ccolamd now installs and works with gtsam - all tests pass

configure.ac

@@ -16,8 +16,10 @@ AC_CONFIG_SRCDIR([gtsam/slam/pose2SLAM.cpp])
 AC_CONFIG_SRCDIR([tests/testTupleValues.cpp])
 AC_CONFIG_SRCDIR([examples/SimpleRotation.cpp])
 
-# pull in all subdirectories of Eigen - FIXME: find a better way of handling this
 AC_CONFIG_SRCDIR([gtsam/3rdparty/Makefile.am])
+AC_CONFIG_SRCDIR([gtsam/3rdparty/ccolamd/Makefile.am])
+
+# pull in all subdirectories of Eigen - FIXME: find a better way of handling this
 AC_CONFIG_SRCDIR([gtsam/3rdparty/Eigen/Makefile.am])
 AC_CONFIG_SRCDIR([gtsam/3rdparty/Eigen/src/Makefile.am])
 AC_CONFIG_SRCDIR([gtsam/3rdparty/Eigen/src/Cholesky/Makefile.am])
@@ -140,21 +142,21 @@ AX_BOOST_BASE([1.40])
 #            ])
 #AC_SUBST([boost])
 
-# ask for ccolamd library include directory
+## ask for ccolamd library include directory
-AC_ARG_WITH([ccolamd-inc],
+#AC_ARG_WITH([ccolamd-inc],
-            [AS_HELP_STRING([--with-ccolamd-inc],
+#            [AS_HELP_STRING([--with-ccolamd-inc],
-              [specify the CCOLAMD library include directory (defaults to /HOME/include/ccolamd)])],
+#              [specify the CCOLAMD library include directory (defaults to /HOME/include/ccolamd)])],
-            [CCOLAMDInc=$withval],
+#            [CCOLAMDInc=$withval],
-            [CCOLAMDInc=${HOME}/include/ccolamd])
+#            [CCOLAMDInc=${HOME}/include/ccolamd])
-AC_SUBST([CCOLAMDInc])
+#AC_SUBST([CCOLAMDInc])
-
+#
-# ask for sparse library lib directory
+## ask for sparse library lib directory
-AC_ARG_WITH([ccolamd-lib],
+#AC_ARG_WITH([ccolamd-lib],
-            [AS_HELP_STRING([--with-ccolamd-lib],
+#            [AS_HELP_STRING([--with-ccolamd-lib],
-              [specify the CCOLAMD library lib directory (defaults to /HOME/lib)])],
+#              [specify the CCOLAMD library lib directory (defaults to /HOME/lib)])],
-            [CCOLAMDLib=$withval],
+#            [CCOLAMDLib=$withval],
-            [CCOLAMDLib=${HOME}/lib])
+#            [CCOLAMDLib=${HOME}/lib])
-AC_SUBST([CCOLAMDLib])
+#AC_SUBST([CCOLAMDLib])
 
 AC_CONFIG_FILES([CppUnitLite/Makefile \
 gtsam/3rdparty/Eigen/src/Cholesky/Makefile \
@@ -183,6 +185,7 @@ gtsam/3rdparty/Eigen/src/Eigen2Support/Makefile \
 gtsam/3rdparty/Eigen/src/Eigen2Support/Geometry/Makefile \
 gtsam/3rdparty/Eigen/src/Makefile \
 gtsam/3rdparty/Eigen/Makefile \
+gtsam/3rdparty/ccolamd/Makefile \
 gtsam/3rdparty/Makefile \
 gtsam/base/Makefile \
 gtsam/geometry/Makefile \

examples/Makefile.am

@@ -22,7 +22,7 @@ SUBDIRS = vSLAMexample # visual SLAM examples with 3D point landmarks and 6D cam
 #----------------------------------------------------------------------------------------------------
 # rules to build local programs
 #----------------------------------------------------------------------------------------------------
-AM_CPPFLAGS = $(BOOST_CPPFLAGS) -I$(CCOLAMDInc) -I$(top_srcdir)
+AM_CPPFLAGS = $(BOOST_CPPFLAGS)  -I$(top_srcdir)
 AM_LDFLAGS = $(BOOST_LDFLAGS)
 LDADD = ../gtsam/libgtsam.la
 AM_DEFAULT_SOURCE_EXT = .cpp

examples/vSLAMexample/Makefile.am

@@ -28,7 +28,7 @@ dist-hook:
 #----------------------------------------------------------------------------------------------------
 # rules to build local programs
 #----------------------------------------------------------------------------------------------------
-AM_CPPFLAGS = $(BOOST_CPPFLAGS) -I$(CCOLAMDInc) -I$(top_srcdir)
+AM_CPPFLAGS = $(BOOST_CPPFLAGS)  -I$(top_srcdir)
 AM_LDFLAGS = $(BOOST_LDFLAGS)
 LDADD = ../../gtsam/libgtsam.la
 AM_DEFAULT_SOURCE_EXT = .cpp

gtsam/3rdparty/Makefile.am

@@ -1,8 +1,7 @@
 # 3rd Party libraries to be built and installed along with gtsam
 
