fix dealii dependencies for Clang 9.1.0 C++17 (#7644)

* fix boost and muparser for Clang 9.1.0 with C++17

* muparser: add C++11 flags

* dealii: temporary disable python by default

* dealii: make CMake find right python

5 files changed, 88 insertions, 4 deletions

diff --git a/var/spack/repos/builtin/packages/boost/array_binary_tree.patch b/var/spack/repos/builtin/packages/boost/array_binary_tree.patch
new file mode 100644
index 0000000000..51e1950528
--- /dev/null
+++ b/var/spack/repos/builtin/packages/boost/array_binary_tree.patch
@@ -0,0 +1,12 @@
+diff --git a/boost/graph/detail/array_binary_tree.hpp b/boost/graph/detail/array_binary_tree.hpp
+index e59da9e..fd403d1 100644
+--- a/boost/graph/detail/array_binary_tree.hpp
++++ b/boost/graph/detail/array_binary_tree.hpp
+@@ -14,6 +14,7 @@
+ #include <iterator>
+ #include <functional>
+ #include <boost/config.hpp>
++#include <boost/iterator.hpp>
+ 
+ namespace boost {
+ 
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index fdee5af217..09e71023b1 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -46,8 +46,10 @@ class Boost(Package):
             branch='develop',
             submodules=True)
 
+    version('1.67.0.b1', '3423a4a3ec5297051fd27091864630e2dce4c159',
+            url='https://dl.bintray.com/boostorg/beta/1.67.0.beta.1/source/boost_1_67_0_b1.tar.gz')
     version('1.66.0', 'b6b284acde2ad7ed49b44e856955d7b1ea4e9459',
-            url='https://dl.bintray.com/boostorg/release/1.66.0/source/boost_1_66_0.tar.bz2')
+            url='https://dl.bintray.com/boostorg/release/1.66.0/source/boost_1_66_0.tar.bz2', preferred=True)
     version('1.65.1', '41d7542ce40e171f3f7982aff008ff0d',
             url='https://dl.bintray.com/boostorg/release/1.65.1/source/boost_1_65_1.tar.bz2')
     version('1.65.0', '5512d3809801b0a1b9dd58447b70915d',
@@ -151,6 +153,9 @@ class Boost(Package):
 
     conflicts('+taggedlayout', when='+versionedlayout')
 
+    # temporary fix https://svn.boost.org/trac10/ticket/13505
+    patch('array_binary_tree.patch', when='@1.67.0.b1')
+
     # Patch fix from https://svn.boost.org/trac/boost/ticket/11856
     patch('boost_11856.patch', when='@1.60.0%gcc@4.4.7')
 
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index b45bb09041..77cd58f9db 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -77,7 +77,7 @@ class Dealii(CMakePackage, CudaPackage):
             description='Compile with Slepc (only with Petsc and MPI)')
     variant('trilinos', default=True,
             description='Compile with Trilinos (only with MPI)')
-    variant('python',   default=True,
+    variant('python',   default=False,
             description='Compile with Python bindings')
     variant('int64',    default=False,
             description='Compile with 64 bit indices support')
@@ -95,12 +95,12 @@ class Dealii(CMakePackage, CudaPackage):
     # https://github.com/dealii/dealii/issues/5262
     # we take the patch from https://github.com/boostorg/serialization/pull/79
     # more precisely its variation https://github.com/dealii/dealii/pull/5572#issuecomment-349742019
-    depends_on('boost@1.59.0:1.63,1.65.1+thread+system+serialization+iostreams',
+    depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams',
                patches=patch('boost_1.65.1_singleton.patch',
                        level=1,
                        when='@1.65.1'),
                when='~python')
-    depends_on('boost@1.59.0:1.63,1.65.1+thread+system+serialization+iostreams+python',
+    depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams+python',
                patches=patch('boost_1.65.1_singleton.patch',
                        level=1,
                        when='@1.65.1'),
@@ -223,6 +223,15 @@ class Dealii(CMakePackage, CudaPackage):
                 '-DDEAL_II_COMPONENT_PYTHON_BINDINGS=%s' %
                 ('ON' if '+python' in spec else 'OFF')
             ])
+            if '+python' in spec:
+                python_exe = spec['python'].command.path
+                python_library = spec['python'].libs[0]
+                python_include = spec['python'].headers.directories[0]
+                options.extend([
+                    '-DPYTHON_EXECUTABLE=%s' % python_exe,
+                    '-DPYTHON_INCLUDE_DIR=%s' % python_include,
+                    '-DPYTHON_LIBRARY=%s' % python_library
+                ])
 
