From e3392de3b900b030d97931f6433bdb1d1d8b06c6 Mon Sep 17 00:00:00 2001
From: "Vladimir S. FONOV" <vladimir.fonov@gmail.com>
Date: Tue, 15 Jan 2019 16:37:59 -0500
Subject: [PATCH 01/10] fixed lite build

---
 CMakeLists.txt | 28 ++++++++++++----------------
 1 file changed, 12 insertions(+), 16 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index cf87c999..35c53b69 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -152,7 +152,9 @@ SET(USE_SUPERBUILD ON)
 INCLUDE(ExternalProject)
 INCLUDE(ConfigureExternalProjects)
 SET(SUPERBUILD_STAGING_PREFIX ${CMAKE_BINARY_DIR}/external)
-
+
+# Fix missing share directory
+file(MAKE_DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/share)
 
 SET(MINC_TEST_ENVIRONMENT
  "PATH=${CMAKE_CURRENT_BINARY_DIR}:${CMAKE_CURRENT_BINARY_DIR}/N3:${CMAKE_CURRENT_BINARY_DIR}/classify:${CMAKE_CURRENT_BINARY_DIR}/minctools/progs:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/mincblur:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/make_phantom:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/minctracc:${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/bin:$ENV{PATH}" 
@@ -564,7 +566,6 @@ IF(MT_BUILD_VISUAL_TOOLS)
     ADD_DEPENDENCIES(Display FREEGLUT)
   ENDIF(NOT USE_SYSTEM_GLUT)
 
-  
   IF(MT_BUILD_SHARED_LIBS)
     ADD_DEPENDENCIES(ray_trace bicgl minc2_static bicpl_static)
     ADD_DEPENDENCIES(Display   bicgl minc2_static bicpl_static)
@@ -582,8 +583,7 @@ IF(MT_BUILD_VISUAL_TOOLS)
     ADD_DEPENDENCIES(xdisp minc2)
   ENDIF(X11_FOUND)
 ENDIF(MT_BUILD_VISUAL_TOOLS)
-
-
+
 IF(MT_BUILD_IM)
     message("Building minimal imagemagick, use with caution!")
     INCLUDE(BuildJPEG)
@@ -597,25 +597,23 @@ IF(MT_BUILD_IM)
     build_im(${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX} ${ZLIB_INCLUDE_DIR} ${ZLIB_LIBRARY} ${ZLIB_DIR})
     ADD_DEPENDENCIES(FREETYPE PNG)
     ADD_DEPENDENCIES(IM FREETYPE PNG JPEG)
-ENDIF(MT_BUILD_IM)
-# DO nothing?
-IF(USE_SUPERBUILD)
+ENDIF(MT_BUILD_IM)
+
   #install external dependencies to final destination
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/bin
+INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/bin
         DESTINATION .
         PATTERN *
         PERMISSIONS OWNER_EXECUTE OWNER_READ OWNER_WRITE GROUP_EXECUTE GROUP_READ WORLD_READ WORLD_EXECUTE )
 
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}
+INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}
         DESTINATION .)
 
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/include
+INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/include
         DESTINATION .)
-
-  # do we really need to install share?
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/share
+
+# share can be created by some packages
+INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/share
         DESTINATION .)
-ENDIF(USE_SUPERBUILD)
 
 
 ADD_SUBDIRECTORY(man-pages)
@@ -634,8 +632,6 @@ ENDIF(APPLE)
 
 INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.sh ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.csh DESTINATION .)
 
-
-
 # setup additional variables for making Debian package
 INCLUDE(DebianPackageAddons)
 

From 02d13bb4a7228621017333df43706000799763e4 Mon Sep 17 00:00:00 2001
From: "Vladimir S. FONOV" <vladimir.fonov@gmail.com>
Date: Sat, 19 Jan 2019 16:55:32 -0500
Subject: [PATCH 02/10] Update BEaST

---
 BEaST | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BEaST b/BEaST
index 1730a283..41907b4d 160000
--- a/BEaST
+++ b/BEaST
@@ -1 +1 @@
-Subproject commit 1730a283836638cac86c26cecaec57a8603a0858
+Subproject commit 41907b4d8d22441bfb8ee035d0ab0575924c2e0c

