diff --git a/configure.ac b/configure.ac
index acf76cd..a9db7bd 100644
--- a/configure.ac
+++ b/configure.ac
@@ -167,7 +167,8 @@ if test "x$enable_gmp" != "xno"; then
     AC_CHECK_HEADER([gmp.h], [
       AC_DEFINE([HAVE_GMP], [1], [Define to 1 if you have the GMP library])
       gmp_support=yes
-      LDFLAGS="${LDFLAGS} -lgmp"
+      GMP_LIBS="-lgmp"
+      AC_SUBST(GMP_LIBS)
       PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -lgmp"
     ])
   ])
@@ -231,24 +232,16 @@ else
 fi
 
 if test "$internal_blas" = "no"; then
-  AC_CHECK_LIB([blas], [daxpy_], [],
-     AC_CHECK_LIB([blas], [daxpy], [],
-        AC_CHECK_LIB([blas], [DAXPY_], [],
-           AC_CHECK_LIB([blas], [DAXPY], [],
-	      [AC_MSG_RESULT(not found, trying to use -lblas anyway.)]))))
-  LDFLAGS="${LDFLAGS} -lblas"
+  PKG_CHECK_MODULES([BLAS],[blas])
+  CPPFLAGS="${CPPFLAGS} ${BLAS_CFLAGS}"
   PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -lblas"
 else
   AC_DEFINE([INTERNAL_BLAS], [1], [Define to 1 if you use the internal BLAS library])
 fi
 
 if test "$internal_lapack" = "no"; then
-  AC_CHECK_LIB([lapack], [dlarnv_], [],
-     AC_CHECK_LIB([lapack], [dlarnv], [],
-        AC_CHECK_LIB([lapack], [DLARNV_], [],
-           AC_CHECK_LIB([lapack], [DLARNV], [],
-	      [AC_MSG_RESULT(not found, trying to use -llapack anyway.)]))))
-  LDFLAGS="${LDFLAGS} -llapack"
+  PKG_CHECK_MODULES([LAPACK],[lapack])
+  CPPFLAGS="${CPPFLAGS} ${LAPACK_CFLAGS}"
   PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -llapack"
 else
   AC_DEFINE([INTERNAL_LAPACK], [1], [Define to 1 if you use the internal LAPACK library])
@@ -258,17 +251,15 @@ if test "$internal_arpack" = "no"; then
   if test "$tls_support" = "yes"; then
     AC_MSG_ERROR([Thread-local storage only supported with internal ARPACK library])
   fi
-  AC_CHECK_LIB([arpack], [dsaupd_], [],
-     AC_CHECK_LIB([arpack], [dsaupd], [],
-        AC_CHECK_LIB([arpack], [DSAUPD_], [],
-           AC_CHECK_LIB([arpack], [DSAUPD], [],
-	      [AC_MSG_RESULT(not found, trying to use -larpack anyway.)]))))
-  LDFLAGS="${LDFLAGS} -larpack"
+  PKG_CHECK_MODULES([ARPACK],[arpack])
+  CPPFLAGS="${CPPFLAGS} ${ARPACK_CFLAGS}"
   PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -larpack"
 else
   AC_DEFINE([INTERNAL_ARPACK], [1], [Define to 1 if you use the internal ARPACK library])
 fi
 
