--- 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) {