various fixes for macOS high sierra (#5647)

* various fixes for macOS high sierra

* add macOS_version() helper function

* flake8 fixes

* update oce and trilinos

* fix bison

var/spack/repos/builtin/packages/gcc/darwin/apfs.patch

@@ -0,0 +1,12 @@
+diff -uNr gcc-7.2.0.orig/libstdc++-v3/include/Makefile.in gcc-7.2.0/libstdc++-v3/include/Makefile.in
+--- gcc-7.2.0.orig/libstdc++-v3/include/Makefile.in     2017-07-25 14:05:07.000000000 -0400
++++ gcc-7.2.0/libstdc++-v3/include/Makefile.in  2017-09-02 12:22:08.000000000 -0400
+@@ -1764,6 +1764,8 @@
+ @GLIBCXX_HOSTED_TRUE@install-data-local: install-headers
+ @GLIBCXX_HOSTED_FALSE@install-data-local: install-freestanding-headers
+ 
++.NOTPARALLEL: install-headers
++
+ # This is a subset of the full install-headers rule.  We only need <ciso646>,
+ # <cstddef>, <cfloat>, <limits>, <climits>, <cstdint>, <cstdlib>, <new>,
+ # <typeinfo>, <exception>, <initializer_list>, <cstdalign>, <cstdarg>,

var/spack/repos/builtin/packages/gcc/package.py

@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+from spack.operating_systems.mac_os import macOS_version
 from llnl.util import tty
 
 import glob
@@ -148,6 +149,10 @@ class Gcc(AutotoolsPackage):
     conflicts('languages=jit', when='@:4')
 
     if sys.platform == 'darwin':
+        # Fix parallel build on APFS filesystem
+        # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81797
+        if macOS_version() >= Version('10.13'):
+            patch('darwin/apfs.patch', when='@7.2.0')
         patch('darwin/gcc-7.1.0-headerpad.patch', when='@5:')
         patch('darwin/gcc-6.1.0-jit.patch', when='@5:')
         patch('darwin/gcc-4.9.patch1', when='@4.9.0:4.9.3')