--- bundled/bliss/configure.pl.orig	2016-07-22 06:23:31.000000000 -0600
+++ bundled/bliss/configure.pl	2017-01-11 07:40:52.589296237 -0700
@@ -32,7 +32,6 @@ sub proceed {
       my $bliss_lib=Polymake::Configure::get_libdir($bliss_path, "bliss");
       if (-f "$bliss_inc/bliss/graph.hh" && -f "$bliss_lib/libbliss.$Config::Config{dlext}" ) {
          $CXXflags="-I$bliss_inc";
-         $LDflags="-L$bliss_lib -Wl,-rpath,$bliss_lib";
       } elsif (-f "$bliss_inc/bliss/graph.hh" && -f "$bliss_lib/libbliss.a" ) {
          $CXXflags="-I$bliss_inc";
          $LDflags="-L$bliss_lib";
--- bundled/cdd/configure.pl.orig	2016-07-22 06:23:31.000000000 -0600
+++ bundled/cdd/configure.pl	2017-01-11 07:42:26.948644436 -0700
@@ -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/group/apps/polytope/src/Makefile.inc.orig	2016-07-22 06:23:31.000000000 -0600
+++ bundled/group/apps/polytope/src/Makefile.inc	2016-07-24 10:28:59.948123191 -0600
@@ -1,11 +1,11 @@
 ifeq (${ImportedIntoExtension},)
-  StaticLibs := sympol
+  # StaticLibs := sympol
 
-  sympol_interface$O : ExtraCXXFLAGS += -I${ExtensionTop}/external/sympol
-  sympol_raycomputation_beneathbeyond$O : ExtraCXXFLAGS += -I${ExtensionTop}/external/sympol
+  sympol_interface$O : ExtraCXXFLAGS += -I/usr/include/sympol
+  sympol_raycomputation_beneathbeyond$O : ExtraCXXFLAGS += -I/usr/include/sympol
   sympol_raycomputation_ppl$O : ExtraCXXFLAGS += -I${ExtensionTop}/external/sympol
 
-  LIBS += ${BuildDir}/staticlib/sympol/libsympol$A $(subst %A,${A},${CddLib} ${LrsLib})
+  LIBS += -lsympol -lcddgmp
 endif
 
 ifneq ($(filter 4.4%,${GCCversion}),)
--- bundled/group/configure.pl.orig	2016-07-22 06:23:31.000000000 -0600
+++ bundled/group/configure.pl	2016-07-24 10:28:59.960122234 -0600
@@ -28,7 +28,7 @@ sub proceed {
    my ($options)=@_;
    my $boost_path;
    # everything can include permlib headers
-   $CXXflags='-I${ExtensionTop}/external/permlib/include';
+   $CXXflags='-I/usr/include/permlib';
 
    if (defined ($boost_path=$options->{boost})) {
       $boost_path .= '/include' if (-d "$boost_path/include/boost");
--- bundled/group/staticlib/sympol/Makefile.inc.orig	2016-07-22 06:23:31.000000000 -0600
+++ bundled/group/staticlib/sympol/Makefile.inc	2016-07-24 10:28:59.960122234 -0600
@@ -4,7 +4,7 @@ src := ${ExtensionTop}/external/sympol/s
 
 vpath %.cpp $(src)
 
-ExtraCXXFLAGS := -I${ExtensionTop}/external/permlib/include -I${ExtensionTop}/external/sympol/sympol ${LrsCflags} -DGMP -DLRS_QUIET ${CddCflags} -DGMPRATIONAL 
+ExtraCXXFLAGS := -I/usr/include/permlib -I/usr/include/sympol ${LrsCflags} -DGMP -DLRS_QUIET ${CddCflags} -DGMPRATIONAL
 
 # Local Variables:
 # mode: Makefile
--- bundled/libnormaliz/apps/polytope/src/Makefile.inc.orig	2016-07-22 06:23:31.000000000 -0600
+++ bundled/libnormaliz/apps/polytope/src/Makefile.inc	2016-07-24 10:28:59.960122234 -0600
@@ -1,4 +1,5 @@
-ExtraCXXFLAGS = -I$(ExtensionTop)/external/libnormaliz
+ExtraCXXFLAGS = -I/usr/include/libnormaliz
+LIBS += -lnormaliz
 
