* Add prefix in Makefiles, not the configure script
* Use AC_SEARCH_LIBS instead of AC_CHECK_LIB,
  as it is more flexible and helps us with LAPACK
* Use correct ZLIB_CFLAGS instead of non-existent ZLIB_CPPFLAGS

--- a/configure.ac
+++ b/configure.ac
@@ -34,7 +34,7 @@
       [--with-pmdir=DIR],
       [install Perl modules in DIR]),
     [PMDIR=${withval}],
-    [PMDIR='${prefix}'/"$pmdir_relative_path"])
+    [PMDIR="$pmdir_relative_path"])
 
 AC_SUBST([PMDIR])
 
@@ -73,9 +73,9 @@
               [pca=${enableval}],
               [pca=no])
 
-if test "x${pca}" = "xyes" ; then
-  AC_CHECK_LIB(lapack, dgeev_)
-fi
+AS_IF([test "x${pca}" = "xyes"],[
+  AC_SEARCH_LIBS([dgeev_], [lapack])
+])
 
 # Generate output.
 AC_CONFIG_FILES([Makefile
--- a/src/cpp/Makefile.am
+++ b/src/cpp/Makefile.am
@@ -1,6 +1,6 @@
 bin_PROGRAMS = vcftools
 
-vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS)
+vcftools_CPPFLAGS = $(ZLIB_CFLAGS)
 vcftools_LDADD = $(ZLIB_LIBS)
 
 vcftools_SOURCES = \
--- a/src/perl/Makefile.am
+++ b/src/perl/Makefile.am
@@ -24,7 +24,7 @@
 	vcf-tstv \
 	vcf-validator
 
-pmdir = $(PMDIR)
+pmdir = $(exec_prefix)/$(PMDIR)
 
 dist_pm_DATA = \
 	FaSlice.pm \