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

6 files changed, 42 insertions, 4 deletions

diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py
index 868268d42b..67b25441af 100644
--- a/var/spack/repos/builtin/packages/bison/package.py
+++ b/var/spack/repos/builtin/packages/bison/package.py
@@ -23,6 +23,8 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+from spack.operating_systems.mac_os import macOS_version
+import sys
 
 
 class Bison(AutotoolsPackage):
@@ -40,4 +42,7 @@ class Bison(AutotoolsPackage):
 
     patch('pgi.patch', when='@3.0.4')
 
+    if sys.platform == 'darwin' and macOS_version() >= Version('10.13'):
+        patch('secure_snprintf.patch', level=0, when='@3.0.4')
+
     build_directory = 'spack-build'
diff --git a/var/spack/repos/builtin/packages/bison/secure_snprintf.patch b/var/spack/repos/builtin/packages/bison/secure_snprintf.patch
new file mode 100644
index 0000000000..0dff749f2a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bison/secure_snprintf.patch
@@ -0,0 +1,15 @@
+With format string strictness, High Sierra also enforces that %n isn't used
+in dynamic format strings, but we should just disable its use on darwin in
+general.
+
+--- lib/vasnprintf.c.orig	2017-06-22 15:19:15.000000000 -0700
++++ lib/vasnprintf.c	2017-06-22 15:20:20.000000000 -0700
+@@ -4869,7 +4869,7 @@ VASNPRINTF (DCHAR_T *resultbuf, size_t *
+ #endif
+                   *fbp = dp->conversion;
+ #if USE_SNPRINTF
+-# if !(((__GLIBC__ > 2 || (__GLIBC__ == 2 && __GLIBC_MINOR__ >= 3)) && !defined __UCLIBC__) || ((defined _WIN32 || defined __WIN32__) && ! defined __CYGWIN__))
++# if !defined(__APPLE__) && !(((__GLIBC__ > 2 || (__GLIBC__ == 2 && __GLIBC_MINOR__ >= 3)) && !defined __UCLIBC__) || ((defined _WIN32 || defined __WIN32__) && ! defined __CYGWIN__))
+                 fbp[1] = '%';
+                 fbp[2] = 'n';
+                 fbp[3] = '\0';
diff --git a/var/spack/repos/builtin/packages/gcc/darwin/apfs.patch b/var/spack/repos/builtin/packages/gcc/darwin/apfs.patch
new file mode 100644
index 0000000000..d1f9d56667
--- /dev/null
+++ b/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>,
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index d690e63683..f5a84873a0 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/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')
diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
index b6e016361e..15bc9ab39e 100644
--- a/var/spack/repos/builtin/packages/oce/package.py
+++ b/var/spack/repos/builtin/packages/oce/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
 import platform
 
 
@@ -61,7 +62,7 @@ class Oce(Package):
     # fix build with Xcode 8 "previous definition of CLOCK_REALTIME"
     # reported 27 Sep 2016 https://github.com/tpaviot/oce/issues/643
     if (platform.system() == "Darwin") and (
-       '.'.join(platform.mac_ver()[0].split('.')[:2]) == '10.12'):
+       macOS_version() == Version('10.12')):
         patch('sierra.patch', when='@0.17.2:0.18.0')
 
     def install(self, spec, prefix):
@@ -91,7 +92,7 @@ class Oce(Package):
                 '-DOCE_OSX_USE_COCOA:BOOL=ON',
             ])
 
-        if '.'.join(platform.mac_ver()[0].split('.')[:2]) == '10.12':
+        if macOS_version() >= Version('10.12'):
             # use @rpath on Sierra due to limit of dynamic loader
             options.append('-DCMAKE_MACOSX_RPATH=ON')
         else:
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 375309207f..784253158f 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -23,9 +23,9 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+from spack.operating_systems.mac_os import macOS_version
 import os
 import sys
-import platform
 
 # Trilinos is complicated to build, as an inspiration a couple of links to
 # other repositories which build it:
@@ -586,7 +586,7 @@ class Trilinos(CMakePackage):
                 '-DTrilinos_ENABLE_FEI=OFF'
             ])
 
-        if '.'.join(platform.mac_ver()[0].split('.')[:2]) == '10.12':
+        if macOS_version() >= Version('10.12'):
             # use @rpath on Sierra due to limit of dynamic loader
             options.append('-DCMAKE_MACOSX_RPATH=ON')
         else: