Merged

cmake-modules/BuildFREEGLUT.cmake

@@ -22,7 +22,7 @@ macro(build_freeglut install_prefix staging_prefix)
 
 ExternalProject_Add(FREEGLUT 
   SOURCE_DIR FREEGLUT
-  URL "http://iweb.dl.sourceforge.net/project/freeglut/freeglut/2.6.0/freeglut-2.6.0.tar.gz"
+  URL "http://downloads.sourceforge.net/project/freeglut/freeglut/2.6.0/freeglut-2.6.0.tar.gz"
   URL_MD5 "39f0f2de89f399529d2b981188082218"
   BUILD_IN_SOURCE 1
   INSTALL_DIR     "${staging_prefix}"

cmake-modules/BuildGIFTI.cmake

@@ -5,19 +5,16 @@ macro(build_gifti install_prefix staging_prefix)
     set(CMAKE_GEN "${CMAKE_GENERATOR}")
   endif()
 
-  SET(GIFTI_CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
   SET(GIFTI_CMAKE_C_FLAGS_RELEASE   ${CMAKE_C_FLAGS_RELEASE})
 
-  SET(GIFTI_CMAKE_CXX_FLAGS_DEBUG   ${CMAKE_CXX_FLAGS_DEBUG})
   SET(GIFTI_CMAKE_C_FLAGS_DEBUG     ${CMAKE_C_FLAGS_DEBUG})
 
-  SET(GIFTI_CMAKE_CXX_FLAGS "-fPIC ${CMAKE_CXX_FLAGS}")
   SET(GIFTI_CMAKE_C_FLAGS   "-fPIC ${CMAKE_C_FLAGS}")
 
 ExternalProject_Add(GIFTI
   SOURCE_DIR GIFTI
   BINARY_DIR GIFTI-build
-  URL "file:///home/rvincent/Dropbox/MCIN/gifticlib-1.0.10-Source.tar.gz"
+  URL "http://packages.bic.mni.mcgill.ca/tgz/gifticlib-1.0.15-Source.tar.gz"
   URL_MD5 ""
   CMAKE_GENERATOR ${CMAKE_GEN}
   CMAKE_ARGS
@@ -27,11 +24,8 @@ ExternalProject_Add(GIFTI
         -DMACOSX_RPATH:BOOL=ON
         -DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
         -DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
-        "-DCMAKE_CXX_FLAGS_RELEASE:STRING=${GIFTI_CMAKE_CXX_FLAGS_RELEASE}"
         "-DCMAKE_C_FLAGS_RELEASE:STRING=${GIFTI_CMAKE_C_FLAGS_RELEASE}"
-        "-DCMAKE_CXX_FLAGS_DEBUG:STRING=${GIFTI_CMAKE_CXX_FLAGS_DEBUG}"
         "-DCMAKE_C_FLAGS_DEBUG:STRING=${GIFTI_CMAKE_C_FLAGS_DEBUG}"
-        "-DCMAKE_CXX_FLAGS:STRING=${GIFTI_CMAKE_CXX_FLAGS}"
         "-DCMAKE_C_FLAGS:STRING=${GIFTI_CMAKE_C_FLAGS}"
         -DCMAKE_EXE_LINKER_FLAGS:STRING=${CMAKE_EXE_LINKER_FLAGS}
         -DCMAKE_MODULE_LINKER_FLAGS:STRING=${CMAKE_MODULE_LINKER_FLAGS}
@@ -42,11 +36,13 @@ ExternalProject_Add(GIFTI
         -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY}
         -DNIFTI_INCLUDE_DIR=${NIFTI_INCLUDE_DIR}
         -DNIFTI_LIBRARY=${NIFTI_LIBRARY}
+        -DZNZ_LIBRARY=${ZNZ_LIBRARY}
+        -DUSE_NIFTI_VERSION_1=ON
    INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
    INSTALL_DIR ${staging_prefix}/${install_prefix}
 )
 
-SET(GIFTI_LIBRARY     ${staging_prefix}/${install_prefix}/lib${LIB_SUFFIX}/libgiftiio.a )
+SET(GIFTI_LIBRARY     ${staging_prefix}/${install_prefix}/lib${LIB_SUFFIX}/libgiftiio.a expat )
 SET(GIFTI_INCLUDE_DIR ${staging_prefix}/${install_prefix}/include/gifti )
 SET(GIFTI_FOUND ON)
 

cmake-modules/BuildHDF5.cmake

@@ -32,7 +32,6 @@ SET(HDF5_INCLUDE_DIR ${staging_prefix}/${install_prefix}/include )
 SET(HDF5_LIBRARY_DIR ${staging_prefix}/${install_prefix}/lib${LIB_SUFFIX} )
 SET(HDF5_LIBRARY     ${staging_prefix}/${install_prefix}/lib${LIB_SUFFIX}/libhdf5${HDF5_LIB_SUFFIX} )
 
-
 SET(HDF5_LIBRARIES    ${HDF5_LIBRARY})
 SET(HDF5_INCLUDE_DIRS ${HDF5_INCLUDE_DIR})
 

cmake-modules/BuildITKv3.cmake

@@ -33,6 +33,7 @@ macro(build_itkv3 install_prefix staging_prefix)
 #    GIT_TAG "537ecca3a2762908c96508ab6f667c049aba44f6"
     URL     "https://github.com/vfonov/ITK/archive/release-3.20-fix-libtiff-v1.tar.gz"
     URL_MD5 "bba1ad3c4d0817f94bb34653acbba9c0"
+    PATCH_COMMAND patch -p 1 -d ${CMAKE_CURRENT_BINARY_DIR}/ITKv3 -u -i ${CMAKE_CURRENT_SOURCE_DIR}/cmake-modules/patch_itkv3_gcc5.patch
     UPDATE_COMMAND ""
     SOURCE_DIR ITKv3
     BINARY_DIR ITKv3-build

cmake-modules/BuildNETCDF.cmake

@@ -26,5 +26,4 @@ SET(NETCDF_LIBRARY     ${staging_prefix}/${install_prefix}/lib${LIB_SUFFIX}/libn
 SET(NETCDF_INCLUDE_DIR ${staging_prefix}/${install_prefix}/include )
 SET(NETCDF_FOUND ON)
 
-
 endmacro(build_netcdf)

cmake-modules/BuildZLIB.cmake

@@ -41,15 +41,11 @@ ExternalProject_Add(ZLIB
 )
 
 
-
-
 SET(ZLIB_INCLUDE_DIR ${staging_prefix}/${install_prefix}/include )
 SET(ZLIB_LIBRARY     ${staging_prefix}/${install_prefix}/lib/libz.a )
 SET(ZLIB_DIR         ${staging_prefix}/${install_prefix}/share/cmake/ZLIB/ )
 SET(ZLIB_FOUND ON)
 
 configure_file(${CMAKE_SOURCE_DIR}/cmake-modules/ZLIB-config.cmake.install.in ${staging_prefix}/${install_prefix}/share/cmake/ZLIB/ZLIBConfig.cmake @ONLY )
 
-
-
 endmacro(build_zlib)