From a279aeccf97053090bc5636656d4b2b308e1ef0f Mon Sep 17 00:00:00 2001
From: "Vladimir S. FONOV" <vladimir.fonov@gmail.com>
Date: Mon, 4 Mar 2019 12:41:50 -0500
Subject: [PATCH 03/10] Updated BEaST

---
 BEaST | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BEaST b/BEaST
index 41907b4d..ae0a023f 160000
--- a/BEaST
+++ b/BEaST
@@ -1 +1 @@
-Subproject commit 41907b4d8d22441bfb8ee035d0ab0575924c2e0c
+Subproject commit ae0a023f6ed13fc769934428b4c550edd13d3bd6

From 9b34a1e843236024222f8ebc5240e3d8ac9a10b6 Mon Sep 17 00:00:00 2001
From: "Vladimir S. FONOV" <vladimir.fonov@gmail.com>
Date: Mon, 4 Mar 2019 12:41:59 -0500
Subject: [PATCH 04/10] Updated mni-perllib

---
 mni-perllib | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mni-perllib b/mni-perllib
index b908472b..170827f5 160000
--- a/mni-perllib
+++ b/mni-perllib
@@ -1 +1 @@
-Subproject commit b908472b4390180ea5d19a121ac5edad6ed88d83
+Subproject commit 170827f5644820b87bcb2b194494c5ebf0928149

From 4557d11f27c9a1693331a70accffcf3042085dbf Mon Sep 17 00:00:00 2001
From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
Date: Thu, 7 Mar 2019 10:40:11 -0500
Subject: [PATCH 05/10] Update OpenBLAS so we don't have to patch anymore

---
 ...e-incorrectly-calculate-page-locatio.patch | 39 -------------------
 cmake-modules/BuildOpenBLAS.cmake             | 22 +++++------
 2 files changed, 10 insertions(+), 51 deletions(-)
 delete mode 100644 cmake-modules/0001-Fix-1705-where-we-incorrectly-calculate-page-locatio.patch

diff --git a/cmake-modules/0001-Fix-1705-where-we-incorrectly-calculate-page-locatio.patch b/cmake-modules/0001-Fix-1705-where-we-incorrectly-calculate-page-locatio.patch
deleted file mode 100644
index a13d3308..00000000
--- a/cmake-modules/0001-Fix-1705-where-we-incorrectly-calculate-page-locatio.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-From 6400868e553f03110890882c78f9f38ee69e4615 Mon Sep 17 00:00:00 2001
-From: Craig Donner <cdonner@google.com>
-Date: Thu, 2 Aug 2018 16:21:19 +0100
-Subject: [PATCH] Fix #1705 where we incorrectly calculate page locations.
-
-Since we now use an allocation size that isn't a multiple of PAGESIZE, finding
-the pages for run_bench wasn't terminating properly.  Now we detect if we've
-found enough pages for the allocation and terminate the loop.
----
- driver/others/memory.c | 5 +++--
- 1 file changed, 3 insertions(+), 2 deletions(-)
-
-diff --git a/driver/others/memory.c b/driver/others/memory.c
-index 98bcfb2..044c7d7 100644
---- a/driver/others/memory.c
-+++ b/driver/others/memory.c
-@@ -637,7 +637,7 @@ static inline BLASULONG run_bench(BLASULONG address, BLASULONG size) {
- 
- static void *alloc_mmap(void *address){
-   void *map_address, *best_address;
--  BLASULONG best, start, current;
-+  BLASULONG best, start, current, original;
-   BLASULONG allocsize;
- 
-   if (address){
-@@ -685,8 +685,9 @@ static void *alloc_mmap(void *address){
- 
- 	start   = (BLASULONG)map_address;
- 	current = (SCALING - 1) * allocation_block_size;
-+	original = current;
- 
--	while(current > 0) {
-+	while(current > 0 && current <= original) {
- 	  *(BLASLONG *)start = (BLASLONG)start + PAGESIZE;
- 	  start += PAGESIZE;
- 	  current -= PAGESIZE;
--- 
-1.7.12.4
-
diff --git a/cmake-modules/BuildOpenBLAS.cmake b/cmake-modules/BuildOpenBLAS.cmake
index c2ef41ec..87e15ae7 100644
--- a/cmake-modules/BuildOpenBLAS.cmake
+++ b/cmake-modules/BuildOpenBLAS.cmake
@@ -3,7 +3,7 @@ macro(build_open_blas install_prefix staging_prefix build_parallel)
   if(NOT CMAKE_Fortran_COMPILER)
     message("Fortran compiler not found! OpenBLAS will not work as expected!")
   endif(NOT CMAKE_Fortran_COMPILER)
-  
+
   if(CMAKE_EXTRA_GENERATOR)
     set(CMAKE_GEN "${CMAKE_EXTRA_GENERATOR} - ${CMAKE_GENERATOR}")
   else()
@@ -52,7 +52,7 @@ macro(build_open_blas install_prefix staging_prefix build_parallel)
         -DCMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO}
         -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
   )
-  
+
   if(APPLE)
     list(APPEND CMAKE_EXTERNAL_PROJECT_ARGS
       -DCMAKE_OSX_ARCHITECTURES:STRING=${CMAKE_OSX_ARCHITECTURES}
@@ -60,18 +60,17 @@ macro(build_open_blas install_prefix staging_prefix build_parallel)
       -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=${CMAKE_OSX_DEPLOYMENT_TARGET}
     )
   endif()
-  
-  
-  
+
+
+
  
