academic/cholmod: Renamed and moved from libraries.

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

6 files changed, 0 insertions, 1798 deletions

diff --git a/libraries/CHOLMOD/CHOLMOD.SlackBuild b/libraries/CHOLMOD/CHOLMOD.SlackBuild
deleted file mode 100644
index 1475bce852..0000000000
--- a/libraries/CHOLMOD/CHOLMOD.SlackBuild
+++ /dev/null
@@ -1,112 +0,0 @@
-#!/bin/sh
-
-# Slackware build script for CHOLMOD
-
-# 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=${VERSION:-2.1.2}
-BUILD=${BUILD:-1}
-TAG=${TAG:-_SBo}
-
-if [ -z "$ARCH" ]; then
-  case "$(uname -m)" in
-    i?86) ARCH=i486 ;;
-    arm*) ARCH=arm ;;
-       *) ARCH=$(uname -m) ;;
-  esac
-fi
-
-CWD=$(pwd)
-TMP=${TMP:-/tmp/SBo}
-PKG=$TMP/package-$PRGNAM
-OUTPUT=${OUTPUT:-/tmp}
-
-DOCS="README.txt Doc/ChangeLog Core/lesser.txt Modify/gpl.txt"
-MODULE_DOCS="Core/License.txt Check/License.txt Cholesky/License.txt Partition/License.txt MatrixOps/License.txt Modify/License.txt Supernodal/License.txt"
-
-if [ "$ARCH" = "i486" ]; then
-  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
-  LIBDIRSUFFIX=""
-elif [ "$ARCH" = "i686" ]; then
-  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
-  LIBDIRSUFFIX=""
-elif [ "$ARCH" = "x86_64" ]; then
-  SLKCFLAGS="-O2 -fPIC"
-  LIBDIRSUFFIX="64"
-else
-  SLKCFLAGS="-O2"
-  LIBDIRSUFFIX=""
-fi
-
-# Recommended by SuiteSparse
-SLKCFLAGS="$SLKCFLAGS -fexceptions -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE"
-
-set -e
-
-rm -rf $PKG
-mkdir -p $TMP $PKG $OUTPUT
-cd $TMP
-rm -rf $PRGNAM
-tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
-cd $PRGNAM
-chown -R root:root .
-find -L . \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
-  -o -perm 511 \) -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
- -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
-
-patch -p1 < $CWD/autotoolize.diff
-patch -p1 < $CWD/atlas-threaded-blas.diff
-autoreconf -vif
-
-CFLAGS="$SLKCFLAGS" \
-FFLAGS="$SLKCFLAGS" \
-./configure \
-  --prefix=/usr \
-  --libdir=/usr/lib${LIBDIRSUFFIX} \
-  --sysconfdir=/etc \
-  --localstatedir=/var \
-  --mandir=/usr/man \
-  --infodir=/usr/info \
-  --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
-cp -a $DOCS $PKG/usr/doc/$PRGNAM-$VERSION
-for i in $MODULE_DOCS; do
-  cp -a $i $PKG/usr/doc/$PRGNAM-$VERSION/$(echo $i | tr / _)
-done
-cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
-
-mkdir -p $PKG/install
-cat $CWD/slack-desc > $PKG/install/slack-desc
-
-cd $PKG
-/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/libraries/CHOLMOD/CHOLMOD.info b/libraries/CHOLMOD/CHOLMOD.info
deleted file mode 100644
index 8551cb3ca1..0000000000
--- a/libraries/CHOLMOD/CHOLMOD.info
+++ /dev/null
@@ -1,10 +0,0 @@
-PRGNAM="CHOLMOD"
-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="%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
deleted file mode 100644
index ebbb152bc3..0000000000
--- a/libraries/CHOLMOD/README
+++ /dev/null
@@ -1,6 +0,0 @@
-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
deleted file mode 100644
index e7f34ef011..0000000000
--- a/libraries/CHOLMOD/atlas-threaded-blas.diff
+++ /dev/null
@@ -1,26 +0,0 @@
-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, $sgemm,
-+				[AC_CHECK_LIB(cblas, cblas_dgemm,
-+					[ax_blas_ok=yes; BLAS_LIBS="-lcblas -lf77blas -latlas"],,
-+					[-lf77blas -latlas])],,
-+				[-latlas])],
