--- bundled/cdd/configure.pl.orig	2017-03-28 03:30:14.000000000 -0600
+++ bundled/cdd/configure.pl	2017-03-28 20:46:01.130083651 -0600
@@ -52,7 +52,6 @@ sub proceed {
       my $cdd_lib=Polymake::Configure::get_libdir($cdd_path, "cddgmp");
       if (-f "$cdd_lib/libcddgmp.$Config::Config{so}" ) {
          $LDflags = "-L$cdd_lib";
-         $LDflags .= " -Wl,-rpath,$cdd_lib" unless ($cdd_path eq "/usr");
       }
       if (!$CXXflags or !$LDflags) {
          die "Invalid installation location of cddlib: header file cdd.h and/or library libcddgmp.$Config::Config{so} not found.\n",
@@ -65,7 +64,6 @@ sub proceed {
       $cdd_path .= "include: $cdd_inc ";
    }
    if (defined ($cdd_lib=$options->{'cdd-lib'})) {
-      $LDflags = "-L$cdd_lib -Wl,-rpath,$cdd_lib";
       $cdd_path .= "lib: $cdd_lib";
    }
 
--- bundled/libnormaliz/apps/polytope/src/Makefile.inc.orig	2017-03-28 03:30:14.000000000 -0600
+++ bundled/libnormaliz/apps/polytope/src/Makefile.inc	2017-03-28 20:58:44.103003083 -0600
@@ -1,4 +1,5 @@
-ExtraCXXFLAGS = -I$(ExtensionTop)/external/libnormaliz
+ExtraCXXFLAGS = -I/usr/include/libnormaliz
+LIBS += -lnormaliz
 
 # Local Variables:
 # mode: Makefile
--- bundled/libnormaliz/apps/polytope/src/normaliz.cc.orig	2017-03-28 03:30:14.000000000 -0600
+++ bundled/libnormaliz/apps/polytope/src/normaliz.cc	2017-03-28 20:52:15.183466846 -0600
@@ -95,7 +95,7 @@ namespace libnormaliz {
 #endif
 #endif
 
-#include "libnormaliz/libnormaliz-all.cpp"
+#include <libnormaliz/cone.h>
 
 #if defined(__GNUC__) && !defined(__clang__)
 #pragma GCC diagnostic pop
--- bundled/lrs/configure.pl.orig	2017-03-28 03:30:14.000000000 -0600
+++ bundled/lrs/configure.pl	2017-03-28 20:47:36.352644537 -0600
@@ -42,7 +42,6 @@ sub proceed {
       my $lrs_lib=Polymake::Configure::get_libdir($lrs_path, "lrs");
       if (-f "$lrs_inc/lrslib.h" && -f "$lrs_lib/liblrsgmp.$Config::Config{so}" ) {
          $CXXflags="-I$lrs_inc";
-         $LDflags="-L$lrs_lib -Wl,-rpath,$lrs_lib";
       } elsif (-f "$lrs_inc/lrslib.h" && -f "$lrs_lib/liblrsgmp.a" ) {
          $CXXflags="-I$lrs_inc";
          $LDflags="-L$lrs_lib";
--- bundled/nauty/apps/graph/src/Makefile.inc.orig	2017-03-28 03:30:14.000000000 -0600
+++ bundled/nauty/apps/graph/src/Makefile.inc	2017-03-28 20:53:17.303208302 -0600
@@ -1,13 +1,13 @@
 ifeq (${ImportedIntoExtension},)
-  StaticLibs := nauty
+  # StaticLibs := nauty
 
   ifeq (${NautySrc},)
     NautySrc := ${ExtensionTop}/external/nauty
   endif
 
-  GraphIso$O : ExtraCXXFLAGS = -DBIGNAUTY -I${BuildDir}/staticlib/nauty -I${NautySrc}
+  GraphIso$O : ExtraCXXFLAGS = -DBIGNAUTY -I/usr/include/nauty
 
-  LIBS += ${BuildDir}/staticlib/nauty/libnauty$A
+  LIBS += -lnauty
 endif
 
 # Local Variables:
--- bundled/nauty/staticlib/nauty/Makefile.inc.orig	2017-03-28 03:30:14.000000000 -0600
+++ bundled/nauty/staticlib/nauty/Makefile.inc	2017-03-28 20:55:16.583711852 -0600
@@ -1,10 +1,10 @@
-OwnLibrary := libnauty
-LibModules := nauty naututil nautil nautinv naugraph rng naurng schreier nausparse nautaux
-ifeq (${NautySrc},)
-  src := ${ExtensionTop}/external/nauty
-else
-  src := ${NautySrc}
-endif
+#OwnLibrary := libnauty
+#LibModules := nauty naututil nautil nautinv naugraph rng naurng schreier nausparse nautaux
+#ifeq (${NautySrc},)
+#  src := ${ExtensionTop}/external/nauty
+#else
+#  src := ${NautySrc}
+#endif
 vpath %.c $(src)
 