-  GET_PACKAGE("https://github.com/xianyi/OpenBLAS/archive/v0.3.2.tar.gz" "686f30a234f81fd768dbad5bbd41ca4f" "openblas_v0.3.2.tar.gz" OPENBLAS_PATH ) 
-  
+  GET_PACKAGE("https://github.com/xianyi/OpenBLAS/archive/v0.3.5.tar.gz" "579bda57f68ea6e9074bf5780e8620bb" "openblas_v0.3.5.tar.gz" OPENBLAS_PATH )
+
   ExternalProject_Add(OpenBLAS
         URL "${OPENBLAS_PATH}"
-        URL_MD5 "686f30a234f81fd768dbad5bbd41ca4f"
+        URL_MD5 "579bda57f68ea6e9074bf5780e8620bb"
         SOURCE_DIR OpenBLAS
         BINARY_DIR OpenBLAS-build
-        PATCH_COMMAND patch -p1 -t -N -i ${CMAKE_SOURCE_DIR}/cmake-modules/0001-Fix-1705-where-we-incorrectly-calculate-page-locatio.patch
         LIST_SEPARATOR :::
         CMAKE_GENERATOR ${CMAKE_GEN}
         CMAKE_ARGS
@@ -89,15 +88,14 @@ macro(build_open_blas install_prefix staging_prefix build_parallel)
         ${CMAKE_EXTERNAL_PROJECT_ARGS}
         "-DCMAKE_CXX_FLAGS:STRING=-fPIC ${CMAKE_CXX_FLAGS}"
         "-DCMAKE_C_FLAGS:STRING=-fPIC ${CMAKE_C_FLAGS}"
-        -DCMAKE_INSTALL_LIBDIR:PATH=${install_prefix}/lib${LIB_SUFFIX} 
+        -DCMAKE_INSTALL_LIBDIR:PATH=${install_prefix}/lib${LIB_SUFFIX}
             INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
             INSTALL_DIR ${staging_prefix}/${install_prefix}
       )
-  
+
   SET(OpenBLAS_INCLUDE_DIRS ${staging_prefix}/${install_prefix}/include )
   SET(OpenBLAS_LIBRARIES    ${staging_prefix}/${install_prefix}/lib${LIB_SUFFIX}/libopenblas.so  )
   SET(OpenBLAS_DIR          ${staging_prefix}/${install_prefix}/lib${LIB_SUFFIX}/cmake/openblas )
   SET(OpenBLAS_FOUND        ON)
 
 endmacro(build_open_blas)
-

From 7979b7c28e2a39459eadefcddfbe98c882bd263b Mon Sep 17 00:00:00 2001
From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
Date: Thu, 7 Mar 2019 12:48:30 -0500
Subject: [PATCH 06/10] Update to ITK 4.13.1

