTERN = '/cholmod_sparse \*cholmod_vertcat/, /\*\) ;/'
++_symmetry.tex: PATTERN = '/int cholmod_symmetry/, /\*\) ;/'
++
++$(PROTO_MATRIXOPS): $(top_srcdir)/Include/cholmod_matrixops.h header.tex rule.awk footer.tex
++	$(getproto)
++
++PROTO_SUPERNODAL = \
++	_super_symbolic.tex \
++	_super_numeric.tex \
++	_super_lsolve.tex \
++	_super_ltsolve.tex
++
++_super_symbolic.tex: PATTERN = '/int cholmod_super_symbolic/, /\*\) ;/'
++_super_numeric.tex: PATTERN = '/int cholmod_super_numeric/, /\*\) ;/'
++_super_lsolve.tex: PATTERN = '/int cholmod_super_lsolve/, /\*\) ;/'
++_super_ltsolve.tex: PATTERN = '/int cholmod_super_ltsolve/, /\*\) ;/'
++
++$(PROTO_SUPERNODAL): $(top_srcdir)/Include/cholmod_supernodal.h header.tex rule.awk footer.tex
++	$(getproto)
++
++PROTO_PARTITION = \
++	_nested_dissection.tex \
++	_metis.tex \
++	_ccolamd.tex \
++	_camd.tex \
++	_csymamd.tex \
++	_bisect.tex \
++	_metis_bisector.tex \
++	_collapse_septree.tex
++
++_nested_dissection.tex: PATTERN = '/long cholmod_nested_dissection/, /\*\) ;/'
++_metis.tex: PATTERN = '/int cholmod_metis/, /\*\) ;/'
++_ccolamd.tex: PATTERN = '/int cholmod_ccolamd/, /\*\) ;/'
++_camd.tex: PATTERN = '/int cholmod_camd/, /\*\) ;/'
++_csymamd.tex: PATTERN = '/int cholmod_csymamd/, /\*\) ;/'
++_bisect.tex: PATTERN = '/long cholmod_bisect/, /\*\) ;/'
++_metis_bisector.tex: PATTERN = '/long cholmod_metis_bisector/, /\*\) ;/'
++_collapse_septree.tex: PATTERN = '/long cholmod_collapse_septree/, /\*\) ;/'
++
++$(PROTO_PARTITION): $(top_srcdir)/Include/cholmod_partition.h header.tex rule.awk footer.tex
++	$(getproto)
++
++PROTO = \
++	$(PROTO_M) \
++	$(PROTO_SIMPLE) \
++	$(PROTO_CORE) \
++	$(PROTO_CHECK) \
++	$(PROTO_CHOLESKY) \
++	$(PROTO_MODIFY) \
++	$(PROTO_MATRIXOPS) \
++	$(PROTO_SUPERNODAL) \
++	$(PROTO_PARTITION)
++
++UserGuide.pdf UserGuide.aux: $(PROTO)
++.INTERMEDIATE: UserGuide.aux $(PROTO)
++
++TEX = TEXINPUTS="$(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 = _*.awk _*.tex *.dvi *.aux *.log *.lof *.lot *.toc *.bak *.bbl *.blg
++MAINTAINERCLEANFILES = $(dist_pdf_DATA)
 diff --git a/Include/Makefile.am b/Include/Makefile.am
 new file mode 100644
 --- /dev/null
@@ -426,8 +637,6 @@ new file mode 100644
 +	License.txt \
 +	README.txt
 +
-+pkgincludedir = $(includedir)/cholmod
-+
 +# Automatically generated headers
 +nodist_pkginclude_HEADERS = \
 +	cholmod_config.h
@@ -435,10 +644,12 @@ new file mode 100644
 +pkginclude_HEADERS = \
 +	cholmod.h \
 +	cholmod_blas.h \
-+	cholmod_complexity.h \
 +	cholmod_core.h \
++	cholmod_io64.h
++
++noinst_HEADERS = \
++	cholmod_complexity.h \
 +	cholmod_internal.h \
-+	cholmod_io64.h \
 +	cholmod_template.h
 +
 +if MOD_CHECK
@@ -450,7 +661,7 @@ new file mode 100644
 +endif
 +
 +if MOD_PARTITION
-+pkginclude_HEADERS += cholmod_partition.h
++pkginclude_HEADERS += cholmod_camd.h cholmod_partition.h
 +endif
 +
 +if MOD_MATRIXOPS
@@ -469,19 +680,47 @@ rename from Include/cholmod_config.h
 rename to Include/cholmod_config.h.in
 --- a/Include/cholmod_config.h
 +++ b/Include/cholmod_config.h.in
-@@ -69,6 +69,12 @@
- #define LONGBLAS long long
- #define NSUNPERF
- */
-+@CHOLMOD_NCHECK@
-+@CHOLMOD_NCHOLESKY@
-+@CHOLMOD_NPARTITION@
-+@CHOLMOD_NMATRIXOPS@
-+@CHOLMOD_NMODIFY@
-+@CHOLMOD_NSUPERNODAL@
+@@ -54,17 +54,31 @@
+ /* Use the compiler flag, or uncomment the definition(s), if you want to use
+  * one or more non-default installation options: */
  
- /* -------------------------------------------------------------------------- */
- /* if NGPL is defined, disable all GNU GPL Modules */
+-/*
+-#define NCHECK
+-#define NCHOLESKY
+-#define NCAMD
+-#define NPARTITION
++/* Define to disable the Check module */
++#undef NCHECK
+ 
+-#define NGPL  
+-#define NMATRIXOPS
+-#define NMODIFY
+-#define NSUPERNODAL
++/* Define to disable the Cholesky module */
++#undef NCHOLESKY
++
++/* Define to disable the Partition module */
++#undef NCAMD
++
++/* Define to disable metis support in the Partition module */
++#undef NPARTITION
+ 
++/* Define to disable GPL-licensed modules */
++#undef NGPL
++
++/* Define to disable the MatrixOps module */
++#undef NMATRIXOPS
++
++/* Define to disable the Modify module */
++#undef NMODIFY
++
++/* Define to disable the Supernodal module */
++#undef NSUPERNODAL
++
++/*
+ #define NPRINT
+ 
+ #define LONGBLAS long
 diff --git a/MATLAB/Makefile.am b/MATLAB/Makefile.am
 new file mode 100644
 --- /dev/null
@@ -527,7 +766,7 @@ new file mode 100644
 +
 +libcholmod_la_SOURCES =
 +libcholmod_la_LIBADD = $(top_builddir)/Core/libcore.la
-+libcholmod_la_LDFLAGS = -no-undefined -version-info 8:3:7
++libcholmod_la_LDFLAGS = -no-undefined -version-number 2:1:2
 +
 +if MOD_CHECK
 +SUBDIRS += Check