 # All the sub-directories that need to be built
-SUBDIRS = Eigen
+SUBDIRS = Eigen ccolamd
 
 # And the corresponding libraries produced
-# TODO add sublibs when something in 3rdparty actually needs compilation
+SUBLIBS = ccolamd/libccolamd.la
-# SUBLIBS = 

gtsam/3rdparty/ccolamd/ChangeLog

@@ -1,3 +1,14 @@
+Changes for GTSAM Distribution
+June 2, 2011:
+	
+		* Moved all source/header files into a single folder within gtsam/3rdparty
+		* Removed demos, matlab examples, original makefiles
+		* Added UFconfig.[c|h] from the UFconfig suitesparse package
+		* Renamed licence file to LGPL.txt - contents remain the same
+		* All code is unchanged from original
+
+
+Original ChangeLog by authors
 Jan 25, 2011: version 2.7.3
 
     * minor fix to "make install"

gtsam/3rdparty/ccolamd/Lib_Makefile.mk

@@ -1,32 +0,0 @@
-#-------------------------------------------------------------------------------
-# CCOLAMD Makefile
-#-------------------------------------------------------------------------------
-
-default: libccolamd.a
-
-include ../../UFconfig/UFconfig.mk
-
-I = -I../Include -I../../UFconfig
-
-INC = ../Include/ccolamd.h ../../UFconfig/UFconfig.h
-
-SRC = ../Source/ccolamd.c ../Source/ccolamd_global.c
-
-# creates libccolamd.a, a C-callable COLAMD library
-libccolamd.a:  $(SRC) $(INC)
-	$(CC) $(CFLAGS) $(I) -c ../Source/ccolamd_global.c
-	$(CC) $(CFLAGS) $(I) -c ../Source/ccolamd.c
-	$(CC) $(CFLAGS) $(I) -c ../Source/ccolamd.c -DDLONG -o ccolamd_l.o
-	$(AR) libccolamd.a ccolamd.o ccolamd_l.o ccolamd_global.o
-
-ccode: libccolamd.a
-
-library: libccolamd.a
-
-clean:
-	- $(RM) $(CLEAN)
-
-purge: distclean
-
-distclean: clean
-	- $(RM) libccolamd.a

gtsam/3rdparty/ccolamd/Makefile.am

@@ -0,0 +1,30 @@
+#----------------------------------------------------------------------------------------------------
+# GTSAM 3rdparty: CCOLAMD
+# Tim Davis' sparse library for column ordering - part of suitesparse
+#----------------------------------------------------------------------------------------------------
+
+# use nostdinc to turn off -I. and -I.., we do not need them because 
+# header files are qualified so they can be included in external projects.
+AUTOMAKE_OPTIONS = nostdinc
+
+headers =
+sources = 
+
+# CCOLAMD (with UFconfig files included)
+headers += ccolamd.h UFconfig.h
+sources += ccolamd.c ccolamd_global.c UFconfig.c 
+
+#----------------------------------------------------------------------------------------------------
+# Create a libtool library that is not installed
+# It will be packaged in the toplevel libgtsam.la as specfied in ../Makefile.am 
+# The headers are installed in $(includedir)/gtsam/3rdparty: 
+#----------------------------------------------------------------------------------------------------
+ccolamddir = $(pkgincludedir)/3rdparty/ccolamd
+ccolamd_HEADERS = $(headers)
+noinst_LTLIBRARIES = libccolamd.la
+libccolamd_la_SOURCES = $(sources)
+
+AM_CPPFLAGS =
+
+AM_CPPFLAGS += $(BOOST_CPPFLAGS) -I$(top_srcdir) -DDLONG 
+AM_LDFLAGS = $(BOOST_LDFLAGS)