---
 cmake-modules/BuildITKv4.cmake | 54 +++++++++++++++++-----------------
 1 file changed, 27 insertions(+), 27 deletions(-)

diff --git a/cmake-modules/BuildITKv4.cmake b/cmake-modules/BuildITKv4.cmake
index a519a7cc..0afa37e4 100644
--- a/cmake-modules/BuildITKv4.cmake
+++ b/cmake-modules/BuildITKv4.cmake
@@ -17,17 +17,17 @@ macro(build_itkv4 install_prefix staging_prefix minc_dir)
   LIST(APPEND EXT_CMAKE_C_FLAGS -D_XOPEN_SOURCE=600)
   LIST(APPEND EXT_CMAKE_CXX_FLAGS -D_XOPEN_SOURCE=600)
   ENDIF(NOT APPLE)
-  
+
   set(CMAKE_EXTERNAL_PROJECT_ARGS
         -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
         -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
         -DCMAKE_LINKER:FILEPATH=${CMAKE_LINKER}
-        -DCMAKE_CXX_FLAGS:STRING=${EXT_CMAKE_CXX_FLAGS} 
+        -DCMAKE_CXX_FLAGS:STRING=${EXT_CMAKE_CXX_FLAGS}
         -DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG}
         -DCMAKE_CXX_FLAGS_MINSIZEREL:STRING=${CMAKE_CXX_FLAGS_MINSIZEREL}
         -DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE}
         -DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO}
-        -DCMAKE_C_FLAGS:STRING=${EXT_CMAKE_C_FLAGS} 
+        -DCMAKE_C_FLAGS:STRING=${EXT_CMAKE_C_FLAGS}
         -DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG}
         -DCMAKE_C_FLAGS_MINSIZEREL:STRING=${CMAKE_C_FLAGS_MINSIZEREL}
         -DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE}
@@ -78,16 +78,16 @@ macro(build_itkv4 install_prefix staging_prefix minc_dir)
   #endif(MT_BUILD_QUIET)
 
   SET(HDF5_LIB_SUFFIX ".a")
-  
-  IF(MT_BUILD_SHARED_LIBS) 
+
+  IF(MT_BUILD_SHARED_LIBS)
     SET(ITK_SHARED_LIBRARY "ON")
-    
+
     IF(APPLE)
         SET(HDF5_LIB_SUFFIX ".dylib")
     ELSE(APPLE)
         SET(HDF5_LIB_SUFFIX ".so")
     ENDIF(APPLE)
-    
+
   ELSE(MT_BUILD_SHARED_LIBS)
       SET(HDF5_LIB_SUFFIX    ".a")
       SET(ITK_SHARED_LIBRARY "OFF")
@@ -136,13 +136,13 @@ macro(build_itkv4 install_prefix staging_prefix minc_dir)
   message("HDF5_HL_CPP_LIBRARY=${HDF5_HL_CPP_LIBRARY}")
   message("HDF5_BIN_DIR=${HDF5_BIN_DIR}")
 
-  GET_PACKAGE("https://sourceforge.net/projects/itk/files/itk/4.13/InsightToolkit-4.13.0.tar.xz" "3badf70cfb0093054453f66c5974c5a4" "InsightToolkit-4.13.0.tar.xz" ITKv4_PATH ) 
-  
+  GET_PACKAGE("https://github.com/InsightSoftwareConsortium/ITK/releases/download/v4.13.1/InsightToolkit-4.13.1.tar.xz" "bc7296e7faccdcb5656a7669d4d875d2" "InsightToolkit-4.13.1.tar.xz" ITKv4_PATH )
+
 
 
   ExternalProject_Add(ITKv4
     URL "${ITKv4_PATH}"
-    URL_MD5 "3badf70cfb0093054453f66c5974c5a4"
+    URL_MD5 "bc7296e7faccdcb5656a7669d4d875d2"
     UPDATE_COMMAND ""
     SOURCE_DIR ITKv4
     BINARY_DIR ITKv4-build
@@ -195,19 +195,19 @@ macro(build_itkv4 install_prefix staging_prefix minc_dir)
     INSTALL_DIR ${staging_prefix}/${install_prefix}
     STEP_TARGETS PatchInstall
   )
-  
-  ExternalProject_Add_Step(ITKv4 PatchInstall 
+
+  ExternalProject_Add_Step(ITKv4 PatchInstall
     COMMAND ${CMAKE_COMMAND} -Dstaging_prefix=${staging_prefix} -Dminc_dir=${minc_dir} -Dinstall_prefix=${install_prefix} -P ${CMAKE_CURRENT_SOURCE_DIR}/cmake-modules/PatchITKv4.cmake
     COMMENT "Patching ITKv4 Build"
     DEPENDEES install
     )
-  
+
   # let's patch targets to remove staging directory
-  
-  
+
+
   SET(ITK_DIR ${CMAKE_CURRENT_BINARY_DIR}/ITKv4-build)
-  
-  SET(ITK_INCLUDE_DIRS 
+
+  SET(ITK_INCLUDE_DIRS
         ${CMAKE_CURRENT_BINARY_DIR}/ITKv4-build
         ${CMAKE_CURRENT_BINARY_DIR}/ITKv4/Code/Algorithms
         ${CMAKE_CURRENT_BINARY_DIR}/ITKv4/Code/BasicFilters
@@ -242,18 +242,18 @@ macro(build_itkv4 install_prefix staging_prefix minc_dir)
 