 # We need to disable avx2 for some gcc versions as it produces invalid relocations
@@ -15,21 +15,21 @@ ifdef GCCversion
   endif
 endif
 
-ifeq "$(wildcard nauty.h)" ""
-  override _system := $(shell uname -s)
-  ifeq "$(_system)" "Darwin"
-    override _hide := mv Makefile Makefile.hidden;
-    override _restore := ;mv Makefile.hidden Makefile
-  endif
-
-  override _dummy := $(shell ${_hide} CC=${CC} CFLAGS="${Cflags}" ${src}/configure --quiet 2>/dev/null; rm makefile ${_restore})
-endif
+#ifeq "$(wildcard nauty.h)" ""
+#  override _system := $(shell uname -s)
+#  ifeq "$(_system)" "Darwin"
+#    override _hide := mv Makefile Makefile.hidden;
+#    override _restore := ;mv Makefile.hidden Makefile
+#  endif
+#
+#  override _dummy := $(shell ${_hide} CC=${CC} CFLAGS="${Cflags}" ${src}/configure --quiet 2>/dev/null; rm makefile ${_restore})
+#endif
 
 # force include nauty headers here on the command line to make sure that we pick
 # up the newly generated ones instead (wrong?) ones from the original tarball
 # (current directory of the source file is always searched first and -I- is deprecated)
-ExtraCFLAGS := -DBIGNAUTY -I. -include $(CURDIR)/nauty.h -include $(CURDIR)/naututil.h -include $(CURDIR)/gtools.h -I${src}
-ExtraCLEAN := nauty.h naututil.h gtools.h config.*
+ExtraCFLAGS := -DBIGNAUTY -I/usr/include/nauty
+#ExtraCLEAN := nauty.h naututil.h gtools.h config.*
 
 # Local Variables:
 # mode: Makefile
--- bundled/ppl/configure.pl.orig	2017-03-28 03:30:14.000000000 -0600
+++ bundled/ppl/configure.pl	2017-03-28 20:46:46.977872227 -0600
@@ -35,7 +35,6 @@ sub proceed {
       my $ppl_lib=Polymake::Configure::get_libdir($ppl_path, "ppl");
       if (-f "$ppl_inc/ppl.hh" && -f "$ppl_lib/libppl.$Config::Config{so}") {
          $CXXflags.="-I$ppl_inc";
-         $LDflags="-L$ppl_lib -Wl,-rpath,$ppl_lib";
       } else {
          die "Invalid installation location of libppl: header file ppl.hh and/or library libppl.$Config::Config{so} not found\n";
       }
--- bundled/singular/configure.pl.orig	2017-03-28 03:30:14.000000000 -0600
+++ bundled/singular/configure.pl	2017-03-28 20:48:06.064507522 -0600
@@ -40,7 +40,6 @@ sub singular_config_approach {
    chomp ($singular_prefix = `$singular_config --prefix`);
    chomp $singular_prefix;
    $LDflags =~ s/ -l\w+//g;
-   $LDflags =~ s/-L(\S+)/-L$1 -Wl,-rpath,$1/g;
    my $libdir = $1;
 
    # newer versions of singular need -lsingular_resources while older ones needed -lresources
@@ -63,9 +62,6 @@ sub pkg_config_approach {
    chomp ($CXXflags=`$pkg_config --cflags Singular`);
    die "$pkg_config failed: $!" if ($?);
    chomp ($LDflags=`$pkg_config --libs-only-other --libs-only-L Singular`);
-   if (defined ($options->{singular})){
-      $LDflags =~ s/-L(\S+)/-L$1 -Wl,-rpath,$1/g;
-   }
    chomp ($Libs=`$pkg_config --libs-only-l Singular`);
    return $pc_singular_prefix;
 }
--- bundled/sympol/configure.pl.orig	2017-03-28 03:30:14.000000000 -0600
+++ bundled/sympol/configure.pl	2017-03-28 20:47:05.905784941 -0600
@@ -47,7 +47,6 @@ sub proceed {
       my $sympol_lib=Polymake::Configure::get_libdir($sympol_path, "sympol");
       if (-f "$sympol_lib/libsympol.$Config::Config{so}" ) {
          $LDflags = "-L$sympol_lib";
-         $LDflags .= " -Wl,-rpath,$sympol_lib" unless ($sympol_path eq "/usr");
       }
       if (!$CXXflags or !$LDflags) {
          die "Invalid installation location of sympol: header file symmetrycomputation.h and/or library libsympol.$Config::Config{so} not found.\n",
@@ -61,7 +60,6 @@ sub proceed {
    }
    if (defined ($sympol_lib=$options->{'sympol-lib'})) {
       $LDflags = " -L$sympol_lib";
-      $LDflags .= " -Wl,-rpath,$sympol_lib" unless ($sympol_lib =~ m#^/usr/lib#);
       $sympol_path .= "lib: $sympol_lib";
    }
 
