--- bundled/cdd/support/configure.pl.orig	2018-02-16 03:27:51.000000000 -0700

+++ bundled/cdd/support/configure.pl	2018-04-15 13:42:47.970012974 -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" if $cdd_path ne "/usr";

       }

       if (!$CFLAGS or !$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/libnormaliz_inst.cc.orig	2018-02-16 03:27:51.000000000 -0700

+++ bundled/libnormaliz/apps/polytope/src/libnormaliz_inst.cc	2018-04-15 13:50:12.744485018 -0600

@@ -135,7 +135,7 @@ inline bool int_quotient(long long& Quot

 #endif

 #endif

-#include "libnormaliz/libnormaliz-all.cpp"

+#include <libnormaliz/cone.h>

 #if defined(__GNUC__)

 #if defined(__clang__)

--- bundled/libnormaliz/support/configure.pl.orig	2018-02-16 03:27:51.000000000 -0700

+++ bundled/libnormaliz/support/configure.pl	2018-04-15 13:45:39.129423452 -0600

@@ -136,6 +136,7 @@ int main (int argc, char *argv[])

          $message .= " [OpenMP support disabled]";

       }

    } else {

+      $CXXFLAGS='-I/usr/include/libnormaliz';

       $LIBS="-lnormaliz";

       $message = "$nmz_version @ ".($nmz_path//"system")

    }

--- bundled/lrs/support/configure.pl.orig	2018-02-16 03:27:51.000000000 -0700

+++ bundled/lrs/support/configure.pl	2018-04-16 21:04:58.916451962 -0600

@@ -45,11 +45,11 @@ sub proceed {

    my $suppress_output=0;

    if (defined ($lrs_path=$options->{lrs}) and $lrs_path ne "bundled") {

-      my $lrs_inc="$lrs_path/include";

+      my $lrs_inc="$lrs_path/include/lrslib";

       my $lrs_lib=Polymake::Configure::get_libdir($lrs_path, "lrsgmp");

       if (-f "$lrs_inc/lrslib.h" && -f "$lrs_lib/liblrsgmp.$Config::Config{so}" ) {

          $CFLAGS = "-I$lrs_inc";

-         $LDFLAGS = "-L$lrs_lib -Wl,-rpath,$lrs_lib";

+         $LDFLAGS = "-L$lrs_lib";

       } elsif (-f "$lrs_inc/lrslib.h" && -f "$lrs_lib/liblrsgmp.a" ) {

          $CFLAGS = "-I$lrs_inc";

          $LDFLAGS = "-L$lrs_lib";

--- bundled/nauty/apps/graph/src/build_flags.pl.orig	2018-02-16 03:27:51.000000000 -0700

+++ bundled/nauty/apps/graph/src/build_flags.pl	2018-04-18 18:51:41.461585057 -0600

@@ -1,25 +1,11 @@

 # input for generate_ninja_targets.pl

-my $foreign_src=$ConfigFlags{'bundled.nauty.NautySrc'};

-my $nauty_src= $foreign_src ? '${bundled.nauty.NautySrc}' : '${root}/bundled/nauty/external/nauty';

-my $generated_dir='${buildroot}/staticlib/nauty';

-my @generated_headers=qw( nauty.h naututil.h gtools.h );

-my @generated_in=map { /\.h$/; "$nauty_src/$`-h.in" } @generated_headers;

-my @generated_out=map { "$generated_dir/$_" } @generated_headers;

-my $include_generated= ($foreign_src && grep { -f "$foreign_src/$_" } @generated_headers)

-                       ? join(" ", map { "-include $_" } @generated_out)

-                       : "-I$generated_dir";

-

-( CXXFLAGS => "-DBIGNAUTY -I$generated_dir -I$nauty_src",

-

-  GENERATED => {

-    out => "@generated_out", in => "@generated_in",

-    command => "cd $generated_dir; CC=\"\${CC}\" CFLAGS=\"\${CFLAGS}\" $nauty_src/configure --quiet >/dev/null 2>/dev/null; rm -f makefile",

-  },

-

-  staticlib => {

-    SOURCEDIR => $nauty_src,

-    SOURCES => [ qw(naugraph.c naurng.c nausparse.c nautaux.c nautil.c nautinv.c naututil.c nauty.c rng.c schreier.c) ],