gtsam/3rdparty/ccolamd/UFconfig.mk

@@ -1,386 +0,0 @@
-#===============================================================================
-# UFconfig.mk:  common configuration file for the SuiteSparse
-#===============================================================================
-
-# This file contains all configuration settings for all packages authored or
-# co-authored by Tim Davis at the University of Florida:
-#
-# Package Version       Description
-# ------- -------       -----------
-# AMD	  1.2 or later  approximate minimum degree ordering
-# COLAMD  2.4 or later  column approximate minimum degree ordering
-# CCOLAMD 1.0 or later  constrained column approximate minimum degree ordering
-# CAMD    any		constrained approximate minimum degree ordering
-# UMFPACK 4.5 or later	sparse LU factorization, with the BLAS
-# CHOLMOD any		sparse Cholesky factorization, update/downdate
-# KLU	  0.8 or later  sparse LU factorization, BLAS-free
-# BTF	  0.8 or later  permutation to block triangular form
-# LDL	  1.2 or later	concise sparse LDL'
-# LPDASA  any		linear program solve (dual active set algorithm)
-# CXSparse any		extended version of CSparse (int/long, real/complex)
-# SuiteSparseQR	any	sparse QR factorization
-#
-# The UFconfig directory and the above packages should all appear in a single
-# directory, in order for the Makefile's within each package to find this file.
-#
-# To enable an option of the form "# OPTION = ...", edit this file and
-# delete the "#" in the first column of the option you wish to use.
-
-#------------------------------------------------------------------------------
-# Generic configuration
-#------------------------------------------------------------------------------
-
-# C compiler and compiler flags:  These will normally not give you optimal
-# performance.  You should select the optimization parameters that are best
-# for your system.  On Linux, use "CFLAGS = -O3 -fexceptions" for example.
-CC = cc
-CFLAGS = -O3 -fexceptions
-
-# C++ compiler (also uses CFLAGS)
-CPLUSPLUS = g++
-
-# ranlib, and ar, for generating libraries
-RANLIB = ranlib
-AR = ar cr
-
-# copy, delete, and rename a file
-CP = cp -f
-RM = rm -f
-MV = mv -f
-
-# Fortran compiler (not normally required)
-F77 = f77
-F77FLAGS = -O
-F77LIB =
-
-# C and Fortran libraries
-LIB = -lm
-
-# For compiling MATLAB mexFunctions (MATLAB 7.5 or later)
-MEX = mex -O -largeArrayDims -lmwlapack -lmwblas
-
-# For compiling MATLAB mexFunctions (MATLAB 7.3 and 7.4)
-# MEX = mex -O -largeArrayDims -lmwlapack
-
-# For MATLAB 7.2 or earlier, you must use one of these options:
-# MEX = mex -O -lmwlapack
-# MEX = mex -O
-
-# Which version of MAKE you are using (default is "make")
-# MAKE = make
-# MAKE = gmake
-
-# For "make install"
-INSTALL_LIB = /usr/local/lib
-INSTALL_INCLUDE = /usr/local/include
-
-#------------------------------------------------------------------------------
-# BLAS and LAPACK configuration:
-#------------------------------------------------------------------------------
-
-# UMFPACK and CHOLMOD both require the BLAS.  CHOLMOD also requires LAPACK.
-# See Kazushige Goto's BLAS at http://www.cs.utexas.edu/users/flame/goto/ or
-# http://www.tacc.utexas.edu/~kgoto/ for the best BLAS to use with CHOLMOD.
-# LAPACK is at http://www.netlib.org/lapack/ .  You can use the standard
-# Fortran LAPACK along with Goto's BLAS to obtain very good performance.
-# CHOLMOD gets a peak numeric factorization rate of 3.6 Gflops on a 3.2 GHz
-# Pentium 4 (512K cache, 4GB main memory) with the Goto BLAS, and 6 Gflops
-# on a 2.5Ghz dual-core AMD Opteron.
-
-# These settings will probably not work, since there is no fixed convention for
-# naming the BLAS and LAPACK library (*.a or *.so) files.
-
-# This is probably slow ... it might connect to the Standard Reference BLAS:
-BLAS = -lblas -lgfortran
-LAPACK = -llapack
-
-# NOTE: this next option for the "Goto BLAS" has nothing to do with a "goto"
-# statement.  Rather, the Goto BLAS is written by Dr. Kazushige Goto.
-# Using the Goto BLAS:
-# BLAS = -lgoto -lgfortran -lgfortranbegin
-
-# Using non-optimized versions:
-# BLAS = -lblas_plain -lgfortran -lgfortranbegin
-# LAPACK = -llapack_plain
-
-# BLAS = -lblas_plain -lgfortran -lgfortranbegin
-# LAPACK = -llapack
-
-# The BLAS might not contain xerbla, an error-handling routine for LAPACK and
-# the BLAS.  Also, the standard xerbla requires the Fortran I/O library, and
-# stops the application program if an error occurs.  A C version of xerbla
-# distributed with this software (UFconfig/xerbla/libcerbla.a) includes a
-# Fortran-callable xerbla routine that prints nothing and does not stop the
-# application program.  This is optional.