 # force a recent C++ standard for normaliz but keep it compatible with older
 # gcc versions and use tr1/unordered_{map,set} for polymake data structures
--- bundled/libnormaliz/apps/polytope/src/normaliz.cc.orig	2016-07-22 06:23:31.000000000 -0600
+++ bundled/libnormaliz/apps/polytope/src/normaliz.cc	2016-07-24 10:28:59.960122234 -0600
@@ -78,7 +78,7 @@ namespace libnormaliz {
    }
 }
 
-#include "libnormaliz/libnormaliz-all.cpp"
+#include <libnormaliz/cone.h>
 
 namespace libnormaliz {
    template<>
--- bundled/lrs/configure.pl.orig	2016-07-22 06:23:31.000000000 -0600
+++ bundled/lrs/configure.pl	2017-01-11 07:41:13.165154107 -0700
@@ -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	2016-07-22 06:23:31.000000000 -0600
+++ bundled/nauty/apps/graph/src/Makefile.inc	2016-07-24 10:28:59.961122154 -0600
@@ -1,9 +1,9 @@
 ifeq (${ImportedIntoExtension},)
-  StaticLibs := nauty
+  # StaticLibs := nauty
 
-  GraphIso$O : ExtraCXXFLAGS = -DBIGNAUTY -I${BuildDir}/staticlib/nauty
+  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	2016-07-22 06:23:31.000000000 -0600
+++ bundled/nauty/staticlib/nauty/Makefile.inc	2016-07-24 10:32:04.655400694 -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
@@ -15,18 +15,18 @@ 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
+#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
+#  override _dummy := $(shell ${_hide} CC=${CC} CFLAGS="${Cflags}" ${src}/configure --quiet 2>/dev/null; rm makefile ${_restore})
+#endif
 
-ExtraCFLAGS := -DBIGNAUTY -I. -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	2016-07-22 06:23:31.000000000 -0600
+++ bundled/ppl/configure.pl	2017-01-11 07:41:52.699881023 -0700
@@ -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	2016-07-22 06:23:31.000000000 -0600
+++ bundled/singular/configure.pl	2017-01-11 07:41:33.684012377 -0700
@@ -48,7 +48,6 @@ sub proceed {
 
    $Libs = join(" ",$LDflags =~ m/(-l\w+)/g) . " -lfactory -lresources -lpolys -lomalloc";
    $LDflags =~ s/ -l\w+//g;
-   $LDflags =~ s/-L(\S+)/-L$1 -Wl,-rpath,$1/g;
    my $libdir = $1;
 
    my $error=Polymake::Configure::build_test_program(<<"---", CXXflags => $CXXflags, LDflags => $LDflags, Libs => $Libs);
--- bundled/soplex/configure.pl.orig	2016-07-22 06:23:31.000000000 -0600
+++ bundled/soplex/configure.pl	2017-01-11 07:40:25.285484842 -0700
@@ -42,7 +42,6 @@ sub proceed {
    if (defined ($path = $options->{soplex}))
    {
       $CXXflags.=" -I$path/src -I$path/include -std=c++11";
-      $LDflags.=" -L$path/lib -Wl,-rpath,$path/lib";
    }
 
    # example code from src/example.cpp
--- perl/polymake-config.orig	2016-07-22 06:23:31.000000000 -0600
+++ perl/polymake-config	2016-07-24 10:28:59.961122154 -0600
@@ -125,9 +125,6 @@ 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: $!\n";
       print CF "int main() { return 0; }\n";
@@ -145,8 +142,6 @@ while (defined ($_=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	2016-07-22 06:23:31.000000000 -0600
+++ support/configure.pl	2016-07-24 10:28:59.962122074 -0600
@@ -389,7 +389,7 @@ if (defined $CC) {
 print "ok ($CXX is ", defined($GCCversion) ? "GCC $GCCversion" : defined($CLANGversion) ? "CLANG $CLANGversion" : "ICC $ICCversion", ")\n";
 
 $PERL     =$vars{PERL}     || $^X;
-$CXXOPT   =$vars{CXXOPT}   || "-O3";
+$CXXOPT   =$vars{CXXOPT}   || "-O2";
 $CXXDEBUG =$vars{CXXDEBUG} || "";
 $Cflags   =$vars{CFLAGS}   || "";
 $CXXflags =$vars{CXXFLAGS} || $Cflags;
@@ -631,10 +631,6 @@ 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};
@@ -643,10 +639,6 @@ 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 ($check_prereq) {