 # The ITK library directories.
   SET(ITK_LIBRARY_DIRS "${CMAKE_CURRENT_BINARY_DIR}/ITKv4-build/bin")
-  
-  SET(ITK_LIBRARIES  
-          ITKAlgorithms ITKStatistics 
-          ITKNumerics 
-          ITKFEM ITKQuadEdgeMesh 
-          ITKBasicFilters  ITKIO ITKNrrdIO 
+
+  SET(ITK_LIBRARIES
+          ITKAlgorithms ITKStatistics
+          ITKNumerics
+          ITKFEM ITKQuadEdgeMesh
+          ITKBasicFilters  ITKIO ITKNrrdIO
           ITKSpatialObject ITKMetaIO
           ITKDICOMParser ITKEXPAT
-          ITKniftiio ITKTransformIOReview  ITKCommon ITKznz 
-          itkgdcm itkpng itktiff itkzlib itkvcl 
-          itkvcl 
-          itkv3p_lsqr  itkvnl_algo itkvnl_inst itkvnl itkv3p_netlib 
+          ITKniftiio ITKTransformIOReview  ITKCommon ITKznz
+          itkgdcm itkpng itktiff itkzlib itkvcl
+          itkvcl
+          itkv3p_lsqr  itkvnl_algo itkvnl_inst itkvnl itkv3p_netlib
           itksys itkjpeg8 itkjpeg12 itkjpeg16 itkopenjpeg  hdf5_cpp hdf5
           ${CMAKE_THREAD_LIBS_INIT}
           )

From f9ad1c0681848a884e0dfdfe6c8a0915aa241f25 Mon Sep 17 00:00:00 2001
From: "Vladimir S. FONOV" <vladimir.fonov@gmail.com>
Date: Tue, 12 Mar 2019 16:35:46 -0400
Subject: [PATCH 07/10] Updated subprojects

---
 EZminc    | 2 +-
 ILT       | 2 +-
 minctools | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/EZminc b/EZminc
index 23db5caf..5e3333ee 160000
--- a/EZminc
+++ b/EZminc
@@ -1 +1 @@
-Subproject commit 23db5caf2f3b605c4c57746372ed9c84022caaa1
+Subproject commit 5e3333ee356f914d34d66d33ea8df809c7f7fa51
diff --git a/ILT b/ILT
index dadababb..e2c611c2 160000
--- a/ILT
+++ b/ILT
@@ -1 +1 @@
-Subproject commit dadababbd8d4fb9da3173f7caa6fb3b91cbf8083
+Subproject commit e2c611c21a8fa577e47f8a62d27603e38596cfe3
diff --git a/minctools b/minctools
index 346ce29b..9bc7e81f 160000
--- a/minctools
+++ b/minctools
@@ -1 +1 @@
-Subproject commit 346ce29b9c9fe4edb5466ba4ce57f3653db6b7c8
+Subproject commit 9bc7e81fb932bdf4218bf5792cd44b640273be9a

From 10f801590b710e573cc792590ffbd25fff1b8da2 Mon Sep 17 00:00:00 2001
From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
Date: Wed, 13 Mar 2019 09:53:14 -0400
Subject: [PATCH 08/10] Fix OpenBLAS build on 32bit

