--- 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)) {