+PKG_CHECK_MODULES([CS],[cxsparse])
+
 glpk_support=no
 AC_ARG_ENABLE(glpk, AC_HELP_STRING([--disable-glpk], [Compile without the GLPK library]))
 if test "x$enable_glpk" != "xno"; then
@@ -283,7 +274,8 @@ if test "x$enable_glpk" != "xno"; then
         ], [
           AC_DEFINE([HAVE_GLPK], [1], [Define to 1 if you have the GLPK library])
           glpk_support=yes
-          LDFLAGS="${LDFLAGS} -lglpk"
+          GLPK_LIBS="-lglpk"
+          AC_SUBST(GLPK_LIBS)
           PKGCONFIG_LIBS_PRIVATE="${PKGCONFIG_LIBS_PRIVATE} -lglpk"
         ])
       ])
diff --git a/examples/simple/igraph_arpack_rnsolve.out b/examples/simple/igraph_arpack_rnsolve.out
index ec38497..6603034 100644
--- a/examples/simple/igraph_arpack_rnsolve.out
+++ b/examples/simple/igraph_arpack_rnsolve.out
@@ -16,7 +16,7 @@
 ---
 22.0483 0
 -21.3281 0
--3.00735 -19.2957
+-3.00735 19.2957
 ---
 0.373224 0.226696 0.204213 0.0473383
 -0.289145 -0.296079 -0.0479785 0.156365
@@ -31,7 +31,7 @@
 ---
 -21.3281 0
 -12.4527 0
--3.00735 -19.2957
+-3.00735 19.2957
 ---
 -0.226696 0.695866 -0.204213 -0.0473383
 0.296079 0.120213 0.0479785 -0.156365
@@ -46,7 +46,7 @@
 ---
 -3.00735 19.2957
 -3.00735 -19.2957
-12.1099 6.27293
+12.1099 -6.27293
 ---
 0.0768616 -0.195028 -0.152389 0.21912
 0.147607 0.0704569 0.346547 0.125122
diff --git a/examples/simple/igraph_layout_merge2.out b/examples/simple/igraph_layout_merge2.out
index dfe2c22..9fe81bf 100644
--- a/examples/simple/igraph_layout_merge2.out
+++ b/examples/simple/igraph_layout_merge2.out
@@ -1,13 +1,13 @@
--2.73912 -2.95429
--0.479512 -4.00008
-1.96326 -3.51798
-3.65613 -1.69214
-3.95248 0.780051
-2.73912 2.95429
-0.479512 4.00008
--1.96326 3.51798
--3.65613 1.69214
--3.95248 -0.780051
+-2.55311 -3.13964
+-0.22007 -4.0407
+2.19703 -3.39835
+3.77493 -1.45795
+3.91094 1.03935
+2.55311 3.13964
+0.22007 4.0407
+-2.19703 3.39835
+-3.77493 1.45795
+-3.91094 -1.03935
 -1.6061 6.30088
 -4.92661 5.80435
 -3.69637 8.92826
diff --git a/examples/simple/igraph_sparsemat2.c b/examples/simple/igraph_sparsemat2.c
index c39d0e5..fdfd264 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_sparsemat.h>
 #include <igraph_blas_internal.h>
diff --git a/examples/simple/igraph_sparsemat3.c b/examples/simple/igraph_sparsemat3.c
index 630bf1a..b23cbe1 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>
 #include <igraph_sparsemat.h>
 
diff --git a/examples/simple/igraph_sparsemat4.c b/examples/simple/igraph_sparsemat4.c
index 4d85bde..7497faf 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>
 #include <igraph_sparsemat.h>
 
diff --git a/src/Makefile.am b/src/Makefile.am
index e7085c5..194f4a0 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
@@ -255,7 +250,7 @@ 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 \
@@ -274,8 +269,8 @@ libigraph_la_SOURCES       = $(SOURCES) $(HEADERS_PRIVATE)
 libigraph_la_CFLAGS        = -I$(top_srcdir)/include -I$(top_builddir)/include $(WARNING_CFLAGS)
 libigraph_la_CXXFLAGS	   = -I$(top_srcdir)/include -I$(top_builddir)/include $(WARNING_CFLAGS)
 libigraph_la_LDFLAGS       = -no-undefined
-libigraph_la_LIBADD        = -lm $(XML2_LIBS) $(F2C_LIB) $(BLAS_LIB) \
-				 $(LAPACK_LIB) $(ARPACK_LIB) $(GLPK_LIB) $(PRPACK_LIB) \
+libigraph_la_LIBADD        = -lm $(XML2_LIBS) $(F2C_LIB) $(BLAS_LIBS) $(GMP_LIBS) \
+				 $(LAPACK_LIBS) $(ARPACK_LIBS) $(GLPK_LIBS) $(PRPACK_LIB) $(CS_LIBS) \
 				 $(PLFIT_LIB)
 
 if INTERNAL_GLPK
diff --git a/src/sparsemat.c b/src/sparsemat.c
index f96d022..6990c91 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 6da83b2..c0b82d6 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..9558d6f 100644
--- a/tests/mt.at
+++ b/tests/mt.at
@@ -29,5 +29,5 @@ 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
diff --git a/tests/types.at b/tests/types.at
index f80a6a2..29ac739 100644
--- a/tests/types.at
+++ b/tests/types.at
@@ -133,7 +133,7 @@ AT_CLEANUP
 AT_SETUP([Sparse matrix, multiplications (igraph_sparsemat_t): ])
 AT_KEYWORDS([sparse matrix igraph_sparsemat_t])
 AT_COMPILE_CHECK([simple/igraph_sparsemat2.c], [simple/igraph_sparsemat2.out],
-                 [], [INTERNAL], [-lblas])
+                 [], [INTERNAL], [$(${PKG_CONFIG} --libs blas)])
 AT_CLEANUP
 
 AT_SETUP([Sparse matrix, indexing (igraph_sparsemat_t): ])
-- 
2.0.0