         # Set directory structure:
         if spec.satisfies('@:8.2.1'):
diff --git a/var/spack/repos/builtin/packages/muparser/auto_ptr.patch b/var/spack/repos/builtin/packages/muparser/auto_ptr.patch
new file mode 100644
index 0000000000..7e39ea603f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/muparser/auto_ptr.patch
@@ -0,0 +1,52 @@
+diff --git a/include/muParserBase.h b/include/muParserBase.h
+index beb15bb..685f59f 100644
+--- a/include/muParserBase.h
++++ b/include/muParserBase.h
+@@ -288,7 +288,7 @@ private:
+     mutable stringbuf_type  m_vStringBuf; ///< String buffer, used for storing string function arguments

+     stringbuf_type  m_vStringVarBuf;

+ 

+-    std::auto_ptr<token_reader_type> m_pTokenReader; ///< Managed pointer to the token reader object.

++    std::unique_ptr<token_reader_type> m_pTokenReader; ///< Managed pointer to the token reader object.

+ 

+     funmap_type  m_FunDef;         ///< Map of function names and pointers.

+     funmap_type  m_PostOprtDef;    ///< Postfix operator callbacks

+diff --git a/include/muParserToken.h b/include/muParserToken.h
+index fc91d78..0cca469 100644
+--- a/include/muParserToken.h
++++ b/include/muParserToken.h
+@@ -69,7 +69,7 @@ namespace mu
+       TString m_strTok;   ///< Token string

+       TString m_strVal;   ///< Value for string variables

+       value_type m_fVal;  ///< the value 

+-      std::auto_ptr<ParserCallback> m_pCallback;

++      std::unique_ptr<ParserCallback> m_pCallback;

+ 

+   public:

+ 

+diff --git a/src/muParserTest.cpp b/src/muParserTest.cpp
+index 4006b27..8feaa2c 100644
+--- a/src/muParserTest.cpp
++++ b/src/muParserTest.cpp
+@@ -1258,7 +1258,7 @@ namespace mu
+ 

+       try

+       {

+-        std::auto_ptr<Parser> p1;

++        std::unique_ptr<Parser> p1;

+         Parser  p2, p3;   // three parser objects

+                           // they will be used for testing copy and assignment operators

+         // p1 is a pointer since i'm going to delete it in order to test if

+diff --git a/src/muParserTokenReader.cpp b/src/muParserTokenReader.cpp
+index 8da1e40..49cee68 100644
+--- a/src/muParserTokenReader.cpp
++++ b/src/muParserTokenReader.cpp
+@@ -147,7 +147,7 @@ namespace mu
+   */

+   ParserTokenReader* ParserTokenReader::Clone(ParserBase *a_pParent) const

+   {

+-    std::auto_ptr<ParserTokenReader> ptr(new ParserTokenReader(*this));

++    std::unique_ptr<ParserTokenReader> ptr(new ParserTokenReader(*this));

+     ptr->SetParent(a_pParent);

+     return ptr.release();

+   }

diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py
index e2e6c22f72..964f47b0cf 100644
--- a/var/spack/repos/builtin/packages/muparser/package.py
+++ b/var/spack/repos/builtin/packages/muparser/package.py
@@ -32,9 +32,15 @@ class Muparser(Package):
 
     version('2.2.5', '02dae671aa5ad955fdcbcd3fee313fb7')
 
+    # Replace std::auto_ptr by std::unique_ptr
+    # https://github.com/beltoforion/muparser/pull/46
+    patch('auto_ptr.patch',
+          when='@2.2.5')
+
     def install(self, spec, prefix):
         options = ['--disable-debug',
                    '--disable-dependency-tracking',
+                   'CXXFLAGS=-std=c++11',
                    '--prefix=%s' % prefix]
 
         configure(*options)