Merge pull request #2238 from stan-dev/eigen339

upgrade to eigen 3.3.9

Author: rok-cesnovar

README.md

@@ -1,4 +1,3 @@
-syntax: glob
 qrc_*cxx
 *.orig
 *.pyc
@@ -28,7 +27,11 @@ activity.png
 *.rej
 log
 patch
+*.patch
 a
 a.*
 lapack/testing
 lapack/reference
+.*project
+.settings
+Makefile

lib/eigen_3.3.7/doc/Pitfalls.dox

@@ -391,22 +391,27 @@ endif()
 
 if(EIGEN_INCLUDE_INSTALL_DIR AND NOT INCLUDE_INSTALL_DIR)
   set(INCLUDE_INSTALL_DIR ${EIGEN_INCLUDE_INSTALL_DIR}
-      CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where Eigen header files are installed")
+      CACHE STRING "The directory relative to CMAKE_PREFIX_PATH where Eigen header files are installed")
 else()
   set(INCLUDE_INSTALL_DIR
       "${CMAKE_INSTALL_INCLUDEDIR}/eigen3"
-      CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where Eigen header files are installed"
+      CACHE STRING "The directory relative to CMAKE_PREFIX_PATH where Eigen header files are installed"
       )
 endif()
 set(CMAKEPACKAGE_INSTALL_DIR
     "${CMAKE_INSTALL_DATADIR}/eigen3/cmake"
-    CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where Eigen3Config.cmake is installed"
+    CACHE STRING "The directory relative to CMAKE_PREFIX_PATH where Eigen3Config.cmake is installed"
     )
 set(PKGCONFIG_INSTALL_DIR
     "${CMAKE_INSTALL_DATADIR}/pkgconfig"
-    CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where eigen3.pc is installed"
+    CACHE STRING "The directory relative to CMAKE_PREFIX_PATH where eigen3.pc is installed"
     )
 
+foreach(var INCLUDE_INSTALL_DIR CMAKEPACKAGE_INSTALL_DIR PKGCONFIG_INSTALL_DIR)
+  if(IS_ABSOLUTE "${${var}}")
+    message(FATAL_ERROR "${var} must be relative to CMAKE_PREFIX_PATH. Got: ${${var}}")
+  endif()
+endforeach()
 
 # similar to set_target_properties but append the property instead of overwriting it
 macro(ei_add_target_property target prop value)

lib/eigen_3.3.7/doc/TopicLazyEvaluation.dox

@@ -4,10 +4,10 @@
 ## # The following are required to uses Dart and the Cdash dashboard
 ##   ENABLE_TESTING()
 ##   INCLUDE(CTest)
-set(CTEST_PROJECT_NAME "Eigen 3.3")
+set(CTEST_PROJECT_NAME "Eigen")
 set(CTEST_NIGHTLY_START_TIME "00:00:00 UTC")
 
 set(CTEST_DROP_METHOD "http")
-set(CTEST_DROP_SITE "manao.inria.fr")
-set(CTEST_DROP_LOCATION "/CDash/submit.php?project=Eigen+3.3")
+set(CTEST_DROP_SITE "my.cdash.org")
+set(CTEST_DROP_LOCATION "/submit.php?project=Eigen")
 set(CTEST_DROP_SITE_CDASH TRUE)

lib/eigen_3.3.7/doc/eigendoxy_footer.html.in

@@ -279,7 +279,10 @@
 #include <cmath>
 #include <cassert>
 #include <functional>
-#include <iosfwd>
+#include <sstream>
+#ifndef EIGEN_NO_IO
+  #include <iosfwd>
+#endif
 #include <cstring>
 #include <string>
 #include <limits>
@@ -375,7 +378,9 @@ using std::ptrdiff_t;
 
 #if defined EIGEN_VECTORIZE_AVX512
   #include "src/Core/arch/SSE/PacketMath.h"
+  #include "src/Core/arch/SSE/MathFunctions.h"
   #include "src/Core/arch/AVX/PacketMath.h"
+  #include "src/Core/arch/AVX/MathFunctions.h"
   #include "src/Core/arch/AVX512/PacketMath.h"
   #include "src/Core/arch/AVX512/MathFunctions.h"
 #elif defined EIGEN_VECTORIZE_AVX

lib/eigen_3.3.7/scripts/buildtests.in

@@ -10,14 +10,14 @@
 
 #include "Core"
 
-#include "src/Core/util/DisableStupidWarnings.h"
-
 #include "Cholesky"
 #include "Jacobi"
 #include "Householder"
 #include "LU"
 #include "Geometry"
 
+#include "src/Core/util/DisableStupidWarnings.h"
+
 /** \defgroup Eigenvalues_Module Eigenvalues module
   *
   *

lib/eigen_3.3.7/test/rvalue_types.cpp

@@ -10,12 +10,12 @@
 
 #include "Core"
 
-#include "src/Core/util/DisableStupidWarnings.h"
-
 #include "SVD"
 #include "LU"
 #include <limits>
 
+#include "src/Core/util/DisableStupidWarnings.h"
+
 /** \defgroup Geometry_Module Geometry module
   *
   * This module provides support for:

lib/eigen_3.3.7/.hgignore lib/eigen_3.3.9/.gitignore

@@ -10,12 +10,12 @@
 
 #include "Core"
 
-#include "src/Core/util/DisableStupidWarnings.h"
-
 #include "Cholesky"
 #include "Jacobi"
 #include "Householder"
 
+#include "src/Core/util/DisableStupidWarnings.h"
+
 /** \defgroup QR_Module QR module
   *
   *

lib/eigen_3.3.7/.hgeol lib/eigen_3.3.9/.hgeol

@@ -28,7 +28,6 @@
   * 
   */
 
-#include "OrderingMethods"
 #include "src/SparseCore/SparseColEtree.h"
 #include "src/SparseQR/SparseQR.h"