-    CFLAGS => "-DBIGNAUTY $include_generated -I$nauty_src",

-  }

+( 

+  $ConfigFlags{'bundled.nauty.UseBundled'}

+  ? ( staticlib => {

+        SOURCEDIR => '${root}/bundled/nauty/external/nauty',

+        SOURCES => [ qw(naugraph.c naurng.c nausparse.c nautaux.c nautil.c nautinv.c naututil.c nauty.c rng.c schreier.c) ],

+        CFLAGS => "-I/usr/include/nauty",

+      } )

+  : ()

 )

--- bundled/nauty/support/configure.pl.orig	2018-02-16 03:27:51.000000000 -0700

+++ bundled/nauty/support/configure.pl	2018-04-17 20:54:14.055618022 -0600

@@ -13,7 +13,7 @@

 #  GNU General Public License for more details.

 #-------------------------------------------------------------------------------

-@conf_vars=qw( NautySrc );

+@conf_vars=qw( UseBundled CFLAGS LDFLAGS LIBS );

 sub allowed_options {

    my ($allowed_options, $allowed_with)=@_;

@@ -28,24 +28,27 @@ sub usage {

                 "                         directory containing the nauty sources.\n";

 }

-sub check_nauty {

-   my $dir = @_ > 0 ? $_[0] : "bundled/nauty/external/nauty";

-   -e "$dir/nauty-h.in"

+sub check_bundled {

+   -e "bundled/nauty/external/nauty/nauty-h.in";

 }

 sub proceed {

    my ($options)=@_;

    my $nautysrc;

+   $UseBundled = 1;

    if (defined ($nautysrc=$options->{"nauty-src"})) {

-      check_nauty($nautysrc) or

-         die "Specified nauty source directory invalid, could not find 'nauty-h.in'.";

-      $NautySrc = $nautysrc;

-   } elsif (!check_nauty()) {

-      die "Bundled nauty directory seems to be missing, to use the nauty interface\n",

-          "with the minimal tarball please specify a nauty source directory\n",

-          "via --with-nauty-src=PATH.";

+      my $nauty_inc="$nautysrc/include/nauty";

+      my $nauty_lib=Polymake::Configure::get_libdir($nautysrc, "nauty");

+      if (-f "$nauty_inc/nauty.h") {

+         $CFLAGS="-I$nauty_inc";

+		 $LDFLAGS="-L$nauty_lib";

+		 $LIBS="-lnauty";

+		 $UseBundled = 0;

+	  } else {

+         die "Could not locate a working nauty installation\n";

+      }

    }

-   return $NautySrc ? "$NautySrc" : "bundled";

+   return $UseBundled ? "bundled" : ($nautysrc//"system");

 }

--- bundled/ppl/support/configure.pl.orig	2018-02-16 03:27:51.000000000 -0700

+++ bundled/ppl/support/configure.pl	2018-04-15 14:00:54.998296923 -0600

@@ -55,7 +55,7 @@ sub proceed {

    }

    if ($ppl_lib) {

       if (-f "$ppl_lib/libppl.$Config::Config{so}") {

-         $LDFLAGS = "-L$ppl_lib -Wl,-rpath,$ppl_lib";

+         $LDFLAGS = "-L$ppl_lib";

       } elsif ("$ppl_lib/libppl.a") {

 	 die "PPL found at $ppl_path is built without shared libraries.\n";

       } else {

--- bundled/singular/support/configure.pl.orig	2018-02-16 03:27:51.000000000 -0700

+++ bundled/singular/support/configure.pl	2018-04-15 14:02:08.374046937 -0600

@@ -42,7 +42,7 @@ sub singular_config_approach {

    # yes we need it twice ...

    chomp ($singular_prefix = `$singular_config --prefix`);

    chomp $singular_prefix;

-   $LDFLAGS =~ s/-L(\S+)/-L$1 -Wl,-rpath,$1/g;

+   $LDFLAGS =~ s/-L(\S+)/-L$1/g;

    my $libdir = $1;

    # newer versions of singular need -lsingular_resources while older ones needed -lresources

@@ -65,9 +65,6 @@ 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/apps/polytope/src/build_flags.pl.orig	2018-02-16 03:27:51.000000000 -0700

+++ bundled/sympol/apps/polytope/src/build_flags.pl	2018-04-15 14:06:35.821171083 -0600

@@ -10,7 +10,7 @@ if ($ConfigFlags{'bundled.sympol.UseBund

        'raycomputationcdd.cpp' => '-DGMPRATIONAL ${bundled.cdd.CFLAGS}',

        'raycomputationlrs.cpp' => '-DGMP ${bundled.lrs.CFLAGS}',

        $ConfigFlags{ExternalHeaders} =~ /\bpermlib\b/

-       ? ( CXXFLAGS => '-I${root}/include/external/permlib' ) : (),

+       ? ( CXXFLAGS => '-I/usr/include/permlib' ) : (),

     },

   )

 } else {

--- bundled/sympol/support/configure.pl.orig	2018-02-16 03:27:51.000000000 -0700

+++ bundled/sympol/support/configure.pl	2018-04-15 14:05:52.837292506 -0600

@@ -146,6 +146,7 @@ int main() {

       undef $LIBS;

       $CXXFLAGS = '-I${root}/bundled/sympol/external/sympol';

    } else {

+      $CXXFLAGS="-I/usr/include/sympol";

       $LIBS="-lsympol";

    }

--- perl/polymake-config.orig	2018-02-16 03:27:51.000000000 -0700

+++ perl/polymake-config	2018-04-15 14:08:13.652894725 -0600

@@ -130,9 +130,6 @@ while (defined ($_=shift)) {

    } elsif ($_ eq "--ldflags") {

       my $ldflags=$ConfigFlags{LDFLAGS};

-      if ($ldflags !~ /(?:^|\s)-L$ConfigFlags{InstallLib}(?:\s|$)/) {

-         $ldflags="-L$ConfigFlags{InstallLib} $ldflags";

-      }

       my $add_rpath=1;

       # collect standard library paths of the C++ compiler and exclude them from the result

@@ -152,8 +149,6 @@ while (defined ($_=shift)) {

       close CC;

       if ($^O eq "darwin") {

          $ldflags="$ConfigFlags{ARCHFLAGS} $ldflags -flat_namespace";

-      } elsif ($add_rpath) {

-         $ldflags.=" -Wl,-rpath,$ConfigFlags{InstallLib}";

       }

       $ldflags=~s/^\s+//; $ldflags=~s/\s+$//; $ldflags=~s/\s{2,}/ /g;

       if ($debug_asked=defined($debug)) {

--- support/configure.pl.orig	2018-02-16 03:27:51.000000000 -0700

+++ support/configure.pl	2018-04-15 14:10:02.468587338 -0600

@@ -454,7 +454,7 @@ sub parse_command_line {

       }

    }

-   $CXXOPT   =$vars{CXXOPT}   // "-O3";

+   $CXXOPT   =$vars{CXXOPT}   // "-O2";

    $CXXDEBUG =$vars{CXXDEBUG} // "";

    $CFLAGS   =$vars{CFLAGS}   // "";

    $CXXFLAGS =$vars{CXXFLAGS} // $CFLAGS;

@@ -668,7 +668,7 @@ sub determine_cxx_library {

       }

       $CFLAGS   .= " -I$options{toolchain}/include";

       $CXXFLAGS .= " -I$options{toolchain}/include";

-      $LDFLAGS  .= " -L$libdir -Wl,-rpath,$libdir";

+      $LDFLAGS  .= " -L$libdir";

    }

    if ($options{libcxx} eq ".true.") {

@@ -993,10 +993,6 @@ sub locate_gmp_and_mpfr_libraries {

       $CXXFLAGS .= " -I$GMP/include";

       my $libdir=get_libdir($GMP, "gmp");

       $LDFLAGS .= " -L$libdir";

-      if (!$FinkBase) {

-         # non-standard location

-         $LDFLAGS .= " -Wl,-rpath,$libdir";

-      }

    }

    my $MPFR=$options{mpfr};

@@ -1005,10 +1001,6 @@ sub locate_gmp_and_mpfr_libraries {

       $CXXFLAGS .= " -I$MPFR/include";

       my $libdir=get_libdir($MPFR, "mpfr");

       $LDFLAGS .= " -L$libdir";

-      if (!$FinkBase) {

-         # non-standard location

-         $LDFLAGS .= " -Wl,-rpath,$libdir";

-      }

    } elsif ($FinkBase) {

       $MPFR=$FinkBase;

    }