diff --git a/configure.ac b/configure.ac
index b422caf..dae8647 100644
--- a/configure.ac
+++ b/configure.ac
@@ -333,6 +333,8 @@ else
   internal_glpk=no
 fi
 
+PKG_CHECK_MODULES([CS],[cxsparse])
+
 # Link time optimization feature in newer gcc/g++
 # based on http://svn.r-project.org/R/trunk/configure.ac
 AC_ARG_ENABLE([lto],
diff --git a/examples/simple/igraph_sparsemat2.c b/examples/simple/igraph_sparsemat2.c
index 24877c2..0f4b45c 100644
--- a/examples/simple/igraph_sparsemat2.c
+++ b/examples/simple/igraph_sparsemat2.c
@@ -21,7 +21,7 @@
 
 */
 
-#include <cs/cs.h>
+#include <cs.h>
 #include <igraph.h>
 #include "igraph_blas_internal.h"
 #include "igraph_arpack_internal.h"
diff --git a/examples/simple/igraph_sparsemat3.c b/examples/simple/igraph_sparsemat3.c
index 09329f0..31d4f1f 100644
--- a/examples/simple/igraph_sparsemat3.c
+++ b/examples/simple/igraph_sparsemat3.c
@@ -21,7 +21,7 @@
 
 */
 
-#include <cs/cs.h>
+#include <cs.h>
 #include <igraph.h>
 
 int permute(const igraph_matrix_t *M,
diff --git a/examples/simple/igraph_sparsemat4.c b/examples/simple/igraph_sparsemat4.c
index 3a33979..c0ea489 100644
--- a/examples/simple/igraph_sparsemat4.c
+++ b/examples/simple/igraph_sparsemat4.c
@@ -21,7 +21,7 @@
 
 */
 
-#include <cs/cs.h>
+#include <cs.h>
 #include <igraph.h>
 
 igraph_bool_t check_solution(const igraph_sparsemat_t *A,
diff --git a/src/Makefile.am b/src/Makefile.am
index f9d02d2..8ab3385 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -9,9 +9,6 @@ AM_YFLAGS = -d
 
 lib_LTLIBRARIES         = libigraph.la
 
-include lapack/blas.inc
-include lapack/lapack.inc
-include lapack/arpack.inc
 include plfit/plfit.inc
 
 F2C =	f2c/abort_.c	  f2c/dolio.c	    f2c/r_sin.c\
@@ -99,8 +96,6 @@ if INTERNAL_ARPACK
   ARPACK_LIB = libarpack.la
 endif
 
-include ../optional/glpk/glpk.inc
-
 if INTERNAL_GLPK
   libglpk_la_SOURCES = 	$(GLPK)
   libglpk_la_CFLAGS = -I$(top_srcdir)/optional/glpk
@@ -365,7 +360,7 @@ SOURCES = 		     basic_query.c games.c cocitation.c iterators.c \
 			     drl_layout_3d.cpp drl_graph_3d.cpp \
 			     DensityGrid_3d.cpp \
 			     foreign-dl-parser.y foreign-dl-lexer.l \
-			     $(CS) sparsemat.c mixing.c bigint.c bignum.c \
+			     sparsemat.c mixing.c bigint.c bignum.c \
 			     version.c optimal_modularity.c \
 			     igraph_fixed_vectorlist.c separators.c \
 			     igraph_marked_queue.c igraph_estack.c st-cuts.c \
@@ -408,7 +403,7 @@ libigraph_la_CXXFLAGS	   = -I$(top_srcdir)/include -I$(top_builddir)/include $(W
 libigraph_la_LDFLAGS       = -no-undefined
 libigraph_la_LIBADD        = -lm $(XML2_LIBS) $(F2C_LIB) $(BLAS_LIB) \
 				 $(LAPACK_LIB) $(ARPACK_LIB) $(GLPK_LIB) $(PRPACK_LIB) \
-				 $(PLFIT_LIB)
+				 $(PLFIT_LIB) $(CS_LIBS)
 
 if INTERNAL_GLPK
   libigraph_la_CFLAGS   += -I$(top_srcdir)/optional/glpk
diff --git a/src/Makefile.in b/src/Makefile.in
index 56703d4..cc30d48 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -2411,7 +2411,7 @@ SOURCES = basic_query.c games.c cocitation.c iterators.c \
 	gengraph_powerlaw.cpp gengraph_random.cpp decomposition.c \
 	bipartite.c drl_layout_3d.cpp drl_graph_3d.cpp \
 	DensityGrid_3d.cpp foreign-dl-parser.y foreign-dl-lexer.l \
-	$(CS) sparsemat.c mixing.c bigint.c bignum.c version.c \
+	sparsemat.c mixing.c bigint.c bignum.c version.c \
 	optimal_modularity.c igraph_fixed_vectorlist.c separators.c \
 	igraph_marked_queue.c igraph_estack.c st-cuts.c \
 	cohesive_blocks.c statusbar.c lapack.c complex.c eigen.c \
diff --git a/src/sparsemat.c b/src/sparsemat.c
index 0ed4678..4fb724d 100644
--- a/src/sparsemat.c
+++ b/src/sparsemat.c
@@ -23,7 +23,7 @@
 
 #include "config.h"
 
-#include "cs/cs.h"
+#include <cs.h>
 
 #include "igraph_sparsemat.h"
 #include "igraph_error.h"
diff --git a/tests/Makefile.am b/tests/Makefile.am
index d350f11..31a1f5a 100644
--- a/tests/Makefile.am
+++ b/tests/Makefile.am
@@ -13,7 +13,7 @@ $(srcdir)/package.m4: $(top_srcdir)/configure.ac
 	  echo 'm4_define([AT_PACKAGE_BUGREPORT], [@PACKAGE_BUGREPORT@])'; \
 	} >$(srcdir)/package.m4
 
-EXTRA_DIST += package.m4
+#EXTRA_DIST += package.m4
 
 TESTSUITE_AT = \
 	testsuite.at \
diff --git a/tests/mt.at b/tests/mt.at
index 050974a..b154ce1 100644
--- a/tests/mt.at
+++ b/tests/mt.at
@@ -23,11 +23,11 @@ AT_BANNER([[Thread-safety tests]])
 
 AT_SETUP([Simple error handling test :])
 AT_KEYWORDS([thread-safe])
-AT_COMPILE_CHECK([simple/tls1.c], [], [], [], [-lpthread])
+AT_COMPILE_CHECK([simple/tls1.c], [], [], [], [-lpthread $(${PKG_CONFIG} --libs arpack)])
 AT_CLEANUP
 
 AT_SETUP([Thread-safe ARPACK:])
 AT_KEYWORDS([thread-safe ARPACK])
 AT_COMPILE_CHECK([simple/tls2.c], [simple/tls2.out], [], [internal], 
-                 [-lpthread])
+                 [-lpthread $(${PKG_CONFIG} --libs arpack)])
 AT_CLEANUP