---
 cmake-modules/2058.patch          | 26 ++++++++++++++++++++++++++
 cmake-modules/BuildOpenBLAS.cmake |  1 +
 2 files changed, 27 insertions(+)
 create mode 100644 cmake-modules/2058.patch

diff --git a/cmake-modules/2058.patch b/cmake-modules/2058.patch
new file mode 100644
index 00000000..98e59e8a
--- /dev/null
+++ b/cmake-modules/2058.patch
@@ -0,0 +1,26 @@
+From c3e30b2bc2234dfafc9e674c8ab5723fabeb04c5 Mon Sep 17 00:00:00 2001
+From: Sacha <xsacha@gmail.com>
+Date: Wed, 13 Mar 2019 23:21:54 +1000
+Subject: [PATCH] Change 64-bit detection as explained in #2056
+
+---
+ cmake/system_check.cmake | 6 +++++-
+ 1 file changed, 5 insertions(+), 1 deletion(-)
+
+diff --git a/cmake/system_check.cmake b/cmake/system_check.cmake
+index 88bb081a6..f30a946b4 100644
+--- a/cmake/system_check.cmake
++++ b/cmake/system_check.cmake
+@@ -39,7 +39,11 @@ elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "ppc.*|power.*|Power.*")
+ elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "mips64.*")
+   set(MIPS64 1)
+ elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "amd64.*|x86_64.*|AMD64.*")
+-  set(X86_64 1)
++  if("${CMAKE_SIZEOF_VOID_P}" EQUAL "8")
++    set(X86_64 1)
++  else()
++    set(X86 1)
++  endif()
+ elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "i686.*|i386.*|x86.*|amd64.*|AMD64.*")
+   set(X86 1)
+ elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(arm.*|ARM.*)")
diff --git a/cmake-modules/BuildOpenBLAS.cmake b/cmake-modules/BuildOpenBLAS.cmake
index 87e15ae7..6a012b71 100644
--- a/cmake-modules/BuildOpenBLAS.cmake
+++ b/cmake-modules/BuildOpenBLAS.cmake
@@ -71,6 +71,7 @@ macro(build_open_blas install_prefix staging_prefix build_parallel)
         URL_MD5 "579bda57f68ea6e9074bf5780e8620bb"
         SOURCE_DIR OpenBLAS
         BINARY_DIR OpenBLAS-build
+        PATCH_COMMAND patch -p1 -t -N -i ${CMAKE_SOURCE_DIR}/cmake-modules/2058.patch
         LIST_SEPARATOR :::
         CMAKE_GENERATOR ${CMAKE_GEN}
         CMAKE_ARGS

From 23413b8d51b44088f4131a8ec0a8b0d6b547c814 Mon Sep 17 00:00:00 2001
From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
Date: Wed, 13 Mar 2019 11:09:41 -0400
Subject: [PATCH 09/10] Patch an ANTS build failure with modern compilers

---
 ...9b2694715bf8204993e032fa132f80cf37bd.patch | 25 +++++++++++++++++++
 cmake-modules/BuildANTS.cmake                 |  1 +
 2 files changed, 26 insertions(+)
 create mode 100644 cmake-modules/89af9b2694715bf8204993e032fa132f80cf37bd.patch

diff --git a/cmake-modules/89af9b2694715bf8204993e032fa132f80cf37bd.patch b/cmake-modules/89af9b2694715bf8204993e032fa132f80cf37bd.patch
new file mode 100644
index 00000000..63c1bd7f
--- /dev/null
+++ b/cmake-modules/89af9b2694715bf8204993e032fa132f80cf37bd.patch
@@ -0,0 +1,25 @@
+From 89af9b2694715bf8204993e032fa132f80cf37bd Mon Sep 17 00:00:00 2001
+From: Martino Pilia <martino.pilia@gmail.com>
+Date: Fri, 1 Jun 2018 18:17:57 +0200
+Subject: [PATCH] BUG: fix a bug in
+ ImageSegmentation/antsAtroposSegmentationImageFilter.h
+
+This should be pretty obvious, the return type of a getter method was
+wrong.
+---
+ ImageSegmentation/antsAtroposSegmentationImageFilter.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/ImageSegmentation/antsAtroposSegmentationImageFilter.h b/ImageSegmentation/antsAtroposSegmentationImageFilter.h
+index e4b32a0cf..adeb4baad 100644
+--- a/ImageSegmentation/antsAtroposSegmentationImageFilter.h
++++ b/ImageSegmentation/antsAtroposSegmentationImageFilter.h
+@@ -518,7 +518,7 @@ class AtroposSegmentationImageFilter :
+   /**
+    * Get the prior label parameters.
+    */
+-  void GetPriorLabelParameterMap()
++  LabelParameterMapType GetPriorLabelParameterMap()
+   {
+     return this->m_PriorLabelParameterMap;
+   }
diff --git a/cmake-modules/BuildANTS.cmake b/cmake-modules/BuildANTS.cmake
index 1480b79a..86a18ad4 100644
--- a/cmake-modules/BuildANTS.cmake
+++ b/cmake-modules/BuildANTS.cmake
@@ -62,6 +62,7 @@ macro(build_ANTS install_prefix staging_prefix itk_dir ) #boost_dir
     #UPDATE_COMMAND ""
     SOURCE_DIR ${CMAKE_SOURCE_DIR}/ANTs
     BINARY_DIR ANTS-build
+    PATCH_COMMAND patch -p1 -t -N -i ${CMAKE_SOURCE_DIR}/cmake-modules/89af9b2694715bf8204993e032fa132f80cf37bd.patch
     #PATCH_COMMAND ${PATCH_QUIET}
     LIST_SEPARATOR :::  
     CMAKE_GENERATOR ${CMAKE_GEN}

From 49650293658a1636916bbe09a02af01a0b387908 Mon Sep 17 00:00:00 2001
From: "Vladimir S. FONOV" <vladimir.fonov@gmail.com>
Date: Wed, 13 Mar 2019 16:34:57 -0400
Subject: [PATCH 10/10] Release date bump

---
 CMakeLists.txt | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 35c53b69..2dcef05a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -27,7 +27,7 @@ ENDIF(COMMAND CMAKE_POLICY)
 SET(MINC_TOOLKIT_PACKAGE_VERSION_MAJOR 1)
 SET(MINC_TOOLKIT_PACKAGE_VERSION_MINOR 9)
 SET(MINC_TOOLKIT_PACKAGE_VERSION_PATCH 17)
-SET(MINC_TOOLKIT_RELEASE_DATE "20181127")
+SET(MINC_TOOLKIT_RELEASE_DATE "20190313")
 
 SET(MINC_TOOLKIT_VERSION_FULL "${MINC_TOOLKIT_PACKAGE_VERSION_MAJOR}.${MINC_TOOLKIT_PACKAGE_VERSION_MINOR}.${MINC_TOOLKIT_PACKAGE_VERSION_PATCH}-${MINC_TOOLKIT_RELEASE_DATE}")
 
@@ -152,9 +152,9 @@ SET(USE_SUPERBUILD ON)
 INCLUDE(ExternalProject)
 INCLUDE(ConfigureExternalProjects)
 SET(SUPERBUILD_STAGING_PREFIX ${CMAKE_BINARY_DIR}/external)
-
-# Fix missing share directory
-file(MAKE_DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/share)
+
+# Fix missing share directory
+file(MAKE_DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/share)
 
 SET(MINC_TEST_ENVIRONMENT
  "PATH=${CMAKE_CURRENT_BINARY_DIR}:${CMAKE_CURRENT_BINARY_DIR}/N3:${CMAKE_CURRENT_BINARY_DIR}/classify:${CMAKE_CURRENT_BINARY_DIR}/minctools/progs:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/mincblur:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/make_phantom:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/minctracc:${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/bin:$ENV{PATH}" 
@@ -583,7 +583,7 @@ IF(MT_BUILD_VISUAL_TOOLS)
     ADD_DEPENDENCIES(xdisp minc2)
   ENDIF(X11_FOUND)
 ENDIF(MT_BUILD_VISUAL_TOOLS)
-
+
 IF(MT_BUILD_IM)
     message("Building minimal imagemagick, use with caution!")
     INCLUDE(BuildJPEG)
@@ -597,7 +597,7 @@ IF(MT_BUILD_IM)
     build_im(${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX} ${ZLIB_INCLUDE_DIR} ${ZLIB_LIBRARY} ${ZLIB_DIR})
     ADD_DEPENDENCIES(FREETYPE PNG)
     ADD_DEPENDENCIES(IM FREETYPE PNG JPEG)
-ENDIF(MT_BUILD_IM)
+ENDIF(MT_BUILD_IM)
 
   #install external dependencies to final destination
 INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/bin
@@ -610,7 +610,7 @@ INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/lib${LIB_
 
 INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/include
         DESTINATION .)
-
+
 # share can be created by some packages
 INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/share
         DESTINATION .)