--- bundled/sympol/staticlib/sympol/Makefile.inc.orig	2017-03-28 03:30:14.000000000 -0600
+++ bundled/sympol/staticlib/sympol/Makefile.inc	2017-03-28 20:50:52.455811162 -0600
@@ -4,10 +4,10 @@ src := ${ExtensionTop}/external/sympol/s
 
 vpath %.cpp $(src)
 
-ExtraCXXFLAGS := -I${ExtensionTop}/external/sympol/sympol ${LrsCflags} -DGMP -DLRS_QUIET ${CddCflags} -DGMPRATIONAL
+ExtraCXXFLAGS := -I/usr/include/sympol ${LrsCflags} -DGMP -DLRS_QUIET ${CddCflags} -DGMPRATIONAL
 
 ifneq ($(filter ${ExternalHeaders},permlib),)
-  ExtraCXXFLAGS += -I${ProjectTop}/include/external/permlib
+  ExtraCXXFLAGS += -I$/usr/include/permlib
 endif
 
 # Local Variables:
--- perl/polymake-config.orig	2017-03-28 03:30:14.000000000 -0600
+++ perl/polymake-config	2017-03-28 20:56:20.646445222 -0600
@@ -127,9 +127,6 @@ while (defined ($_=shift)) {
 
    } elsif ($_ eq "--ldflags") {
       my $ldflags=$conf{LDflags};
-      if ($ldflags !~ /(?:^|\s)-L$conf{InstallLib}(?:\s|$)/) {
-         $ldflags="-L$conf{InstallLib} $ldflags";
-      }
       my $add_rpath=1;
       open CF, ">$tmpfile.cc" or die "can't create temporary file $tmpfile.cc: $!\n";
       print CF "int main() { return 0; }\n";
@@ -147,8 +144,6 @@ while (defined ($_=shift)) {
       close CC;
       if ($^O eq "darwin") {
          $ldflags="$conf{ARCHFLAGS} $ldflags -flat_namespace";
-      } elsif ($add_rpath) {
-         $ldflags.=" -Wl,-rpath,$conf{InstallLib}";
       }
       $ldflags=~s/^\s+//; $ldflags=~s/\s+$//; $ldflags=~s/\s{2,}/ /g;
       if ($debug_asked=defined($debug)) {
--- support/configure.pl.orig	2017-03-28 03:30:14.000000000 -0600
+++ support/configure.pl	2017-03-28 20:57:46.759165080 -0600
@@ -442,7 +442,7 @@ if (defined($GCCversion) or defined($CLA
 }
 
 $PERL     =$vars{PERL}     || $^X;
-$CXXOPT   =$vars{CXXOPT}   || "-O3";
+$CXXOPT   =$vars{CXXOPT}   || "-O2";
 $CXXDEBUG =$vars{CXXDEBUG} || "";
 $Cflags   =$vars{CFLAGS}   || "";
 $CXXflags =$vars{CXXFLAGS} || $Cflags;
@@ -763,10 +763,6 @@ if (defined $GMP) {
    $CXXflags .= " -I$GMP/include";
    my $libdir=get_libdir($GMP, "gmp");
    $LDflags .= " -L$libdir";
-   if (($^O ne "darwin" || $options{fink} eq ".none.") && exists $options{gmp}) {
-      # non-standard location
-      $LDflags .= " -Wl,-rpath,$libdir";
-   }
 }
 
 my $MPFR=$options{mpfr};
@@ -775,10 +771,6 @@ if (defined($MPFR) && $MPFR ne $GMP) {
    $CXXflags .= " -I$MPFR/include";
    my $libdir=get_libdir($MPFR, "mpfr");
    $LDflags .= " -L$libdir";
-   if ($^O ne "darwin" || $options{fink} eq ".none.") {
-      # non-standard location
-      $LDflags .= " -Wl,-rpath,$libdir";
-   }
 }
 
 if (defined($boost_path)) {