-+			[-latlas])])
- fi
- 
- # BLAS in PhiPACK libraries? (requires generic BLAS lib, too)
diff --git a/libraries/CHOLMOD/autotoolize.diff b/libraries/CHOLMOD/autotoolize.diff
deleted file mode 100644
index 5e93cf2f1c..0000000000
--- a/libraries/CHOLMOD/autotoolize.diff
+++ /dev/null
@@ -1,1625 +0,0 @@
-diff --git a/Check/Makefile.am b/Check/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Check/Makefile.am
-@@ -0,0 +1,24 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
-+
-+EXTRA_DIST = \
-+	License.txt \
-+	lesser.txt
-+
-+CHECKSRC = \
-+	cholmod_check.c \
-+	cholmod_read.c \
-+	cholmod_write.c
-+
-+noinst_LTLIBRARIES = \
-+	libchecki.la \
-+	libcheckl.la \
-+	libcheck.la
-+
-+libchecki_la_SOURCES = $(CHECKSRC)
-+libchecki_la_CPPFLAGS= $(AM_CPPFLAGS)
-+
-+libcheckl_la_SOURCES = $(CHECKSRC)
-+libcheckl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG
-+
-+libcheck_la_SOURCES =
-+libcheck_la_LIBADD = libchecki.la libcheckl.la
-diff --git a/Cholesky/Makefile.am b/Cholesky/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Cholesky/Makefile.am
-@@ -0,0 +1,41 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(COLAMD_CFLAGS) $(AMD_CFLAGS) $(SUITESPARSECONFIG_CFLAGS)
-+
-+EXTRA_DIST = \
-+	License.txt \
-+	lesser.txt
-+
-+CHOLESKYSRC = \
-+	cholmod_amd.c \
-+	cholmod_analyze.c \
-+	cholmod_colamd.c \
-+	cholmod_etree.c \
-+	cholmod_factorize.c \
-+	cholmod_postorder.c \
-+	cholmod_rcond.c \
-+	cholmod_resymbol.c \
-+	cholmod_rowcolcounts.c \
-+	cholmod_rowfac.c \
-+	cholmod_solve.c \
-+	cholmod_spsolve.c
-+
-+noinst_HEADERS = \
-+	t_cholmod_lsolve.c \
-+	t_cholmod_ltsolve.c \
-+	t_cholmod_rowfac.c \
-+	t_cholmod_solve.c
-+
-+noinst_LTLIBRARIES = \
-+	libcholeskyi.la \
-+	libcholeskyl.la \
-+	libcholesky.la
-+
-+libcholeskyi_la_SOURCES = $(CHOLESKYSRC)
-+libcholeskyi_la_LIBADD = $(COLAMD_LIBS) $(AMD_LIBS) -lm
-+libcholeskyi_la_CPPFLAGS = $(AM_CPPFLAGS)
-+
-+libcholeskyl_la_SOURCES = $(CHOLESKYSRC)
-+libcholeskyl_la_LIBADD = $(COLAMD_LIBS) $(AMD_LIBS) -lm
-+libcholeskyl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG
-+
-+libcholesky_la_SOURCES =
-+libcholesky_la_LIBADD = libcholeskyi.la libcholeskyl.la
-diff --git a/Core/Makefile.am b/Core/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Core/Makefile.am
-@@ -0,0 +1,44 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
-+
-+EXTRA_DIST = \
-+	License.txt \
-+	lesser.txt
-+
-+CORESRC = \
-+	cholmod_aat.c \
-+	cholmod_add.c \
-+	cholmod_band.c \
-+	cholmod_change_factor.c \
-+	cholmod_common.c \
-+	cholmod_complex.c \
-+	cholmod_copy.c \
-+	cholmod_dense.c \
-+	cholmod_error.c \
-+	cholmod_factor.c \
-+	cholmod_memory.c \
-+	cholmod_sparse.c \
-+	cholmod_transpose.c \
-+	cholmod_triplet.c \
-+	cholmod_version.c
-+
-+noinst_HEADERS = \
-+	t_cholmod_change_factor.c \
-+	t_cholmod_dense.c \
-+	t_cholmod_transpose.c \
-+	t_cholmod_triplet.c
-+
-+noinst_LTLIBRARIES = \
-+	libcorei.la \
-+	libcorel.la \
-+	libcore.la
-+
-+libcorei_la_SOURCES = $(CORESRC)
-+libcorei_la_LIBADD = -lm
-+libcorei_la_CPPFLAGS = $(AM_CPPFLAGS)
-+
-+libcorel_la_SOURCES = $(CORESRC)
-+libcorel_la_LIBADD = -lm
-+libcorel_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG
-+
-+libcore_la_SOURCES =
-+libcore_la_LIBADD = libcorei.la libcorel.la
-diff --git a/Demo/Makefile.am b/Demo/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Demo/Makefile.am
-@@ -0,0 +1,60 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
-+
-+EXTRA_DIST = \
-+	License.txt \
-+	gpl.txt
-+
-+dist_noinst_HEADERS = \
-+	cholmod_demo.h
-+
-+dist_noinst_DATA = \
-+	Matrix/bcsstk01.tri \
-+	Matrix/lp_afiro.tri \
-+	Matrix/can___24.mtx \
-+	Matrix/c.tri
-+
-+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 $(SUITESPARSECONFIG_LIBS)
-+
-+cholmod_l_demo_SOURCES = cholmod_l_demo.c
-+cholmod_l_demo_LDADD = $(top_builddir)/libcholmod.la $(SUITESPARSECONFIG_LIBS)
-+
-+cholmod_simple_SOURCES = cholmod_simple.c
-+cholmod_simple_LDADD = $(top_builddir)/libcholmod.la
-+
-+check-local: $(check_PROGRAMS) $(dist_noinst_DATA)
-+	./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 +1,436 @@
-+EXTRA_DIST = \
-+	ChangeLog
-+
-+dist_noinst_DATA = \
-+	UserGuide.bib \
-+	UserGuide.tex \
-+	header.tex \
-+	footer.tex \
-+	mheader.tex \
-+	mfooter.tex \
-+	mfile.awk \
-+	rule.awk
-+
-+dist_pdf_DATA = \
-+	UserGuide.pdf
-+
-+dist_noinst_SCRIPTS = \
-+	getmproto \
-+	getproto
-+
-+# ./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 $@).awk
-+endef
-+
-+PROTO_M = \
-+	_analyze_m.tex \
-+	_bisect_m.tex \
-+	_chol2_m.tex \
-+	_cholmod2_m.tex \
-+	_cholmod_demo_m.tex \
-+	_cholmod_make_m.tex \
-+	_etree2_m.tex \
-+	_graph_demo_m.tex \
-+	_lchol_m.tex \
-+	_ldl_normest_m.tex \
-+	_ldlchol_m.tex \
-+	_ldlsolve_m.tex \
-+	_ldlsplit_m.tex \
-+	_ldlupdate_m.tex \
-+	_metis_m.tex \
-+	_mread_m.tex \
-+	_mwrite_m.tex \
-+	_nesdis_m.tex \
-+	_resymbol_m.tex \
-+	_sdmult_m.tex \
-+	_sparse2_m.tex \
-+	_spsym_m.tex \
-+	_symbfact2_m.tex
-+
-+$(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
-+++ b/Include/Makefile.am
-@@ -0,0 +1,42 @@
-+EXTRA_DIST = \
-+	License.txt \
-+	README.txt
-+
-+# Automatically generated headers
-+nodist_pkginclude_HEADERS = \
-+	cholmod_config.h
-+
-+pkginclude_HEADERS = \
-+	cholmod.h \
-+	cholmod_blas.h \
-+	cholmod_core.h \
-+	cholmod_io64.h
-+
-+noinst_HEADERS = \
-+	cholmod_complexity.h \
-+	cholmod_internal.h \
-+	cholmod_template.h
-+
-+if MOD_CHECK
-+pkginclude_HEADERS += cholmod_check.h
-+endif
-+
-+if MOD_CHOLESKY
-+pkginclude_HEADERS += cholmod_cholesky.h
-+endif
-+
-+if MOD_PARTITION
-+pkginclude_HEADERS += cholmod_camd.h cholmod_partition.h
-+endif
-+
-+if MOD_MATRIXOPS
-+pkginclude_HEADERS += cholmod_matrixops.h
-+endif
-+
-+if MOD_MODIFY
-+pkginclude_HEADERS += cholmod_modify.h
-+endif
-+
-+if MOD_SUPERNODAL
-+pkginclude_HEADERS += cholmod_supernodal.h
-+endif
-diff --git a/Include/cholmod_config.h b/Include/cholmod_config.h.in
-rename from Include/cholmod_config.h
-rename to Include/cholmod_config.h.in
---- a/Include/cholmod_config.h
-+++ b/Include/cholmod_config.h.in
-@@ -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: */
- 
--/*
--#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
-+++ b/MATLAB/Makefile.am
-@@ -0,0 +1,25 @@
-+# Needed by Doc/Makefile.am
-+EXTRA_DIST = \
-+	analyze.m \
-+	bisect.m \
-+	chol2.m \
-+	cholmod2.m \
-+	cholmod_demo.m \
-+	cholmod_make.m \
-+	etree2.m \
-+	graph_demo.m \
-+	lchol.m \
-+	ldl_normest.m \
-+	ldlchol.m \
-+	ldlsolve.m \
-+	ldlsplit.m \
-+	ldlupdate.m \
-+	metis.m \
-+	mread.m \
-+	mwrite.m \
-+	nesdis.m \
-+	resymbol.m \
-+	sdmult.m \
-+	sparse2.m \
-+	spsym.m \
-+	symbfact2.m
-diff --git a/Makefile.am b/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Makefile.am
-@@ -0,0 +1,43 @@
-+SUBDIRS = Include Core
-+EXTRA_DIST = README.txt
-+
-+pkgconfigdir = $(libdir)/pkgconfig
-+pkgconfig_DATA = cholmod.pc
-+
-+lib_LTLIBRARIES = libcholmod.la
-+
-+libcholmod_la_SOURCES =
-+libcholmod_la_LIBADD = $(top_builddir)/Core/libcore.la
-+libcholmod_la_LDFLAGS = -no-undefined -version-number 2:1:2
-+
-+if MOD_CHECK
-+SUBDIRS += Check
-+libcholmod_la_LIBADD += $(top_builddir)/Check/libcheck.la
-+endif
-+
-+if MOD_CHOLESKY
-+SUBDIRS += Cholesky
-+libcholmod_la_LIBADD += $(top_builddir)/Cholesky/libcholesky.la
-+endif
-+
-+if MOD_PARTITION
-+SUBDIRS += Partition
-+libcholmod_la_LIBADD += $(top_builddir)/Partition/libpartition.la
-+endif
-+
-+if MOD_MATRIXOPS
-+SUBDIRS += MatrixOps
-+libcholmod_la_LIBADD += $(top_builddir)/MatrixOps/libmatrixops.la
-+endif
-+
-+if MOD_MODIFY
-+SUBDIRS += Modify
-+libcholmod_la_LIBADD += $(top_builddir)/Modify/libmodify.la
-+endif
-+
-+if MOD_SUPERNODAL
-+SUBDIRS += Supernodal
-+libcholmod_la_LIBADD += $(top_builddir)/Supernodal/libsupernodal.la
-+endif
-+
-+SUBDIRS += MATLAB Demo Doc
-diff --git a/MatrixOps/Makefile.am b/MatrixOps/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/MatrixOps/Makefile.am
-@@ -0,0 +1,35 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
-+
-+EXTRA_DIST = \
-+	License.txt \
-+	gpl.txt
-+
-+MATRIXOPSSRC = \
-+	cholmod_drop.c \
-+	cholmod_horzcat.c \
-+	cholmod_norm.c \
-+	cholmod_scale.c \
-+	cholmod_sdmult.c \
-+	cholmod_ssmult.c \
-+	cholmod_submatrix.c \
-+	cholmod_symmetry.c \
-+	cholmod_vertcat.c
-+
-+noinst_HEADERS = \
-+	t_cholmod_sdmult.c
-+
-+noinst_LTLIBRARIES = \
-+	libmatrixopsi.la \
-+	libmatrixopsl.la \
-+	libmatrixops.la
-+
-+libmatrixopsi_la_SOURCES = $(MATRIXOPSSRC)
-+libmatrixopsi_la_LIBADD = -lm
-+libmatrixopsi_la_CPPFLAGS = $(AM_CPPFLAGS)
-+
-+libmatrixopsl_la_SOURCES = $(MATRIXOPSSRC)
-+libmatrixopsl_la_LIBADD = -lm
-+libmatrixopsl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG
-+
-+libmatrixops_la_SOURCES =
-+libmatrixops_la_LIBADD = libmatrixopsi.la libmatrixopsl.la
-diff --git a/Modify/Makefile.am b/Modify/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Modify/Makefile.am
-@@ -0,0 +1,30 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
-+
-+EXTRA_DIST = \
-+	License.txt \
-+	gpl.txt
-+
-+MODIFYSRC = \
-+	cholmod_rowadd.c \
-+	cholmod_rowdel.c \
-+	cholmod_updown.c
-+
-+noinst_HEADERS = \
-+	t_cholmod_updown.c \
-+	t_cholmod_updown_numkr.c
-+
-+noinst_LTLIBRARIES = \
-+	libmodifyi.la \
-+	libmodifyl.la \
-+	libmodify.la
-+
-+libmodifyi_la_SOURCES = $(MODIFYSRC)
-+libmodifyi_la_LIBADD = -lm
-+libmodifyi_la_CPPFLAGS = $(AM_CPPFLAGS)
-+
-+libmodifyl_la_SOURCES = $(MODIFYSRC)
-+libmodifyl_la_LIBADD = -lm
-+libmodifyl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG
-+
-+libmodify_la_SOURCES =
-+libmodify_la_LIBADD = libmodifyi.la libmodifyl.la
-diff --git a/Partition/Makefile.am b/Partition/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Partition/Makefile.am
-@@ -0,0 +1,28 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(METIS_CFLAGS) $(CCOLAMD_CFLAGS) $(CAMD_CFLAGS) $(SUITESPARSECONFIG_CFLAGS)
-+
-+EXTRA_DIST = \
-+	License.txt \
-+	lesser.txt
-+
-+PARTITIONSRC = \
-+	cholmod_camd.c \
-+	cholmod_ccolamd.c \
-+	cholmod_csymamd.c \
-+	cholmod_metis.c \
-+	cholmod_nesdis.c
-+
-+noinst_LTLIBRARIES = \
-+	libpartitioni.la \
-+	libpartitionl.la \
-+	libpartition.la
-+
-+libpartitioni_la_SOURCES = $(PARTITIONSRC)
-+libpartitioni_la_LIBADD = $(METIS_LIBS) $(CCOLAMD_LIBS) $(CAMD_LIBS) -lm
