From 5b0ad235891027b8b6f6995a6f5d140d17a53744 Mon Sep 17 00:00:00 2001
From: Roland Schulz <roland@utk.edu>
Date: Sun, 6 Jul 2014 00:40:14 -0400
Subject: [PATCH] Fix Cygwin build

Doesn't work with AVX but I suspect this to be Cygwin's/GCC's fault.

GCC Bug 61730

Change-Id: I171e8414a8d65800804226034604a9973770bfdd
---
 cmake/gmxCFlags.cmake             |  3 +++
 cmake/gmxTestCXX11.cmake          | 10 ++++++----
 src/gromacs/utility/cstringutil.h | 18 ------------------
 3 files changed, 9 insertions(+), 22 deletions(-)

diff --git a/cmake/gmxCFlags.cmake b/cmake/gmxCFlags.cmake
index 5ed91032c4..64f10ced52 100644
--- a/cmake/gmxCFlags.cmake
+++ b/cmake/gmxCFlags.cmake
@@ -112,6 +112,9 @@ MACRO(gmx_c_flags)
         GMX_TEST_CFLAG(CFLAGS_WARN_REL "-Wno-array-bounds" GMXC_CFLAGS_RELEASE_ONLY)
         # Since gcc 4.8 strict - false postives with old gmx_fatal. TODO: Remove in master
         GMX_TEST_CFLAG(CFLAGS_WARN_UNINIT "-Wno-maybe-uninitialized" GMXC_CFLAGS)
+        if(CYGWIN)
+            GMX_TEST_CFLAG(CFLAGS_WARN_SUBSCRIPT "-Wno-char-subscripts" GMXC_CFLAGS)
+        endif()
         # new in gcc 4.5
         GMX_TEST_CFLAG(CFLAGS_EXCESS_PREC "-fexcess-precision=fast" GMXC_CFLAGS_RELEASE)
         GMX_TEST_CFLAG(CFLAGS_COPT "-fomit-frame-pointer -funroll-all-loops"
diff --git a/cmake/gmxTestCXX11.cmake b/cmake/gmxTestCXX11.cmake
index fdcc07f591..eaa8888e48 100644
--- a/cmake/gmxTestCXX11.cmake
+++ b/cmake/gmxTestCXX11.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -34,10 +34,12 @@
 
 include(CheckCXXSourceCompiles)
 MACRO(GMX_TEST_CXX11 VARIABLE FLAG)
-    if(NOT WIN32)
-        set(CXX11_FLAG "-std=c++0x")
-    else()
+    if(WIN32)
         set(CXX11_FLAG "/Qstd=c++0x")
+    elseif(CYGWIN)
+        set(CXX11_FLAG "-std=gnu++0x") #required for strdup
+    else()
+        set(CXX11_FLAG "-std=c++0x")
     endif()
     CHECK_CXX_COMPILER_FLAG("${CXX11_FLAG}" CXXFLAG_STD_CXX0X)
     if(NOT CXXFLAG_STD_CXX0X)
diff --git a/src/gromacs/utility/cstringutil.h b/src/gromacs/utility/cstringutil.h
index 6d8f94b4e7..8cba1a370b 100644
--- a/src/gromacs/utility/cstringutil.h
+++ b/src/gromacs/utility/cstringutil.h
@@ -50,24 +50,6 @@
 
 #include "gmx_header_config.h"
 
-/* Suppress Cygwin compiler warnings from using newlib version of
- * ctype.h */
-#ifdef GMX_CYGWIN
-#include <ctype.h>
-
-#undef isdigit
-#undef isstring
-#undef isspace
-#undef isalnum
-#undef isalpha
-#undef ispunct
-#undef isxdigit
-#undef isupper
-#undef islower
-#undef toupper
-#undef tolower
-#endif
-
 #ifdef __cplusplus
 extern "C" {
 #endif
-- 
2.22.0