-# XERBLA = ../../UFconfig/xerbla/libcerbla.a 
-
-# If you wish to use the XERBLA in LAPACK and/or the BLAS instead,
-# use this option:
-XERBLA = 
-
-# If you wish to use the Fortran UFconfig/xerbla/xerbla.f instead, use this:
-# XERBLA = ../../UFconfig/xerbla/libxerbla.a 
-
-#------------------------------------------------------------------------------
-# METIS, optionally used by CHOLMOD
-#------------------------------------------------------------------------------
-
-# If you do not have METIS, or do not wish to use it in CHOLMOD, you must
-# compile CHOLMOD with the -DNPARTITION flag.  You must also use the
-# "METIS =" option, below.
-
-# The path is relative to where it is used, in CHOLMOD/Lib, CHOLMOD/MATLAB, etc.
-# You may wish to use an absolute path.  METIS is optional.  Compile
-# CHOLMOD with -DNPARTITION if you do not wish to use METIS.
-METIS_PATH = ../../metis-4.0
-METIS = ../../metis-4.0/libmetis.a
-
-# If you use CHOLMOD_CONFIG = -DNPARTITION then you must use the following
-# options:
-# METIS_PATH =
-# METIS =
-
-#------------------------------------------------------------------------------
-# UMFPACK configuration:
-#------------------------------------------------------------------------------
-
-# Configuration flags for UMFPACK.  See UMFPACK/Source/umf_config.h for details.
-#
-# -DNBLAS	do not use the BLAS.  UMFPACK will be very slow.
-# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
-#  		LAPACK and the BLAS (defaults to 'int')
-# -DNSUNPERF	do not use the Sun Perf. Library (default is use it on Solaris)
-# -DNPOSIX	do not use POSIX routines sysconf and times.
-# -DGETRUSAGE	use getrusage
-# -DNO_TIMER	do not use any timing routines
-# -DNRECIPROCAL	do not multiply by the reciprocal
-# -DNO_DIVIDE_BY_ZERO	do not divide by zero
-
-UMFPACK_CONFIG = 
-
-#------------------------------------------------------------------------------
-# CHOLMOD configuration
-#------------------------------------------------------------------------------
-
-# CHOLMOD Library Modules, which appear in libcholmod.a:
-# Core		requires: none
-# Check		requires: Core
-# Cholesky	requires: Core, AMD, COLAMD.  optional: Partition, Supernodal
-# MatrixOps	requires: Core
-# Modify	requires: Core
-# Partition	requires: Core, CCOLAMD, METIS.  optional: Cholesky
-# Supernodal	requires: Core, BLAS, LAPACK
-#
-# CHOLMOD test/demo Modules (all are GNU GPL, do not appear in libcholmod.a):
-# Tcov		requires: Core, Check, Cholesky, MatrixOps, Modify, Supernodal
-#		optional: Partition
-# Valgrind	same as Tcov
-# Demo		requires: Core, Check, Cholesky, MatrixOps, Supernodal
-#		optional: Partition
-#
-# Configuration flags:
-# -DNCHECK	    do not include the Check module.	   License GNU LGPL
-# -DNCHOLESKY	    do not include the Cholesky module.	   License GNU LGPL
-# -DNPARTITION	    do not include the Partition module.   License GNU LGPL
-#		    also do not include METIS.
-# -DNGPL	    do not include any GNU GPL Modules in the CHOLMOD library:
-# -DNMATRIXOPS	    do not include the MatrixOps module.   License GNU GPL
-# -DNMODIFY	    do not include the Modify module.      License GNU GPL
-# -DNSUPERNODAL     do not include the Supernodal module.  License GNU GPL
-#
-# -DNPRINT	    do not print anything.
-# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
-#  		    	LAPACK and the BLAS (defaults to 'int')
-# -DNSUNPERF	    for Solaris only.  If defined, do not use the Sun
-#			Performance Library
-
-CHOLMOD_CONFIG =
-
-#------------------------------------------------------------------------------
-# SuiteSparseQR configuration:
-#------------------------------------------------------------------------------
-
-# The SuiteSparseQR library can be compiled with the following options:
-#
-# -DNPARTITION      do not include the CHOLMOD partition module
-# -DNEXPERT         do not include the functions in SuiteSparseQR_expert.cpp
-# -DTIMING          enable timing and flop counts
-# -DHAVE_TBB        enable the use of Intel's Threading Building Blocks (TBB)
-
-# default, without timing, without TBB:
-SPQR_CONFIG =
-# with timing and TBB:
-# SPQR_CONFIG = -DTIMING -DHAVE_TBB
-# with timing
-# SPQR_CONFIG = -DTIMING
-
-# This is needed for IBM AIX: (but not for and C codes, just C++)
-# SPQR_CONFIG = -DBLAS_NO_UNDERSCORE
-
-# with TBB, you must select this:
-# TBB = -ltbb
-# without TBB:
-TBB =
-
-# with timing, you must include the timing library:
-# RTLIB = -lrt
-# without timing
-RTLIB =
-
-#------------------------------------------------------------------------------
-# Linux
-#------------------------------------------------------------------------------
-
-# Using default compilers:
-# CC = gcc
-# CFLAGS = -O3 -fexceptions
-
-# alternatives:
-# CFLAGS = -g -fexceptions \
-   	-Wall -W -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
-    	-Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi \
-        -funit-at-a-time
-# CFLAGS = -O3 -fexceptions \
-   	-Wall -W -Werror -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
-    	-Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi
-# CFLAGS = -O3 -fexceptions -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
-# CFLAGS = -O3
-# CFLAGS = -O3 -g -fexceptions
-# CFLAGS = -g -fexceptions \
-   	-Wall -W -Wshadow \
-    	-Wredundant-decls -Wdisabled-optimization -ansi
-
-# consider:
-# -fforce-addr -fmove-all-movables -freduce-all-givs -ftsp-ordering
-# -frename-registers -ffast-math -funroll-loops
-
-# Using the Goto BLAS:
-# BLAS = -lgoto -lfrtbegin -lg2c $(XERBLA) -lpthread
-
-# Using Intel's icc and ifort compilers:
-#   (does not work for mexFunctions unless you add a mexopts.sh file)
-# F77 = ifort
-# CC = icc
-# CFLAGS = -O3 -xN -vec_report=0
-# CFLAGS = -g
-# old (broken): CFLAGS = -ansi -O3 -ip -tpp7 -xW -vec_report0
-
-# 64bit:
-# F77FLAGS = -O -m64
-# CFLAGS = -O3 -fexceptions -m64
-# BLAS = -lgoto64 -lfrtbegin -lg2c -lpthread $(XERBLA)
-# LAPACK = -llapack64
-
-
-# SUSE Linux 10.1, AMD Opteron, with GOTO Blas
-# F77 = gfortran
-# BLAS = -lgoto_opteron64 -lgfortran
-
-# SUSE Linux 10.1, Intel Pentium, with GOTO Blas
-# F77 = gfortran
-# BLAS = -lgoto -lgfortran
-
-#------------------------------------------------------------------------------
-# Mac
-#------------------------------------------------------------------------------
-
-# As recommended by macports, http://suitesparse.darwinports.com/
-# I've tested them myself on Mac OSX 10.6.1 (Snow Leopard), on my MacBook Air.
-# F77 = gfortran
-# CFLAGS = -O3 -fno-common -no-cpp-precomp -fexceptions
-# BLAS = -framework Accelerate
-# LAPACK = -framework Accelerate
-
-# Using netlib.org LAPACK and BLAS compiled by gfortran, with and without
-# optimzation:
-# BLAS = -lblas_plain -lgfortran
-# LAPACK = -llapack_plain
-# BLAS = -lblas_optimized -lgfortran
-# LAPACK = -llapack_optimized
-
-#------------------------------------------------------------------------------
-# Solaris
-#------------------------------------------------------------------------------
-
-# 32-bit
-# CFLAGS = -KPIC -dalign -xc99=%none -Xc -xlibmieee -xO5 -xlibmil -m32
-
-# 64-bit
-# CFLAGS = -fast -KPIC -xc99=%none -xlibmieee -xlibmil -m64 -Xc
-
-# FFLAGS = -fast -KPIC -dalign -xlibmil -m64
-
-# The Sun Performance Library includes both LAPACK and the BLAS:
-# BLAS = -xlic_lib=sunperf
-# LAPACK =
-
-
-#------------------------------------------------------------------------------
-# Compaq Alpha
-#------------------------------------------------------------------------------
-
-# 64-bit mode only
-# CFLAGS = -O2 -std1
-# BLAS = -ldxml
-# LAPACK =
-
-#------------------------------------------------------------------------------
-# Macintosh
-#------------------------------------------------------------------------------
-
-# CC = gcc
-# CFLAGS = -O3 -fno-common -no-cpp-precomp -fexceptions
-# LIB = -lstdc++
-# BLAS = -framework Accelerate
-# LAPACK = -framework Accelerate
-
-#------------------------------------------------------------------------------
-# IBM RS 6000
-#------------------------------------------------------------------------------
-
-# BLAS = -lessl
-# LAPACK =
-
-# 32-bit mode:
-# CFLAGS   = -O4 -qipa -qmaxmem=16384 -qproto
-# F77FLAGS = -O4 -qipa -qmaxmem=16384
-
-# 64-bit mode:
-# CFLAGS   = -O4 -qipa -qmaxmem=16384 -q64 -qproto
-# F77FLAGS = -O4 -qipa -qmaxmem=16384 -q64
-# AR = ar -X64
-
-#------------------------------------------------------------------------------
-# SGI IRIX
-#------------------------------------------------------------------------------
-
-# BLAS = -lscsl
-# LAPACK =
-
-# 32-bit mode
-# CFLAGS = -O
-
-# 64-bit mode (32 bit int's and 64-bit long's):
-# CFLAGS = -64
-# F77FLAGS = -64
-
-# SGI doesn't have ranlib
-# RANLIB = echo
-
-#------------------------------------------------------------------------------
-# AMD Opteron (64 bit)
-#------------------------------------------------------------------------------
-
-# BLAS = -lgoto_opteron64 -lg2c
-# LAPACK = -llapack_opteron64
-
-# SUSE Linux 10.1, AMD Opteron
-# F77 = gfortran
-# BLAS = -lgoto_opteron64 -lgfortran
-# LAPACK = -llapack_opteron64
-
-#------------------------------------------------------------------------------
-# remove object files and profile output
-#------------------------------------------------------------------------------
-
-CLEAN = *.o *.obj *.ln *.bb *.bbg *.da *.tcov *.gcov gmon.out *.bak *.d *.gcda *.gcno