-+libpartitioni_la_CPPFLAGS = $(AM_CPPFLAGS)
-+
-+libpartitionl_la_SOURCES = $(PARTITIONSRC)
-+libpartitionl_la_LIBADD = $(METIS_LIBS) $(CCOLAMD_LIBS) $(CAMD_LIBS) -lm
-+libpartitionl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG
-+
-+libpartition_la_SOURCES =
-+libpartition_la_LIBADD = libpartitioni.la libpartitionl.la
-diff --git a/Partition/cholmod_camd.c b/Partition/cholmod_camd.c
---- a/Partition/cholmod_camd.c
-+++ b/Partition/cholmod_camd.c
-@@ -32,6 +32,7 @@
-  * Supports any xtype (pattern, real, complex, or zomplex)
-  */
- 
-+#include "cholmod_config.h"
- #ifndef NCAMD
- 
- #include "cholmod_internal.h"
-diff --git a/Partition/cholmod_ccolamd.c b/Partition/cholmod_ccolamd.c
---- a/Partition/cholmod_ccolamd.c
-+++ b/Partition/cholmod_ccolamd.c
-@@ -22,6 +22,7 @@
-  * Supports any xtype (pattern, real, complex, or zomplex).
-  */
- 
-+#include "cholmod_config.h"
- #ifndef NCAMD
- 
- #include "cholmod_internal.h"
-diff --git a/Partition/cholmod_csymamd.c b/Partition/cholmod_csymamd.c
---- a/Partition/cholmod_csymamd.c
-+++ b/Partition/cholmod_csymamd.c
-@@ -21,6 +21,7 @@
-  * Supports any xtype (pattern, real, complex, or zomplex).
-  */
- 
-+#include "cholmod_config.h"
- #ifndef NCAMD
- 
- #include "cholmod_internal.h"
-diff --git a/Partition/cholmod_metis.c b/Partition/cholmod_metis.c
---- a/Partition/cholmod_metis.c
-+++ b/Partition/cholmod_metis.c
-@@ -43,6 +43,7 @@
-  * Supports any xtype (pattern, real, complex, or zomplex).
-  */
- 
-+#include "cholmod_config.h"
- #ifndef NPARTITION
- 
- #include "cholmod_internal.h"
-diff --git a/Partition/cholmod_nesdis.c b/Partition/cholmod_nesdis.c
---- a/Partition/cholmod_nesdis.c
-+++ b/Partition/cholmod_nesdis.c
-@@ -38,6 +38,7 @@
-  * Supports any xtype (pattern, real, complex, or zomplex).
-  */
- 
-+#include "cholmod_config.h"
- #ifndef NPARTITION
- 
- #include "cholmod_internal.h"
-diff --git a/Supernodal/Makefile.am b/Supernodal/Makefile.am
-new file mode 100644
---- /dev/null
-+++ b/Supernodal/Makefile.am
-@@ -0,0 +1,39 @@
-+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS)
-+
-+EXTRA_DIST = \
-+	License.txt \
-+	gpl.txt
-+
-+SUPERNODALSRC = \
-+	cholmod_super_numeric.c \
-+	cholmod_super_solve.c \
-+	cholmod_super_symbolic.c
-+
-+noinst_HEADERS = \
-+	t_cholmod_gpu.c \
-+	t_cholmod_super_numeric.c \
-+	t_cholmod_super_solve.c
-+
-+noinst_LTLIBRARIES = \
-+	libsupernodali.la \
-+	libsupernodall.la \
-+	libsupernodal.la
-+
-+libsupernodali_la_SOURCES = $(SUPERNODALSRC)
-+libsupernodali_la_LIBADD = $(LAPACK_LIBS) $(BLAS_LIBS)
-+libsupernodali_la_CPPFLAGS = $(AM_CPPFLAGS)
-+
-+libsupernodall_la_SOURCES = $(SUPERNODALSRC)
-+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/ax_blas.m4 b/ax_blas.m4
-new file mode 100644
---- /dev/null
-+++ b/ax_blas.m4
-@@ -0,0 +1,238 @@
-+# ===========================================================================
-+#          http://www.gnu.org/software/autoconf-archive/ax_blas.html
-+# ===========================================================================
-+#
-+# SYNOPSIS
-+#
-+#   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.
-+#
-+#   To link with BLAS, you should link with:
-+#
-+#     $BLAS_LIBS $LIBS $FLIBS
-+#
-+#   in that order. 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.
-+#
-+#   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.