cmake-modules/FindOpenJPEG.cmake

@@ -0,0 +1,57 @@
+###
+# -*- cmake -*-
+#
+# File:  FindOpenJPEG.cmake
+#
+# Original script was copied from:
+# http://code.google.com/p/emeraldviewer/source/browse/indra/cmake
+#
+# $Id$
+###
+
+# - Find OpenJPEG
+# Find the OpenJPEG includes and library
+# This module defines
+#  OPENJPEG_INCLUDE_DIR, where to find openjpeg.h, etc.
+#  OPENJPEG_LIBRARIES, the libraries needed to use OpenJPEG.
+#  OPENJPEG_FOUND, If false, do not try to use OpenJPEG.
+# also defined, but not for general use are
+#  OPENJPEG_LIBRARY, where to find the OpenJPEG library.
+
+FIND_PATH(OPENJPEG_INCLUDE_DIR openjpeg.h
+  PATHS
+    /usr/local/include/openjpeg
+    /usr/local/include
+    /usr/include/openjpeg
+    /usr/include
+  PATH_SUFFIXES
+    openjpeg-2.1
+  DOC "Location of OpenJPEG Headers"
+)
+
+SET(OPENJPEG_NAMES ${OPENJPEG_NAMES} openjpeg)
+SET(OPENJPEG_NAMES ${OPENJPEG_NAMES} openjp2)
+FIND_LIBRARY(OPENJPEG_LIBRARY
+  NAMES ${OPENJPEG_NAMES}
+  PATHS /usr/lib /usr/local/lib
+  )
+
+IF (OPENJPEG_LIBRARY AND OPENJPEG_INCLUDE_DIR)
+    SET(OPENJPEG_LIBRARIES ${OPENJPEG_LIBRARY})
+    SET(OPENJPEG_FOUND "YES")
+ELSE (OPENJPEG_LIBRARY AND OPENJPEG_INCLUDE_DIR)
+  SET(OPENJPEG_FOUND "NO")
+ENDIF (OPENJPEG_LIBRARY AND OPENJPEG_INCLUDE_DIR)
+
+
+IF (OPENJPEG_FOUND)
+   IF (NOT OPENJPEG_FIND_QUIETLY)
+      MESSAGE(STATUS "Found OpenJPEG: ${OPENJPEG_LIBRARIES}")
+   ENDIF (NOT OPENJPEG_FIND_QUIETLY)
+ELSE (OPENJPEG_FOUND)
+   IF (OPENJPEG_FIND_REQUIRED)
+      MESSAGE(FATAL_ERROR "Could not find OpenJPEG library")
+   ENDIF (OPENJPEG_FIND_REQUIRED)
+ENDIF (OPENJPEG_FOUND)
+
+MARK_AS_ADVANCED(OPENJPEG_LIBRARY OPENJPEG_INCLUDE_DIR)

cmake-modules/patch_itkv3_gcc5.patch

@@ -0,0 +1,26 @@
+diff -ru ITKv3/Utilities/vxl/vcl/vcl_compiler.h ITKv3-patched/Utilities/vxl/vcl/vcl_compiler.h
+--- ITKv3/Utilities/vxl/vcl/vcl_compiler.h	2015-02-24 10:54:54.000000000 -0500
++++ ITKv3-patched/Utilities/vxl/vcl/vcl_compiler.h	2016-07-07 17:40:03.015651756 -0400
+@@ -119,6 +119,8 @@
+ #  else
+ #   define VCL_GCC_40
+ #  endif
++# elif (__GNUC__==5)
++#  define VCL_GCC_50
+ # else
+ #  error "Dunno about this gcc"
+ # endif
+Only in ITKv3-patched/Utilities/vxl/vcl: vcl_compiler.h~
+diff -ru ITKv3/Utilities/vxl/vcl/vcl_new.h ITKv3-patched/Utilities/vxl/vcl/vcl_new.h
+--- ITKv3/Utilities/vxl/vcl/vcl_new.h	2015-02-24 10:54:54.000000000 -0500
++++ ITKv3-patched/Utilities/vxl/vcl/vcl_new.h	2016-07-07 17:42:49.579871279 -0400
+@@ -15,7 +15,7 @@
+ # include <new.h>
+
+ // -------------------- gcc with old library
+-#elif defined(VCL_GCC) && !defined(GNU_LIBSTDCXX_V3)
++#elif defined(VCL_GCC) && !defined(GNU_LIBSTDCXX_V3) && !defined(VCL_GCC_50)
+ # include <new.h>
+
+ // -------------------- old MSVC
+Only in ITKv3-patched/Utilities/vxl/vcl: vcl_new.h~