gtsam/3rdparty/ccolamd/ccolamd_Makefile.mk

@@ -1,63 +0,0 @@
-#------------------------------------------------------------------------------
-# CCOLAMD Makefile
-#------------------------------------------------------------------------------
-
-VERSION = 2.7.3
-
-default: demos
-
-include ../UFconfig/UFconfig.mk
-
-# Compile all C code, including the C-callable routine and the mexFunctions.
-# Do not the MATLAB interface.
-demos:
-	( cd Lib    ; $(MAKE) )
-	( cd Demo   ; $(MAKE) )
-
-# Compile all C code, including the C-callable routine and the mexFunctions.
-all:
-	( cd Lib    ; $(MAKE) )
-	( cd Demo   ; $(MAKE) )
-	( cd MATLAB ; $(MAKE) )
-
-# compile just the C-callable libraries (not mexFunctions or Demos)
-library:
-	( cd Lib    ; $(MAKE) )
-
-# remove object files, but keep the compiled programs and library archives
-clean:
-	( cd Lib    ; $(MAKE) clean )
-	( cd Demo   ; $(MAKE) clean )
-	( cd MATLAB ; $(MAKE) clean )
-
-# clean, and then remove compiled programs and library archives
-purge:
-	( cd Lib    ; $(MAKE) purge )
-	( cd Demo   ; $(MAKE) purge )
-	( cd MATLAB ; $(MAKE) purge )
-
-distclean: purge
-
-# get ready for distribution
-dist: purge
-	( cd Demo   ; $(MAKE) dist )
-
-ccode: library
-
-lib: library
-
-# compile the MATLAB mexFunction
-mex:
-	( cd MATLAB ; $(MAKE) )
-
-# install CCOLAMD
-install:
-	$(CP) Lib/libccolamd.a $(INSTALL_LIB)/libccolamd.$(VERSION).a
-	( cd $(INSTALL_LIB) ; ln -sf libccolamd.$(VERSION).a libccolamd.a )
-	$(CP) Include/ccolamd.h $(INSTALL_INCLUDE)
-
-# uninstall CCOLAMD
-uninstall:
-	$(RM) $(INSTALL_LIB)/libccolamd*.a
-	$(RM) $(INSTALL_INCLUDE)/ccolamd.h
-

gtsam/3rdparty/ccolamd/core_ufconfig_Makefile.mk

@@ -1,36 +0,0 @@
-# Makefile for UFconfig.c
-
-VERSION = 3.6.0
-
-default: ccode
-
-include UFconfig.mk
-
-ccode: libufconfig.a
-
-all: libufconfig.a
-
-libufconfig.a: UFconfig.c UFconfig.h
-	$(CC) $(CFLAGS) -c UFconfig.c
-	$(AR) libufconfig.a UFconfig.o
-	- $(RM) UFconfig.o
-
-distclean: purge
-
-purge: clean
-	- $(RM) *.o *.a
-
-clean:
-	- $(RM) -r $(CLEAN)
-
-# install UFconfig
-install:
-	$(CP) libufconfig.a $(INSTALL_LIB)/libufconfig.$(VERSION).a
-	( cd $(INSTALL_LIB) ; ln -sf libufconfig.$(VERSION).a libufconfig.a )
-	$(CP) UFconfig.h $(INSTALL_INCLUDE)
-
-# uninstall UFconfig
-uninstall:
-	$(RM) $(INSTALL_LIB)/libufconfig*.a
-	$(RM) $(INSTALL_INCLUDE)/UFconfig.h
-

gtsam/Makefile.am

@@ -1,14 +1,15 @@
 
 # All the sub-directories that need to be built
-SUBDIRS = base geometry inference linear nonlinear slam 3rdparty 
+SUBDIRS = 3rdparty base geometry inference linear nonlinear slam 
 
 # And the corresponding libraries produced
-SUBLIBS = base/libbase.la geometry/libgeometry.la inference/libinference.la \
+SUBLIBS = 3rdparty/ccolamd/libccolamd.la base/libbase.la geometry/libgeometry.la \
-          linear/liblinear.la nonlinear/libnonlinear.la slam/libslam.la
+					inference/libinference.la linear/liblinear.la nonlinear/libnonlinear.la \
+					 slam/libslam.la 
 
 # The following lines specify the actual shared library to be built with libtool
 lib_LTLIBRARIES = libgtsam.la
 libgtsam_la_SOURCES = 
 nodist_EXTRA_libgtsam_la_SOURCES = dummy.cxx
-libgtsam_la_LIBADD = $(SUBLIBS) -L$(CCOLAMDLib) $(BOOST_LDFLAGS) -lccolamd
+libgtsam_la_LIBADD = $(SUBLIBS) $(BOOST_LDFLAGS) 
 libgtsam_la_LDFLAGS = -no-undefined -version-info 0:0:0

gtsam/base/Makefile.am

@@ -55,7 +55,7 @@ libbase_la_SOURCES = $(sources)
 
 AM_CPPFLAGS =
 
-AM_CPPFLAGS += $(BOOST_CPPFLAGS) -I$(CCOLAMDInc) -I$(top_srcdir)
+AM_CPPFLAGS += $(BOOST_CPPFLAGS) -I$(top_srcdir)
 AM_LDFLAGS = $(BOOST_LDFLAGS)
 
 #----------------------------------------------------------------------------------------------------
@@ -63,8 +63,8 @@ AM_LDFLAGS = $(BOOST_LDFLAGS)
 #----------------------------------------------------------------------------------------------------
 TESTS = $(check_PROGRAMS)
 AM_DEFAULT_SOURCE_EXT = .cpp
-AM_LDFLAGS += $(boost_serialization) -L$(CCOLAMDLib) -lccolamd
+AM_LDFLAGS += $(boost_serialization) 
-LDADD = libbase.la ../../CppUnitLite/libCppUnitLite.a
+LDADD = libbase.la ../../CppUnitLite/libCppUnitLite.a ../3rdparty/ccolamd/libccolamd.la
 
 # rule to run an executable
 %.run: % $(LDADD)

gtsam/inference/Makefile.am

@@ -43,17 +43,6 @@ check_PROGRAMS += tests/testEliminationTree
 check_PROGRAMS += tests/testClusterTree
 check_PROGRAMS += tests/testJunctionTree
 
-#----------------------------------------------------------------------------------------------------
-# discrete
-#----------------------------------------------------------------------------------------------------
-
-# Binary Inference
-#headers += BinaryConditional.h
-#check_PROGRAMS += tests/testBinaryBayesNet
-
-# Timing tests
-#noinst_PROGRAMS = tests/timeSymbolMaps
-
 #----------------------------------------------------------------------------------------------------
 # Create a libtool library that is not installed
 # It will be packaged in the toplevel libgtsam.la as specfied in ../Makefile.am 
@@ -64,7 +53,7 @@ inferencedir = $(pkgincludedir)/inference
 inference_HEADERS = $(headers)
 noinst_LTLIBRARIES = libinference.la
 libinference_la_SOURCES = $(sources)
-AM_CPPFLAGS = $(BOOST_CPPFLAGS) -I$(CCOLAMDInc) -I$(top_srcdir)
+AM_CPPFLAGS = $(BOOST_CPPFLAGS) -I$(top_srcdir)
 AM_LDFLAGS = $(BOOST_LDFLAGS)
 AM_CXXFLAGS =
 
@@ -73,7 +62,7 @@ AM_CXXFLAGS =
 #----------------------------------------------------------------------------------------------------
 TESTS = $(check_PROGRAMS)
 AM_LDFLAGS += $(boost_serialization)
-LDADD = libinference.la ../base/libbase.la
+LDADD = libinference.la ../base/libbase.la ../3rdparty/ccolamd/libccolamd.la
 LDADD += ../../CppUnitLite/libCppUnitLite.a 
 AM_DEFAULT_SOURCE_EXT = .cpp
 

gtsam/inference/inference.cpp

@@ -23,7 +23,7 @@
 #include <iostream>
 #include <vector>
 
-#include <ccolamd.h>
+#include <gtsam/3rdparty/ccolamd/ccolamd.h>
 
 using namespace std;
 

gtsam/linear/Makefile.am

@@ -55,7 +55,7 @@ lineardir = $(pkgincludedir)/linear
 linear_HEADERS = $(headers)
 noinst_LTLIBRARIES = liblinear.la
 liblinear_la_SOURCES = $(sources)
-AM_CPPFLAGS = $(BOOST_CPPFLAGS) -I$(CCOLAMDInc) -I$(top_srcdir)
+AM_CPPFLAGS = $(BOOST_CPPFLAGS)  -I$(top_srcdir)
 AM_LDFLAGS = $(BOOST_LDFLAGS)
 AM_CXXFLAGS =
 
@@ -64,7 +64,7 @@ AM_CXXFLAGS =
 #----------------------------------------------------------------------------------------------------
 TESTS = $(check_PROGRAMS)
 AM_LDFLAGS += $(boost_serialization)
-LDADD = liblinear.la ../inference/libinference.la ../base/libbase.la
+LDADD = liblinear.la ../inference/libinference.la ../base/libbase.la ../3rdparty/ccolamd/libccolamd.la
 LDADD += ../../CppUnitLite/libCppUnitLite.a
 AM_DEFAULT_SOURCE_EXT = .cpp
 

gtsam/nonlinear/Makefile.am

@@ -43,7 +43,7 @@ nonlineardir = $(pkgincludedir)/nonlinear
 nonlinear_HEADERS = $(headers)
 noinst_LTLIBRARIES = libnonlinear.la
 libnonlinear_la_SOURCES = $(sources)
-AM_CPPFLAGS = $(BOOST_CPPFLAGS) -I$(CCOLAMDInc) -I$(top_srcdir)
+AM_CPPFLAGS = $(BOOST_CPPFLAGS)  -I$(top_srcdir)
 AM_LDFLAGS = $(BOOST_LDFLAGS)
 AM_CXXFLAGS =
 
@@ -52,7 +52,7 @@ AM_CXXFLAGS =
 #----------------------------------------------------------------------------------------------------
 TESTS = $(check_PROGRAMS)
 AM_LDFLAGS += $(boost_serialization)
-LDADD = libnonlinear.la ../linear/liblinear.la ../inference/libinference.la ../base/libbase.la
+LDADD = libnonlinear.la ../linear/liblinear.la ../inference/libinference.la ../base/libbase.la ../3rdparty/ccolamd/libccolamd.la
 LDADD += ../../CppUnitLite/libCppUnitLite.a
 AM_DEFAULT_SOURCE_EXT = .cpp
 

gtsam/slam/Makefile.am

@@ -64,7 +64,7 @@ slamdir = $(pkgincludedir)/slam
 slam_HEADERS = $(headers)
 noinst_LTLIBRARIES = libslam.la
 libslam_la_SOURCES = $(sources)
-AM_CPPFLAGS = $(BOOST_CPPFLAGS) -I$(CCOLAMDInc) -I$(top_srcdir)
+AM_CPPFLAGS = $(BOOST_CPPFLAGS)  -I$(top_srcdir)
 AM_LDFLAGS = $(BOOST_LDFLAGS)
 
 #----------------------------------------------------------------------------------------------------
@@ -72,8 +72,8 @@ AM_LDFLAGS = $(BOOST_LDFLAGS)
 #----------------------------------------------------------------------------------------------------
 TESTS = $(check_PROGRAMS)
 AM_DEFAULT_SOURCE_EXT = .cpp
-AM_LDFLAGS += $(boost_serialization) -L$(CCOLAMDLib) -lccolamd
+AM_LDFLAGS += $(boost_serialization) 
-LDADD = libslam.la ../geometry/libgeometry.la  ../nonlinear/libnonlinear.la ../linear/liblinear.la ../inference/libinference.la ../base/libbase.la
+LDADD = libslam.la ../geometry/libgeometry.la  ../nonlinear/libnonlinear.la ../linear/liblinear.la ../inference/libinference.la ../base/libbase.la ../3rdparty/ccolamd/libccolamd.la 
 LDADD += ../../CppUnitLite/libCppUnitLite.a
 
 # rule to run an executable

tests/Makefile.am

@@ -34,7 +34,7 @@ noinst_PROGRAMS = timeGaussianFactorGraph timeSequentialOnDataset timeMultifront
 #----------------------------------------------------------------------------------------------------
 TESTS = $(check_PROGRAMS)
 AM_LDFLAGS = $(BOOST_LDFLAGS)
-AM_CPPFLAGS = $(BOOST_CPPFLAGS) -I$(CCOLAMDInc) -I$(top_srcdir)
+AM_CPPFLAGS = $(BOOST_CPPFLAGS)  -I$(top_srcdir)
 
 # link to serialization library for test 
 if ENABLE_SERIALIZATION