-+#
-+# LICENSE
-+#
-+#   Copyright (c) 2008 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 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.
-+#
-+#   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.
-+#
-+#   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
-+
-+AU_ALIAS([ACX_BLAS], [AX_BLAS])
-+AC_DEFUN([AX_BLAS], [
-+AC_PREREQ(2.50)
-+AC_REQUIRE([AC_F77_LIBRARY_LDFLAGS])
-+AC_REQUIRE([AC_CANONICAL_HOST])
-+ax_blas_ok=no
-+
-+AC_ARG_WITH(blas,
-+	[AS_HELP_STRING([--with-blas=<lib>], [use BLAS library <lib>])])
-+case $with_blas in
-+	yes | "") ;;
-+	no) ax_blas_ok=disable ;;
-+	-* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;;
-+	*) BLAS_LIBS="-l$with_blas" ;;
-+esac
-+
-+# Get fortran linker names of BLAS functions to check for.
-+AC_F77_FUNC(sgemm)
-+AC_F77_FUNC(dgemm)
-+
-+ax_blas_save_LIBS="$LIBS"
-+LIBS="$LIBS $FLIBS"
-+
-+# First, check BLAS_LIBS environment variable
-+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, [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 $ax_blas_ok = no; then
-+	save_LIBS="$LIBS"; LIBS="$LIBS"
-+	AC_MSG_CHECKING([if $sgemm is being linked in already])
-+	AC_TRY_LINK_FUNC($sgemm, [ax_blas_ok=yes])
-+	AC_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 $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])])
-+fi
-+
-+# BLAS in PhiPACK libraries? (requires generic BLAS lib, too)
-+if test $ax_blas_ok = no; then
-+	AC_CHECK_LIB(blas, $sgemm,
-+		[AC_CHECK_LIB(dgemm, $dgemm,
-+		[AC_CHECK_LIB(sgemm, $sgemm,
-+			[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 $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 $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 $ax_blas_ok = no; then
-+	if test "x$GCC" != xyes; then # only works with Sun CC
-+		AC_CHECK_LIB(sunmath, acosp,
-+			[AC_CHECK_LIB(sunperf, $sgemm,
-+				[BLAS_LIBS="-xlic_lib=sunperf -lsunmath"
-+                                 ax_blas_ok=yes],[],[-lsunmath])])
-+	fi
-+fi
-+
-+# BLAS in SCSL library?  (SGI/Cray Scientific Library)
-+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 $ax_blas_ok = no; then
-+	AC_CHECK_LIB(complib.sgimath, $sgemm,
-+		     [ax_blas_ok=yes; BLAS_LIBS="-lcomplib.sgimath"])
-+fi
-+
-+# BLAS in IBM ESSL library? (requires generic BLAS lib, too)
-+if test $ax_blas_ok = no; then
-+	AC_CHECK_LIB(blas, $sgemm,
-+		[AC_CHECK_LIB(essl, $sgemm,
-+			[ax_blas_ok=yes; BLAS_LIBS="-lessl -lblas"],
-+			[], [-lblas $FLIBS])])
-+fi
-+
-+# Generic BLAS library?
-+if test $ax_blas_ok = no; then
-+	AC_CHECK_LIB(blas, $sgemm, [ax_blas_ok=yes; BLAS_LIBS="-lblas"])
-+fi
-+
-+AC_SUBST(BLAS_LIBS)
-+
-+LIBS="$ax_blas_save_LIBS"
-+
-+# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
-+if test x"$ax_blas_ok" = xyes; then
-+        ifelse([$1],,AC_DEFINE(HAVE_BLAS,1,[Define if you have a BLAS library.]),[$1])
-+        :
-+else
-+        ax_blas_ok=no
-+        $2
-+fi
-+])dnl AX_BLAS
-diff --git a/ax_lapack.m4 b/ax_lapack.m4
-new file mode 100644
---- /dev/null
-+++ b/ax_lapack.m4
-@@ -0,0 +1,131 @@
-+# ===========================================================================
-+#         http://www.gnu.org/software/autoconf-archive/ax_lapack.html
-+# ===========================================================================
-+#
-+# SYNOPSIS
-+#
-+#   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.
-+#
-+#   To link with LAPACK, you should link with:
-+#
-+#     $LAPACK_LIBS $BLAS_LIBS $LIBS $FLIBS
-+#
-+#   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.
-+#
-+#   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.
-+#
-+# LICENSE
-+#
-+#   Copyright (c) 2009 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 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.
-+#
-+#   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.