@@ -565,7 +804,7 @@ new file mode 100644
 --- /dev/null
 +++ b/MatrixOps/Makefile.am
 @@ -0,0 +1,35 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(UFCONFIG_CFLAGS)
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
 +
 +EXTRA_DIST = \
 +	License.txt \
@@ -605,7 +844,7 @@ new file mode 100644
 --- /dev/null
 +++ b/Modify/Makefile.am
 @@ -0,0 +1,30 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(UFCONFIG_CFLAGS)
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
 +
 +EXTRA_DIST = \
 +	License.txt \
@@ -640,7 +879,7 @@ new file mode 100644
 --- /dev/null
 +++ b/Partition/Makefile.am
 @@ -0,0 +1,28 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(METIS_CFLAGS) $(CCOLAMD_CFLAGS) $(CAMD_CFLAGS) $(UFCONFIG_CFLAGS)
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(METIS_CFLAGS) $(CCOLAMD_CFLAGS) $(CAMD_CFLAGS) $(SUITESPARSECONFIG_CFLAGS)
 +
 +EXTRA_DIST = \
 +	License.txt \
@@ -668,12 +907,67 @@ new file mode 100644
 +
 +libpartition_la_SOURCES =
 +libpartition_la_LIBADD = libpartitioni.la libpartitionl.la
+diff --git a/Partition/cholmod_camd.c b/Partition/cholmod_camd.c
+--- a/Partition/cholmod_camd.c
++++ b/Partition/cholmod_camd.c
+@@ -32,6 +32,7 @@
+  * Supports any xtype (pattern, real, complex, or zomplex)
+  */
+ 
++#include "cholmod_config.h"
+ #ifndef NCAMD
+ 
+ #include "cholmod_internal.h"
+diff --git a/Partition/cholmod_ccolamd.c b/Partition/cholmod_ccolamd.c
+--- a/Partition/cholmod_ccolamd.c
++++ b/Partition/cholmod_ccolamd.c
+@@ -22,6 +22,7 @@
+  * Supports any xtype (pattern, real, complex, or zomplex).
+  */
+ 
++#include "cholmod_config.h"
+ #ifndef NCAMD
+ 
+ #include "cholmod_internal.h"
+diff --git a/Partition/cholmod_csymamd.c b/Partition/cholmod_csymamd.c
+--- a/Partition/cholmod_csymamd.c
++++ b/Partition/cholmod_csymamd.c
+@@ -21,6 +21,7 @@
+  * Supports any xtype (pattern, real, complex, or zomplex).
+  */
+ 
++#include "cholmod_config.h"
+ #ifndef NCAMD
+ 
+ #include "cholmod_internal.h"
+diff --git a/Partition/cholmod_metis.c b/Partition/cholmod_metis.c
+--- a/Partition/cholmod_metis.c
++++ b/Partition/cholmod_metis.c
+@@ -43,6 +43,7 @@
+  * Supports any xtype (pattern, real, complex, or zomplex).
+  */
+ 
++#include "cholmod_config.h"
+ #ifndef NPARTITION
+ 
+ #include "cholmod_internal.h"
+diff --git a/Partition/cholmod_nesdis.c b/Partition/cholmod_nesdis.c
+--- a/Partition/cholmod_nesdis.c
++++ b/Partition/cholmod_nesdis.c
+@@ -38,6 +38,7 @@
+  * Supports any xtype (pattern, real, complex, or zomplex).
+  */
+ 
++#include "cholmod_config.h"
+ #ifndef NPARTITION
+ 
+ #include "cholmod_internal.h"
 diff --git a/Supernodal/Makefile.am b/Supernodal/Makefile.am
 new file mode 100644
 --- /dev/null
 +++ b/Supernodal/Makefile.am
-@@ -0,0 +1,30 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(UFCONFIG_CFLAGS)
+@@ -0,0 +1,39 @@
++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
 +
 +EXTRA_DIST = \
 +	License.txt \
@@ -685,6 +979,7 @@ new file mode 100644
 +	cholmod_super_symbolic.c
 +
 +noinst_HEADERS = \
++	t_cholmod_gpu.c \
 +	t_cholmod_super_numeric.c \
 +	t_cholmod_super_solve.c
 +
@@ -701,97 +996,100 @@ new file mode 100644
 +libsupernodall_la_LIBADD = $(LAPACK_LIBS) $(BLAS_LIBS)
 +libsupernodall_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG
 +
++if TIMING
++libsupernodali_la_LIBADD += $(SUITESPARSECONFIG_LIBS)
++libsupernodall_la_LIBADD += $(SUITESPARSECONFIG_LIBS)
++else
++libsupernodali_la_CPPFLAGS += -DNTIMER
++libsupernodall_la_CPPFLAGS += -DNTIMER
++endif
++
 +libsupernodal_la_SOURCES =
 +libsupernodal_la_LIBADD = libsupernodali.la libsupernodall.la
-diff --git a/acx_blas.m4 b/acx_blas.m4
+diff --git a/ax_blas.m4 b/ax_blas.m4
 new file mode 100644
 --- /dev/null
-+++ b/acx_blas.m4
-@@ -0,0 +1,191 @@
-+##### http://autoconf-archive.cryp.to/acx_blas.html
++++ b/ax_blas.m4
+@@ -0,0 +1,238 @@
++# ===========================================================================
++#          http://www.gnu.org/software/autoconf-archive/ax_blas.html
++# ===========================================================================
 +#
 +# SYNOPSIS
 +#
-+#   ACX_BLAS([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]])
++#   AX_BLAS([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]])
 +#
 +# DESCRIPTION
 +#
-+#   This macro looks for a library that implements the BLAS
-+#   linear-algebra interface (see http://www.netlib.org/blas/). On
-+#   success, it sets the BLAS_LIBS output variable to hold the
-+#   requisite library linkages.
++#   This macro looks for a library that implements the BLAS linear-algebra
++#   interface (see http://www.netlib.org/blas/). On success, it sets the
++#   BLAS_LIBS output variable to hold the requisite library linkages.
 +#
 +#   To link with BLAS, you should link with:
 +#
-+#   	$BLAS_LIBS $LIBS $FLIBS
++#     $BLAS_LIBS $LIBS $FLIBS
 +#
 +#   in that order. FLIBS is the output variable of the
-+#   AC_F77_LIBRARY_LDFLAGS macro (called if necessary by ACX_BLAS), and
-+#   is sometimes necessary in order to link with F77 libraries. Users
-+#   will also need to use AC_F77_DUMMY_MAIN (see the autoconf manual),
-+#   for the same reason.
-+#
-+#   Many libraries are searched for, from ATLAS to CXML to ESSL. The
-+#   user may also use --with-blas=<lib> in order to use some specific
-+#   BLAS library <lib>. In order to link successfully, however, be
-+#   aware that you will probably need to use the same Fortran compiler
-+#   (which can be set via the F77 env. var.) as was used to compile the
-+#   BLAS library.
-+#
-+#   ACTION-IF-FOUND is a list of shell commands to run if a BLAS
-+#   library is found, and ACTION-IF-NOT-FOUND is a list of commands to
-+#   run it if it is not found. If ACTION-IF-FOUND is not specified, the
-+#   default action will define HAVE_BLAS.
++#   AC_F77_LIBRARY_LDFLAGS macro (called if necessary by AX_BLAS), and is
++#   sometimes necessary in order to link with F77 libraries. Users will also
++#   need to use AC_F77_DUMMY_MAIN (see the autoconf manual), for the same
++#   reason.
 +#
-+#   This macro requires autoconf 2.50 or later.
++#   Many libraries are searched for, from ATLAS to CXML to ESSL. The user
++#   may also use --with-blas=<lib> in order to use some specific BLAS
++#   library <lib>. In order to link successfully, however, be aware that you
++#   will probably need to use the same Fortran compiler (which can be set
++#   via the F77 env. var.) as was used to compile the BLAS library.
 +#
-+# LAST MODIFICATION
++#   ACTION-IF-FOUND is a list of shell commands to run if a BLAS library is
++#   found, and ACTION-IF-NOT-FOUND is a list of commands to run it if it is
++#   not found. If ACTION-IF-FOUND is not specified, the default action will
++#   define HAVE_BLAS.
 +#
-+#   2007-07-29
++# LICENSE
 +#
-+# COPYLEFT
++#   Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu>
 +#
-+#   Copyright (c) 2007 Steven G. Johnson <stevenj@alum.mit.edu>
-+#
-+#   This program is free software: you can redistribute it and/or
-+#   modify it under the terms of the GNU General Public License as
-+#   published by the Free Software Foundation, either version 3 of the
-+#   License, or (at your option) any later version.
++#   This program is free software: you can redistribute it and/or modify it
++#   under the terms of the GNU General Public License as published by the
++#   Free Software Foundation, either version 3 of the License, or (at your
++#   option) any later version.
 +#
 +#   This program 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
-+#   General Public License for more details.
++#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
++#   Public License for more details.
 +#
-+#   You should have received a copy of the GNU General Public License
-+#   along with this program. If not, see
-+#   <http://www.gnu.org/licenses/>.
++#   You should have received a copy of the GNU General Public License along
++#   with this program. If not, see <http://www.gnu.org/licenses/>.
 +#
-+#   As a special exception, the respective Autoconf Macro's copyright
-+#   owner gives unlimited permission to copy, distribute and modify the
-+#   configure scripts that are the output of Autoconf when processing
-+#   the Macro. You need not follow the terms of the GNU General Public
-+#   License when using or distributing such scripts, even though
-+#   portions of the text of the Macro appear in them. The GNU General
-+#   Public License (GPL) does govern all other use of the material that
-+#   constitutes the Autoconf Macro.
++#   As a special exception, the respective Autoconf Macro's copyright owner
++#   gives unlimited permission to copy, distribute and modify the configure
++#   scripts that are the output of Autoconf when processing the Macro. You
++#   need not follow the terms of the GNU General Public License when using
++#   or distributing such scripts, even though portions of the text of the
++#   Macro appear in them. The GNU General Public License (GPL) does govern
++#   all other use of the material that constitutes the Autoconf Macro.
 +#
-+#   This special exception to the GPL applies to versions of the
-+#   Autoconf Macro released by the Autoconf Macro Archive. When you
-+#   make and distribute a modified version of the Autoconf Macro, you
-+#   may extend this special exception to the GPL to apply to your
-+#   modified version as well.
++#   This special exception to the GPL applies to versions of the Autoconf
++#   Macro released by the Autoconf Archive. When you make and distribute a
++#   modified version of the Autoconf Macro, you may extend this special
++#   exception to the GPL to apply to your modified version as well.
++
++#serial 14
 +
-+AC_DEFUN([ACX_BLAS], [
++AU_ALIAS([ACX_BLAS], [AX_BLAS])
++AC_DEFUN([AX_BLAS], [
 +AC_PREREQ(2.50)
 +AC_REQUIRE([AC_F77_LIBRARY_LDFLAGS])
-+acx_blas_ok=no
++AC_REQUIRE([AC_CANONICAL_HOST])
++ax_blas_ok=no
 +
 +AC_ARG_WITH(blas,
-+	[AC_HELP_STRING([--with-blas=<lib>], [use BLAS library <lib>])])
++	[AS_HELP_STRING([--with-blas=<lib>], [use BLAS library <lib>])])
 +case $with_blas in
 +	yes | "") ;;
-+	no) acx_blas_ok=disable ;;
++	no) ax_blas_ok=disable ;;
 +	-* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;;
 +	*) BLAS_LIBS="-l$with_blas" ;;
 +esac
@@ -800,191 +1098,240 @@ new file mode 100644
 +AC_F77_FUNC(sgemm)
 +AC_F77_FUNC(dgemm)
 +
-+acx_blas_save_LIBS="$LIBS"
++ax_blas_save_LIBS="$LIBS"
 +LIBS="$LIBS $FLIBS"
 +
 +# First, check BLAS_LIBS environment variable
-+if test $acx_blas_ok = no; then
++if test $ax_blas_ok = no; then
 +if test "x$BLAS_LIBS" != x; then
 +	save_LIBS="$LIBS"; LIBS="$BLAS_LIBS $LIBS"
 +	AC_MSG_CHECKING([for $sgemm in $BLAS_LIBS])
-+	AC_TRY_LINK_FUNC($sgemm, [acx_blas_ok=yes], [BLAS_LIBS=""])
-+	AC_MSG_RESULT($acx_blas_ok)
++	AC_TRY_LINK_FUNC($sgemm, [ax_blas_ok=yes], [BLAS_LIBS=""])
++	AC_MSG_RESULT($ax_blas_ok)
 +	LIBS="$save_LIBS"
 +fi
 +fi
 +
 +# BLAS linked to by default?  (happens on some supercomputers)
-+if test $acx_blas_ok = no; then
++if test $ax_blas_ok = no; then
 +	save_LIBS="$LIBS"; LIBS="$LIBS"
-+	AC_CHECK_FUNC($sgemm, [acx_blas_ok=yes])
++	AC_MSG_CHECKING([if $sgemm is being linked in already])
++	AC_TRY_LINK_FUNC($sgemm, [ax_blas_ok=yes])
++	AC_MSG_RESULT($ax_blas_ok)
 +	LIBS="$save_LIBS"
 +fi
 +
++# BLAS in OpenBLAS library? (http://xianyi.github.com/OpenBLAS/)
++if test $ax_blas_ok = no; then
++	AC_CHECK_LIB(openblas, $sgemm, [ax_blas_ok=yes
++			                BLAS_LIBS="-lopenblas"])
++fi
++
 +# BLAS in ATLAS library? (http://math-atlas.sourceforge.net/)
-+if test $acx_blas_ok = no; then
++if test $ax_blas_ok = no; then
 +	AC_CHECK_LIB(atlas, ATL_xerbla,
 +		[AC_CHECK_LIB(f77blas, $sgemm,
 +		[AC_CHECK_LIB(cblas, cblas_dgemm,
-+			[acx_blas_ok=yes
++			[ax_blas_ok=yes
 +			 BLAS_LIBS="-lcblas -lf77blas -latlas"],
 +			[], [-lf77blas -latlas])],
 +			[], [-latlas])])
 +fi
 +
 +# BLAS in PhiPACK libraries? (requires generic BLAS lib, too)
-+if test $acx_blas_ok = no; then
++if test $ax_blas_ok = no; then
 +	AC_CHECK_LIB(blas, $sgemm,
 +		[AC_CHECK_LIB(dgemm, $dgemm,
 +		[AC_CHECK_LIB(sgemm, $sgemm,
-+			[acx_blas_ok=yes; BLAS_LIBS="-lsgemm -ldgemm -lblas"],
++			[ax_blas_ok=yes; BLAS_LIBS="-lsgemm -ldgemm -lblas"],
 +			[], [-lblas])],
 +			[], [-lblas])])
 +fi
 +
++# BLAS in Intel MKL library?
++if test $ax_blas_ok = no; then
++	# MKL for gfortran
++	if test x"$ac_cv_fc_compiler_gnu" = xyes; then
++		# 64 bit
++		if test $host_cpu = x86_64; then
++			AC_CHECK_LIB(mkl_gf_lp64, $sgemm,
++			[ax_blas_ok=yes;BLAS_LIBS="-lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread"],,
++			[-lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread])
++		# 32 bit
++		elif test $host_cpu = i686; then
++			AC_CHECK_LIB(mkl_gf, $sgemm,
++				[ax_blas_ok=yes;BLAS_LIBS="-lmkl_gf -lmkl_sequential -lmkl_core -lpthread"],,
++				[-lmkl_gf -lmkl_sequential -lmkl_core -lpthread])
++		fi
++	# MKL for other compilers (Intel, PGI, ...?)
++	else
++		# 64-bit
++		if test $host_cpu = x86_64; then
++			AC_CHECK_LIB(mkl_intel_lp64, $sgemm,
++				[ax_blas_ok=yes;BLAS_LIBS="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread"],,
++				[-lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread])
++		# 32-bit
++		elif test $host_cpu = i686; then
++			AC_CHECK_LIB(mkl_intel, $sgemm,
++				[ax_blas_ok=yes;BLAS_LIBS="-lmkl_intel -lmkl_sequential -lmkl_core -lpthread"],,
++				[-lmkl_intel -lmkl_sequential -lmkl_core -lpthread])
++		fi
++	fi
++fi
++# Old versions of MKL
++if test $ax_blas_ok = no; then
++	AC_CHECK_LIB(mkl, $sgemm, [ax_blas_ok=yes;BLAS_LIBS="-lmkl -lguide -lpthread"],,[-lguide -lpthread])
++fi
++
++# BLAS in Apple vecLib library?
++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_MSG_RESULT($ax_blas_ok)
++	LIBS="$save_LIBS"
++fi
++
 +# BLAS in Alpha CXML library?
-+if test $acx_blas_ok = no; then
-+	AC_CHECK_LIB(cxml, $sgemm, [acx_blas_ok=yes;BLAS_LIBS="-lcxml"])
++if test $ax_blas_ok = no; then
++	AC_CHECK_LIB(cxml, $sgemm, [ax_blas_ok=yes;BLAS_LIBS="-lcxml"])
 +fi
 +
 +# BLAS in Alpha DXML library? (now called CXML, see above)
-+if test $acx_blas_ok = no; then
-+	AC_CHECK_LIB(dxml, $sgemm, [acx_blas_ok=yes;BLAS_LIBS="-ldxml"])
++if test $ax_blas_ok = no; then
++	AC_CHECK_LIB(dxml, $sgemm, [ax_blas_ok=yes;BLAS_LIBS="-ldxml"])
 +fi
 +
 +# BLAS in Sun Performance library?
-+if test $acx_blas_ok = no; then
++if test $ax_blas_ok = no; then
 +	if test "x$GCC" != xyes; then # only works with Sun CC
 +		AC_CHECK_LIB(sunmath, acosp,
 +			[AC_CHECK_LIB(sunperf, $sgemm,
-+        			[BLAS_LIBS="-xlic_lib=sunperf -lsunmath"
-+                                 acx_blas_ok=yes],[],[-lsunmath])])
++				[BLAS_LIBS="-xlic_lib=sunperf -lsunmath"
++                                 ax_blas_ok=yes],[],[-lsunmath])])
 +	fi
 +fi
 +
 +# BLAS in SCSL library?  (SGI/Cray Scientific Library)
-+if test $acx_blas_ok = no; then
-+	AC_CHECK_LIB(scs, $sgemm, [acx_blas_ok=yes; BLAS_LIBS="-lscs"])
++if test $ax_blas_ok = no; then
++	AC_CHECK_LIB(scs, $sgemm, [ax_blas_ok=yes; BLAS_LIBS="-lscs"])
 +fi
 +
 +# BLAS in SGIMATH library?
-+if test $acx_blas_ok = no; then
++if test $ax_blas_ok = no; then
 +	AC_CHECK_LIB(complib.sgimath, $sgemm,
-+		     [acx_blas_ok=yes; BLAS_LIBS="-lcomplib.sgimath"])
++		     [ax_blas_ok=yes; BLAS_LIBS="-lcomplib.sgimath"])
 +fi
 +
 +# BLAS in IBM ESSL library? (requires generic BLAS lib, too)
-+if test $acx_blas_ok = no; then
++if test $ax_blas_ok = no; then
 +	AC_CHECK_LIB(blas, $sgemm,
 +		[AC_CHECK_LIB(essl, $sgemm,
-+			[acx_blas_ok=yes; BLAS_LIBS="-lessl -lblas"],
++			[ax_blas_ok=yes; BLAS_LIBS="-lessl -lblas"],
 +			[], [-lblas $FLIBS])])
 +fi
 +
 +# Generic BLAS library?
-+if test $acx_blas_ok = no; then
-+	AC_CHECK_LIB(blas, $sgemm, [acx_blas_ok=yes; BLAS_LIBS="-lblas"])
++if test $ax_blas_ok = no; then
++	AC_CHECK_LIB(blas, $sgemm, [ax_blas_ok=yes; BLAS_LIBS="-lblas"])
 +fi
 +
 +AC_SUBST(BLAS_LIBS)
 +
-+LIBS="$acx_blas_save_LIBS"
++LIBS="$ax_blas_save_LIBS"
 +
 +# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
-+if test x"$acx_blas_ok" = xyes; then
++if test x"$ax_blas_ok" = xyes; then
 +        ifelse([$1],,AC_DEFINE(HAVE_BLAS,1,[Define if you have a BLAS library.]),[$1])
 +        :
 +else
-+        acx_blas_ok=no
++        ax_blas_ok=no
 +        $2
 +fi
-+])dnl ACX_BLAS
-diff --git a/acx_lapack.m4 b/acx_lapack.m4
++])dnl AX_BLAS
+diff --git a/ax_lapack.m4 b/ax_lapack.m4
 new file mode 100644
 --- /dev/null
-+++ b/acx_lapack.m4
-@@ -0,0 +1,133 @@
-+##### http://autoconf-archive.cryp.to/acx_lapack.html
++++ b/ax_lapack.m4
+@@ -0,0 +1,131 @@
++# ===========================================================================
++#         http://www.gnu.org/software/autoconf-archive/ax_lapack.html
++# ===========================================================================
 +#
 +# SYNOPSIS
 +#
-+#   ACX_LAPACK([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]])
++#   AX_LAPACK([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]])
 +#
 +# DESCRIPTION
 +#
-+#   This macro looks for a library that implements the LAPACK
-+#   linear-algebra interface (see http://www.netlib.org/lapack/). On
-+#   success, it sets the LAPACK_LIBS output variable to hold the
-+#   requisite library linkages.
++#   This macro looks for a library that implements the LAPACK linear-algebra
++#   interface (see http://www.netlib.org/lapack/). On success, it sets the
++#   LAPACK_LIBS output variable to hold the requisite library linkages.
 +#
 +#   To link with LAPACK, you should link with:
 +#
-+#       $LAPACK_LIBS $BLAS_LIBS $LIBS $FLIBS
++#     $LAPACK_LIBS $BLAS_LIBS $LIBS $FLIBS
 +#
-+#   in that order. BLAS_LIBS is the output variable of the ACX_BLAS
-+#   macro, called automatically. FLIBS is the output variable of the
-+#   AC_F77_LIBRARY_LDFLAGS macro (called if necessary by ACX_BLAS), and
-+#   is sometimes necessary in order to link with F77 libraries. Users
-+#   will also need to use AC_F77_DUMMY_MAIN (see the autoconf manual),
-+#   for the same reason.
++#   in that order. BLAS_LIBS is the output variable of the AX_BLAS macro,
++#   called automatically. FLIBS is the output variable of the
++#   AC_F77_LIBRARY_LDFLAGS macro (called if necessary by AX_BLAS), and is
++#   sometimes necessary in order to link with F77 libraries. Users will also
++#   need to use AC_F77_DUMMY_MAIN (see the autoconf manual), for the same
++#   reason.
 +#
-+#   The user may also use --with-lapack=<lib> in order to use some
-+#   specific LAPACK library <lib>. In order to link successfully,
-+#   however, be aware that you will probably need to use the same
-+#   Fortran compiler (which can be set via the F77 env. var.) as was
-+#   used to compile the LAPACK and BLAS libraries.
++#   The user may also use --with-lapack=<lib> in order to use some specific
++#   LAPACK library <lib>. In order to link successfully, however, be aware
++#   that you will probably need to use the same Fortran compiler (which can
++#   be set via the F77 env. var.) as was used to compile the LAPACK and BLAS
++#   libraries.
 +#
-+#   ACTION-IF-FOUND is a list of shell commands to run if a LAPACK
-+#   library is found, and ACTION-IF-NOT-FOUND is a list of commands to
-+#   run it if it is not found. If ACTION-IF-FOUND is not specified, the
-+#   default action will define HAVE_LAPACK.
++#   ACTION-IF-FOUND is a list of shell commands to run if a LAPACK library
++#   is found, and ACTION-IF-NOT-FOUND is a list of commands to run it if it
++#   is not found. If ACTION-IF-FOUND is not specified, the default action
++#   will define HAVE_LAPACK.
 +#
-+# LAST MODIFICATION
++# LICENSE
 +#
-+#   2007-07-29
++#   Copyright (c) 2009 Steven G. Johnson <stevenj@alum.mit.edu>
 +#
-+# COPYLEFT
-+#
-+#   Copyright (c) 2007 Steven G. Johnson <stevenj@alum.mit.edu>
-+#
-+#   This program is free software: you can redistribute it and/or
-+#   modify it under the terms of the GNU General Public License as
-+#   published by the Free Software Foundation, either version 3 of the
-+#   License, or (at your option) any later version.
++#   This program is free software: you can redistribute it and/or modify it
++#   under the terms of the GNU General Public License as published by the
++#   Free Software Foundation, either version 3 of the License, or (at your
++#   option) any later version.
 +#
 +#   This program 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
-+#   General Public License for more details.
++#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
++#   Public License for more details.
 +#
-+#   You should have received a copy of the GNU General Public License
-+#   along with this program. If not, see
-+#   <http://www.gnu.org/licenses/>.
++#   You should have received a copy of the GNU General Public License along
++#   with this program. If not, see <http://www.gnu.org/licenses/>.
 +#
-+#   As a special exception, the respective Autoconf Macro's copyright
-+#   owner gives unlimited permission to copy, distribute and modify the
-+#   configure scripts that are the output of Autoconf when processing
-+#   the Macro. You need not follow the terms of the GNU General Public
-+#   License when using or distributing such scripts, even though
-+#   portions of the text of the Macro appear in them. The GNU General
-+#   Public License (GPL) does govern all other use of the material that
-+#   constitutes the Autoconf Macro.
++#   As a special exception, the respective Autoconf Macro's copyright owner
++#   gives unlimited permission to copy, distribute and modify the configure
++#   scripts that are the output of Autoconf when processing the Macro. You
++#   need not follow the terms of the GNU General Public License when using
++#   or distributing such scripts, even though portions of the text of the
++#   Macro appear in them. The GNU General Public License (GPL) does govern
++#   all other use of the material that constitutes the Autoconf Macro.
 +#
-+#   This special exception to the GPL applies to versions of the
-+#   Autoconf Macro released by the Autoconf Macro Archive. When you
-+#   make and distribute a modified version of the Autoconf Macro, you
-+#   may extend this special exception to the GPL to apply to your
-+#   modified version as well.
++#   This special exception to the GPL applies to versions of the Autoconf
++#   Macro released by the Autoconf Archive. When you make and distribute a
++#   modified version of the Autoconf Macro, you may extend this special
++#   exception to the GPL to apply to your modified version as well.
 +
-+AC_DEFUN([ACX_LAPACK], [
-+AC_REQUIRE([ACX_BLAS])
-+acx_lapack_ok=no
++#serial 7
++
++AU_ALIAS([ACX_LAPACK], [AX_LAPACK])
++AC_DEFUN([AX_LAPACK], [
++AC_REQUIRE([AX_BLAS])
++ax_lapack_ok=no
 +
 +AC_ARG_WITH(lapack,
-+        [AC_HELP_STRING([--with-lapack=<lib>], [use LAPACK library <lib>])])
++        [AS_HELP_STRING([--with-lapack=<lib>], [use LAPACK library <lib>])])
 +case $with_lapack in
 +        yes | "") ;;
-+        no) acx_lapack_ok=disable ;;
++        no) ax_lapack_ok=disable ;;
 +        -* | */* | *.a | *.so | *.so.* | *.o) LAPACK_LIBS="$with_lapack" ;;
 +        *) LAPACK_LIBS="-l$with_lapack" ;;
 +esac
@@ -993,35 +1340,36 @@ new file mode 100644
 +AC_F77_FUNC(cheev)
 +
 +# We cannot use LAPACK if BLAS is not found
-+if test "x$acx_blas_ok" != xyes; then
-+        acx_lapack_ok=noblas
++if test "x$ax_blas_ok" != xyes; then
++        ax_lapack_ok=noblas
++        LAPACK_LIBS=""
 +fi
 +
 +# First, check LAPACK_LIBS environment variable
 +if test "x$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, [acx_lapack_ok=yes], [LAPACK_LIBS=""])
-+        AC_MSG_RESULT($acx_lapack_ok)
++        AC_TRY_LINK_FUNC($cheev, [ax_lapack_ok=yes], [LAPACK_LIBS=""])
++        AC_MSG_RESULT($ax_lapack_ok)
 +        LIBS="$save_LIBS"
-+        if test acx_lapack_ok = no; then
++        if test $ax_lapack_ok = no; then
 +                LAPACK_LIBS=""
 +        fi
 +fi
 +
 +# LAPACK linked to by default?  (is sometimes included in BLAS lib)
-+if test $acx_lapack_ok = no; then
++if test $ax_lapack_ok = no; then
 +        save_LIBS="$LIBS"; LIBS="$LIBS $BLAS_LIBS $FLIBS"
-+        AC_CHECK_FUNC($cheev, [acx_lapack_ok=yes])
++        AC_CHECK_FUNC($cheev, [ax_lapack_ok=yes])
 +        LIBS="$save_LIBS"
 +fi
 +
 +# Generic LAPACK library?
 +for lapack in lapack lapack_rs6k; do
-+        if test $acx_lapack_ok = no; then
++        if test $ax_lapack_ok = no; then
 +                save_LIBS="$LIBS"; LIBS="$BLAS_LIBS $LIBS"
 +                AC_CHECK_LIB($lapack, $cheev,
-+                    [acx_lapack_ok=yes; LAPACK_LIBS="-l$lapack"], [], [$FLIBS])
++                    [ax_lapack_ok=yes; LAPACK_LIBS="-l$lapack"], [], [$FLIBS])
 +                LIBS="$save_LIBS"
 +        fi
 +done
@@ -1029,19 +1377,19 @@ new file mode 100644
 +AC_SUBST(LAPACK_LIBS)
 +
 +# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
-+if test x"$acx_lapack_ok" = xyes; then
++if test x"$ax_lapack_ok" = xyes; then
 +        ifelse([$1],,AC_DEFINE(HAVE_LAPACK,1,[Define if you have LAPACK library.]),[$1])
 +        :
 +else
-+        acx_lapack_ok=no
++        ax_lapack_ok=no
 +        $2
 +fi
-+])dnl ACX_LAPACK
++])dnl AX_LAPACK
 diff --git a/cholmod.pc.in b/cholmod.pc.in
 new file mode 100644
 --- /dev/null
 +++ b/cholmod.pc.in
-@@ -0,0 +1,12 @@
+@@ -0,0 +1,13 @@
 +prefix=@prefix@
 +exec_prefix=@exec_prefix@
 +libdir=@libdir@
@@ -1050,6 +1398,7 @@ new file mode 100644
 +Name: @PACKAGE_NAME@
 +Description: Sparse Cholesky factorization
 +Version: @PACKAGE_VERSION@
++URL: @PACKAGE_URL@
 +Requires.private: @CHOLMOD_REQUIRES@
 +Libs: -L${libdir} -lcholmod
 +Libs.private: @LAPACK_LIBS@ @BLAS_LIBS@ -lm
@@ -1058,23 +1407,37 @@ diff --git a/configure.ac b/configure.ac
 new file mode 100644
 --- /dev/null
 +++ b/configure.ac
-@@ -0,0 +1,177 @@
-+AC_PREREQ([2.68])
-+AC_INIT([CHOLMOD],[1.7.3],[davis@cise.ufl.edu])
+@@ -0,0 +1,215 @@
++#                                               -*- Autoconf -*-
++# Process this file with autoconf to produce a configure script.
++
++AC_PREREQ([2.69])
++AC_INIT([CHOLMOD],[2.1.2],[DrTimothyAldenDavis@gmail.com],[cholmod],[http://www.suitesparse.com/])
 +AC_CONFIG_SRCDIR([Core/cholmod_common.c])
-+AC_CONFIG_HEADER([config.h])
++AC_CONFIG_HEADERS([config.h Include/cholmod_config.h])
 +AM_INIT_AUTOMAKE([foreign])
 +LT_INIT
 +
++# Checks for programs.
 +AC_PROG_INSTALL
 +AC_PROG_CC
 +AC_PROG_F77
++AC_PROG_AWK
++
++AC_MSG_CHECKING([whether to build GPL-licensed modules])
++AC_ARG_ENABLE([gpl-modules],
++	[AS_HELP_STRING(
++		[--disable-gpl-modules],
++		[do not build GPL-licensed modules])],
++	[mod_gpl=$enableval],
++	[mod_gpl="yes"])
++AC_MSG_RESULT([$mod_gpl])
 +
 +AC_MSG_CHECKING([whether to build mod-check])
 +AC_ARG_ENABLE([mod-check],
 +	[AS_HELP_STRING(
-+		[--enable-mod-check],
-+		[build the Check module @<:@default=yes@:>@])],
++		[--disable-mod-check],
++		[do not build the Check module])],
 +	[mod_check=$enableval],
 +	[mod_check="yes"])
 +AC_MSG_RESULT([$mod_check])
@@ -1082,8 +1445,8 @@ new file mode 100644
 +AC_MSG_CHECKING([whether to build mod-cholesky])
 +AC_ARG_ENABLE([mod-cholesky],
 +	[AS_HELP_STRING(
-+		[--enable-mod-cholesky],
-+		[build the Cholesky module @<:@default=yes@:>@])],
++		[--disable-mod-cholesky],
++		[do not build the Cholesky module])],
 +	[mod_cholesky=$enableval],
 +	[mod_cholesky="yes"])
 +AC_MSG_RESULT([$mod_cholesky])
@@ -1091,8 +1454,8 @@ new file mode 100644
 +AC_MSG_CHECKING([whether to build mod-partition])
 +AC_ARG_ENABLE([mod-partition],
 +	[AS_HELP_STRING(
-+		[--enable-mod-partition],
-+		[build the Partition module @<:@default=yes@:>@])],
++		[--disable-mod-partition],
++		[do not build the Partition module])],
 +	[mod_partition=$enableval],
 +	[mod_partition="yes"])
 +AC_MSG_RESULT([$mod_partition])
@@ -1100,123 +1463,148 @@ new file mode 100644
 +AC_MSG_CHECKING([whether to build mod-matrixops])
 +AC_ARG_ENABLE([mod-matrixops],
 +	[AS_HELP_STRING(
-+		[--enable-mod-matrixops],
-+		[build the MatrixOps module @<:@default=yes@:>@])],
++		[--disable-mod-matrixops],
++		[do not build the MatrixOps module])],
 +	[mod_matrixops=$enableval],
-+	[mod_matrixops="yes"])
++	[mod_matrixops=$mod_gpl])
 +AC_MSG_RESULT([$mod_matrixops])
 +
 +AC_MSG_CHECKING([whether to build mod-modify])
 +AC_ARG_ENABLE([mod-modify],
 +	[AS_HELP_STRING(
-+		[--enable-mod-modify],
-+		[build the Modify module @<:@default=yes@:>@])],
++		[--disable-mod-modify],
++		[do not build the Modify module])],
 +	[mod_modify=$enableval],
-+	[mod_modify="yes"])
++	[mod_modify=$mod_gpl])
 +AC_MSG_RESULT([$mod_modify])
 +
 +AC_MSG_CHECKING([whether to build mod-supernodal])
 +AC_ARG_ENABLE([mod-supernodal],
 +	[AS_HELP_STRING(
-+		[--enable-mod-supernodal],
-+		[build the Supernodal module @<:@default=yes@:>@])],
++		[--disable-mod-supernodal],
++		[do not build the Supernodal module])],
 +	[mod_supernodal=$enableval],
-+	[mod_supernodal="yes"])
++	[mod_supernodal=$mod_gpl])
 +AC_MSG_RESULT([$mod_supernodal])
 +
-+if test "x$mod_check" = "xno"; then
-+	AC_DEFINE([NCHECK], [], [Define to disable the Check module])
-+	AC_SUBST([CHOLMOD_NCHECK], ["#define NCHECK"])
-+fi
-+
-+if test "x$mod_cholesky" = "xno"; then
-+	AC_DEFINE([NCHOLESKY], [], [Define to disable the Cholesky module])
-+	AC_SUBST([CHOLMOD_NCHOLESKY], ["#define NCHOLESKY"])
-+fi
-+
-+if test "x$mod_partition" = "xno"; then
-+	AC_DEFINE([NPARTITION], [], [Define to disable the Partition module])
-+	AC_SUBST([CHOLMOD_NPARTITION], ["#define NPARTITION"])
-+fi
-+
-+if test "x$mod_matrixops" = "xno"; then
-+	AC_DEFINE([NMATRIXOPS], [], [Define to disable the MatrixOps module])
-+	AC_SUBST([CHOLMOD_NMATRIXOPS], ["#define NMATRIXOPS"])
-+fi
-+
-+if test "x$mod_modify" = "xno"; then
-+	AC_DEFINE([NMODIFY], [], [Define to disable the Modify module])
-+	AC_SUBST([CHOLMOD_NMODIFY], ["#define NMODIFY"])
-+fi
-+
-+if test "x$mod_supernodal" = "xno"; then
-+	AC_DEFINE([NSUPERNODAL], [], [Define to disable the Supernodal module])
-+	AC_SUBST([CHOLMOD_NSUPERNODAL], ["#define NSUPERNODAL"])
-+fi
++AC_MSG_CHECKING([whether to use timing routines])
++AC_ARG_ENABLE([timing],
++	[AS_HELP_STRING(
++		[--disable-timing],
++		[do not use timing routines])],
++	[timing=$enableval],
++	[timing="yes"])
++AC_MSG_RESULT([$timing])
 +
 +LIBS_SAVED=$LIBS
 +
++# Checks for libraries.
 +AC_CHECK_LIB([m], [sqrt])
 +
-+AC_CHECK_HEADERS([stddef.h stdlib.h string.h])
-+
 +PKG_PROG_PKG_CONFIG
-+PKG_CHECK_MODULES([UFCONFIG],[ufconfig],
++PKG_CHECK_MODULES([SUITESPARSECONFIG],[suitesparseconfig],
 +	[],
-+	[AC_MSG_ERROR([cannot find ufconfig])])
-+CHOLMOD_REQUIRES="ufconfig"
++	[AC_MSG_ERROR([cannot find suitesparseconfig])])
++CHOLMOD_REQUIRES="suitesparseconfig"
 +
 +if test "x$mod_cholesky" = "xyes"; then
 +	PKG_CHECK_MODULES([AMD],[amd],
-+		[CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES amd"],
++		[],
 +		[AC_MSG_ERROR([cannot find amd (required by mod-cholesky)])])
++	CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES amd"
 +
 +	PKG_CHECK_MODULES([COLAMD],[colamd],
-+		[CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES colamd"],
++		[],
 +		[AC_MSG_ERROR([cannot find colamd (required by mod-cholesky)])])
++	CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES colamd"
 +fi
 +
 +if test "x$mod_partition" = "xyes"; then
-+	PKG_CHECK_MODULES([METIS],[metis],
-+		[CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES metis"],
-+		[AC_MSG_ERROR([cannot find metis (required by mod-partition)])])
-+
-+PKG_CHECK_MODULES([CAMD],[camd],
-+		[CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES camd"],
++	PKG_CHECK_MODULES([CAMD],[camd],
++		[],
 +		[AC_MSG_ERROR([cannot find camd (required by mod-partition)])])
++	CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES camd"
 +
-+PKG_CHECK_MODULES([CCOLAMD],[ccolamd],
-+		[CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES ccolamd"],
++	PKG_CHECK_MODULES([CCOLAMD],[ccolamd],
++		[],
 +		[AC_MSG_ERROR([cannot find ccolamd (required by mod-partition)])])
++	CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES ccolamd"
++
++	PKG_CHECK_MODULES([METIS],[metis],
++		[metis="yes"],
++		[metis="no"])
++	if test "x$metis" = "xyes"; then
++		CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES metis"
++	else
++		AC_MSG_WARN([cannot find metis (used by mod-partition), disabling some functionality])
++	fi
 +fi
 +
 +if test "x$mod_supernodal" = "xyes"; then
-+	sinclude([acx_blas.m4])
-+	sinclude([acx_lapack.m4])
-+	ACX_LAPACK
-+
-+	if test "x$BLAS_LIBS" = "x"; then
++	sinclude([ax_blas.m4])
++	AX_BLAS
++	if test "x$ax_blas_ok" != "xyes"; then
 +		AC_MSG_ERROR([cannot find blas (required by mod-supernodal)])
 +	fi
 +
-+	if test "x$LAPACK_LIBS" = "x"; then
++	sinclude([ax_lapack.m4])
++	AX_LAPACK
++	if test "x$ax_lapack_ok" != "xyes"; then
 +		AC_MSG_ERROR([cannot find lapack (required by mod-supernodal)])
 +	fi
 +fi
 +
++# Checks for header files.
++AC_CHECK_HEADERS([float.h limits.h stddef.h stdlib.h string.h])
++
++# Checks for typedefs, structures, and compiler characteristics.
 +AC_TYPE_SIZE_T
 +
++# Checks for library functions.
 +AC_FUNC_MALLOC
 +AC_CHECK_FUNCS([sqrt])
 +
 +LIBS=$LIBS_SAVED
 +
++if test "x$mod_check" != "xyes"; then
++	AC_DEFINE([NCHECK], [], [Define to disable the Check module])
++fi
++
++if test "x$mod_cholesky" != "xyes"; then
++	AC_DEFINE([NCHOLESKY], [], [Define to disable the Cholesky module])
++fi
++
++if test "x$mod_partition" != "xyes"; then
++	AC_DEFINE([NCAMD], [], [Define to disable the Partition module])
++fi
++
++if test "x$metis" != "xyes"; then
++	AC_DEFINE([NPARTITION], [], [Define to disable metis support in the Partition module])
++fi
++
++if test "x$mod_gpl" != "xyes"; then
++	AC_DEFINE([NGPL], [], [Define to disable GPL-licensed modules])
++fi
++
++if test "x$mod_matrixops" != "xyes"; then
++	AC_DEFINE([NMATRIXOPS], [], [Define to disable the MatrixOps module])
++fi
++
++if test "x$mod_modify" != "xyes"; then
++	AC_DEFINE([NMODIFY], [], [Define to disable the Modify module])
++fi
++
++if test "x$mod_supernodal" != "xyes"; then
++	AC_DEFINE([NSUPERNODAL], [], [Define to disable the Supernodal module])
++fi
++
 +AM_CONDITIONAL([MOD_CHECK], [test "x$mod_check" = "xyes"])
 +AM_CONDITIONAL([MOD_CHOLESKY], [test "x$mod_cholesky" = "xyes"])
 +AM_CONDITIONAL([MOD_PARTITION], [test "x$mod_partition" = "xyes"])
 +AM_CONDITIONAL([MOD_MATRIXOPS], [test "x$mod_matrixops" = "xyes"])
 +AM_CONDITIONAL([MOD_MODIFY], [test "x$mod_modify" = "xyes"])
 +AM_CONDITIONAL([MOD_SUPERNODAL], [test "x$mod_supernodal" = "xyes"])
++AM_CONDITIONAL([TIMING], [test "x$timing" = "xyes"])
 +
 +AC_SUBST([CHOLMOD_REQUIRES])
 +
@@ -1228,7 +1616,6 @@ new file mode 100644
 +	Core/Makefile
 +	Demo/Makefile
 +	Doc/Makefile
-+	Include/cholmod_config.h
 +	Include/Makefile
 +	MATLAB/Makefile
 +	MatrixOps/Makefile