-+#
-+#   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 7
-+
-+AU_ALIAS([ACX_LAPACK], [AX_LAPACK])
-+AC_DEFUN([AX_LAPACK], [
-+AC_REQUIRE([AX_BLAS])
-+ax_lapack_ok=no
-+
-+AC_ARG_WITH(lapack,
-+        [AS_HELP_STRING([--with-lapack=<lib>], [use LAPACK library <lib>])])
-+case $with_lapack in
-+        yes | "") ;;
-+        no) ax_lapack_ok=disable ;;
-+        -* | */* | *.a | *.so | *.so.* | *.o) LAPACK_LIBS="$with_lapack" ;;
-+        *) LAPACK_LIBS="-l$with_lapack" ;;
-+esac
-+
-+# Get fortran linker name of LAPACK function to check for.
-+AC_F77_FUNC(cheev)
-+
-+# We cannot use LAPACK if BLAS is not found
-+if test "x$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, [ax_lapack_ok=yes], [LAPACK_LIBS=""])
-+        AC_MSG_RESULT($ax_lapack_ok)
-+        LIBS="$save_LIBS"
-+        if test $ax_lapack_ok = no; then
-+                LAPACK_LIBS=""
-+        fi
-+fi
-+
-+# LAPACK linked to by default?  (is sometimes included in BLAS lib)
-+if test $ax_lapack_ok = no; then
-+        save_LIBS="$LIBS"; LIBS="$LIBS $BLAS_LIBS $FLIBS"
-+        AC_CHECK_FUNC($cheev, [ax_lapack_ok=yes])
-+        LIBS="$save_LIBS"
-+fi
-+
-+# Generic LAPACK library?
-+for lapack in lapack lapack_rs6k; do
-+        if test $ax_lapack_ok = no; then
-+                save_LIBS="$LIBS"; LIBS="$BLAS_LIBS $LIBS"
-+                AC_CHECK_LIB($lapack, $cheev,
-+                    [ax_lapack_ok=yes; LAPACK_LIBS="-l$lapack"], [], [$FLIBS])
-+                LIBS="$save_LIBS"
-+        fi
-+done
-+
-+AC_SUBST(LAPACK_LIBS)
-+
-+# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
-+if test x"$ax_lapack_ok" = xyes; then
-+        ifelse([$1],,AC_DEFINE(HAVE_LAPACK,1,[Define if you have LAPACK library.]),[$1])
-+        :
-+else
-+        ax_lapack_ok=no
-+        $2
-+fi
-+])dnl AX_LAPACK
-diff --git a/cholmod.pc.in b/cholmod.pc.in
-new file mode 100644
---- /dev/null
-+++ b/cholmod.pc.in
-@@ -0,0 +1,13 @@
-+prefix=@prefix@
-+exec_prefix=@exec_prefix@
-+libdir=@libdir@
-+includedir=@includedir@
-+
-+Name: @PACKAGE_NAME@
-+Description: Sparse Cholesky factorization
-+Version: @PACKAGE_VERSION@
-+URL: @PACKAGE_URL@
-+Requires.private: @CHOLMOD_REQUIRES@
-+Libs: -L${libdir} -lcholmod
-+Libs.private: @LAPACK_LIBS@ @BLAS_LIBS@ -lm
-+Cflags: -I${includedir}/cholmod
-diff --git a/configure.ac b/configure.ac
-new file mode 100644
---- /dev/null
-+++ b/configure.ac
-@@ -0,0 +1,215 @@
-+#                                               -*- Autoconf -*-
-+# Process this file with autoconf to produce a configure script.
-+
-+AC_PREREQ([2.69])
-+AC_INIT([CHOLMOD],[2.1.2],[DrTimothyAldenDavis@gmail.com],[cholmod],[http://www.suitesparse.com/])
-+AC_CONFIG_SRCDIR([Core/cholmod_common.c])
-+AC_CONFIG_HEADERS([config.h Include/cholmod_config.h])
-+AM_INIT_AUTOMAKE([foreign])
-+LT_INIT
-+
-+# Checks for programs.
-+AC_PROG_INSTALL
-+AC_PROG_CC
-+AC_PROG_F77
-+AC_PROG_AWK
-+
-+AC_MSG_CHECKING([whether to build GPL-licensed modules])
-+AC_ARG_ENABLE([gpl-modules],
-+	[AS_HELP_STRING(
-+		[--disable-gpl-modules],
-+		[do not build GPL-licensed modules])],
-+	[mod_gpl=$enableval],
-+	[mod_gpl="yes"])
-+AC_MSG_RESULT([$mod_gpl])
-+
-+AC_MSG_CHECKING([whether to build mod-check])
-+AC_ARG_ENABLE([mod-check],
-+	[AS_HELP_STRING(
-+		[--disable-mod-check],
-+		[do not build the Check module])],
-+	[mod_check=$enableval],
-+	[mod_check="yes"])
-+AC_MSG_RESULT([$mod_check])
-+
-+AC_MSG_CHECKING([whether to build mod-cholesky])
-+AC_ARG_ENABLE([mod-cholesky],
-+	[AS_HELP_STRING(
-+		[--disable-mod-cholesky],
-+		[do not build the Cholesky module])],
-+	[mod_cholesky=$enableval],
-+	[mod_cholesky="yes"])
-+AC_MSG_RESULT([$mod_cholesky])
-+
-+AC_MSG_CHECKING([whether to build mod-partition])
-+AC_ARG_ENABLE([mod-partition],
-+	[AS_HELP_STRING(
-+		[--disable-mod-partition],
-+		[do not build the Partition module])],
-+	[mod_partition=$enableval],
-+	[mod_partition="yes"])
-+AC_MSG_RESULT([$mod_partition])
-+
-+AC_MSG_CHECKING([whether to build mod-matrixops])
-+AC_ARG_ENABLE([mod-matrixops],
-+	[AS_HELP_STRING(
-+		[--disable-mod-matrixops],
-+		[do not build the MatrixOps module])],
-+	[mod_matrixops=$enableval],
-+	[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(
-+		[--disable-mod-modify],
-+		[do not build the Modify module])],
-+	[mod_modify=$enableval],
-+	[mod_modify=$mod_gpl])
-+AC_MSG_RESULT([$mod_modify])
-+
-+AC_MSG_CHECKING([whether to build mod-supernodal])
-+AC_ARG_ENABLE([mod-supernodal],
-+	[AS_HELP_STRING(
-+		[--disable-mod-supernodal],
-+		[do not build the Supernodal module])],
-+	[mod_supernodal=$enableval],
-+	[mod_supernodal=$mod_gpl])
-+AC_MSG_RESULT([$mod_supernodal])
-+
-+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=$LIBS
-+
-+# Checks for libraries.
-+AC_CHECK_LIB([m], [sqrt])
-+
-+PKG_PROG_PKG_CONFIG
-+PKG_CHECK_MODULES([SUITESPARSECONFIG],[suitesparseconfig],
-+	[],
-+	[AC_MSG_ERROR([cannot find suitesparseconfig])])
-+CHOLMOD_REQUIRES="suitesparseconfig"
-+
-+if test "x$mod_cholesky" = "xyes"; then
-+	PKG_CHECK_MODULES([AMD],[amd],
-+		[],
-+		[AC_MSG_ERROR([cannot find amd (required by mod-cholesky)])])
-+	CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES amd"
-+
-+	PKG_CHECK_MODULES([COLAMD],[colamd],
-+		[],
-+		[AC_MSG_ERROR([cannot find colamd (required by mod-cholesky)])])
-+	CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES colamd"
-+fi
-+
-+if test "x$mod_partition" = "xyes"; then
-+	PKG_CHECK_MODULES([CAMD],[camd],
-+		[],
-+		[AC_MSG_ERROR([cannot find camd (required by mod-partition)])])
-+	CHOLMOD_REQUIRES="$CHOLMOD_REQUIRES camd"
-+
-+	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([ax_blas.m4])
-+	AX_BLAS
-+	if test "x$ax_blas_ok" != "xyes"; then
-+		AC_MSG_ERROR([cannot find blas (required by mod-supernodal)])
-+	fi
-+
-+	sinclude([ax_lapack.m4])
-+	AX_LAPACK
-+	if test "x$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])
-+
-+AC_CONFIG_FILES([
-+	cholmod.pc
-+	Makefile
-+	Check/Makefile
-+	Cholesky/Makefile
-+	Core/Makefile
-+	Demo/Makefile
-+	Doc/Makefile
-+	Include/Makefile
-+	MATLAB/Makefile
-+	MatrixOps/Makefile
-+	Modify/Makefile
-+	Partition/Makefile
-+	Supernodal/Makefile])
-+AC_OUTPUT
diff --git a/libraries/CHOLMOD/slack-desc b/libraries/CHOLMOD/slack-desc
deleted file mode 100644
index 489bbf1ae8..0000000000
--- a/libraries/CHOLMOD/slack-desc
+++ /dev/null
@@ -1,19 +0,0 @@
-# HOW TO EDIT THIS FILE:
-# The "handy ruler" below makes it easier to edit a package description.
-# Line up the first '|' above the ':' following the base package name, and
-# the '|' on the right side marks the last column you can put a character in.
-# You must make exactly 11 lines for the formatting to be correct.  It's also
-# customary to leave one space after the ':' except on otherwise blank lines.
-
-       |-----handy-ruler------------------------------------------------------|
-CHOLMOD: CHOLMOD (sparse matrix factoring routines)
-CHOLMOD:
-CHOLMOD: CHOLMOD is a set of ANSI C routines for sparse Cholesky
-CHOLMOD: factorization and update/downdate.
-CHOLMOD:
-CHOLMOD:
-CHOLMOD:
-CHOLMOD:
-CHOLMOD:
-CHOLMOD:
-CHOLMOD: