debian/patches/use_system_eigen.patch → debian/patches/prevent_cmake_downloading.patch

-Description: use libeigen-dev
- This patch modifies some of the cmake files in order to use the system available libeigen-dev library instead of cmake downloading, building and linking.
+Description: prevent third party downloads
+ This patch will modify some of the cmake files to prevent cmake from using git and downloading third party libraries / files as these can be accomplished by either safely integrating as patches or by using a packaged library.
 Author: Shayan Doust <hello@shayandoust.me>
 Last-Update: 2019-08-08
 ---
 
 Index: fast/cmake/ExternalEigen.cmake
 ===================================================================
---- fast.orig/cmake/ExternalEigen.cmake	2019-08-08 14:52:02.618696327 +0100
-+++ fast/cmake/ExternalEigen.cmake	2019-08-08 14:52:02.614696293 +0100
+--- fast.orig/cmake/ExternalEigen.cmake	2019-08-08 16:04:41.462374017 +0100
++++ fast/cmake/ExternalEigen.cmake	2019-08-08 16:04:41.458373984 +0100
 @@ -1,21 +1,21 @@
  # Download and set up Eigen
  
@@ -48,44 +48,89 @@ Index: fast/cmake/ExternalEigen.cmake
 \ No newline at end of file
 +#list(APPEND FAST_INCLUDE_DIRS ${FAST_EXTERNAL_INSTALL_DIR}/include/eigen3/)
 +#list(APPEND FAST_EXTERNAL_DEPENDENCIES eigen)
-Index: fast/cmake/InstallFAST.cmake
+Index: fast/cmake/ExternalOpenSlide.cmake
 ===================================================================
---- fast.orig/cmake/InstallFAST.cmake	2019-08-08 14:52:02.618696327 +0100
-+++ fast/cmake/InstallFAST.cmake	2019-08-08 14:52:02.614696293 +0100
-@@ -185,10 +185,10 @@
- )
+--- fast.orig/cmake/ExternalOpenSlide.cmake	2019-08-08 16:04:41.462374017 +0100
++++ fast/cmake/ExternalOpenSlide.cmake	2019-08-08 16:04:41.458373984 +0100
+@@ -1,17 +1,17 @@
+ # Download and set up OpenSlide
  
- # Eigen
--file(GLOB LICENSE_FILES ${FAST_EXTERNAL_BUILD_DIR}/eigen/src/eigen/COPYING.*)
--install(FILES ${LICENSE_FILES}
--		DESTINATION fast/licenses/eigen/
+-include(cmake/Externals.cmake)
++#include(cmake/Externals.cmake)
+ 
+-if(WIN32)
++#if(WIN32)
+ 
+-ExternalProject_Add(openslide
+-        PREFIX ${FAST_EXTERNAL_BUILD_DIR}/openslide
+-        BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/openslide
+-        URL "https://github.com/openslide/openslide-winbuild/releases/download/v20171122/openslide-win64-20171122.zip"
+-        CONFIGURE_COMMAND ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/openslide/src/openslide/ ${FAST_EXTERNAL_INSTALL_DIR}
+-        BUILD_COMMAND ""
+-        INSTALL_COMMAND ""
 -)
-+#file(GLOB LICENSE_FILES ${FAST_EXTERNAL_BUILD_DIR}/eigen/src/eigen/COPYING.*)
-+#install(FILES ${LICENSE_FILES}
-+#		DESTINATION fast/licenses/eigen/
++#ExternalProject_Add(openslide
++#       PREFIX ${FAST_EXTERNAL_BUILD_DIR}/openslide
++#       BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/openslide
++#       URL "https://github.com/openslide/openslide-winbuild/releases/download/v20171122/openslide-win64-20171122.zip"
++#       CONFIGURE_COMMAND ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/openslide/src/openslide/ ${FAST_EXTERNAL_INSTALL_DIR}
++#       BUILD_COMMAND ""
++#       INSTALL_COMMAND ""
 +#)
- # zlib
- install(FILES ${FAST_EXTERNAL_BUILD_DIR}/zlib/src/zlib/README
- 		DESTINATION fast/licenses/zlib/
-Index: fast/CMakeLists.txt
+ 
+-list(APPEND FAST_EXTERNAL_DEPENDENCIES openslide)
+-endif()
+\ No newline at end of file
++#list(APPEND FAST_EXTERNAL_DEPENDENCIES openslide)
++#endif()
+Index: fast/cmake/ExternalZlib.cmake
 ===================================================================
---- fast.orig/CMakeLists.txt	2019-08-08 14:52:02.618696327 +0100
-+++ fast/CMakeLists.txt	2019-08-08 14:52:02.614696293 +0100
-@@ -153,7 +153,7 @@
-     endif()
- endif()
+--- fast.orig/cmake/ExternalZlib.cmake	2019-08-08 16:04:41.462374017 +0100
++++ fast/cmake/ExternalZlib.cmake	2019-08-08 16:04:41.458373984 +0100
+@@ -1,24 +1,24 @@
+ # Download and set up zlib
  
--
-+find_package(Eigen3 REQUIRED)
+-include(cmake/Externals.cmake)
++#include(cmake/Externals.cmake)
  
- #### Create FAST library and executables
- add_library(FAST SHARED ${FAST_SOURCE_FILES} ${HEADERS_MOC})
-@@ -169,7 +169,7 @@
- if(FAST_MODULE_Visualization AND FAST_BUILD_QT5)
-     qt5_use_modules(FAST Widgets OpenGL) # Add Qt 5 modules
- endif()
--
-+target_link_libraries(FAST PUBLIC Eigen3::Eigen)
- ## Build test executable
- if(FAST_BUILD_TESTS)
-     add_executable(testFAST ${FAST_TEST_SOURCE_FILES} source/FAST/Algorithms/CoherentPointDrift/Rigid.cpp source/FAST/Algorithms/CoherentPointDrift/Rigid.hpp source/FAST/Algorithms/CoherentPointDrift/Affine.cpp source/FAST/Algorithms/CoherentPointDrift/Affine.hpp)
+-ExternalProject_Add(zlib
+-        PREFIX ${FAST_EXTERNAL_BUILD_DIR}/zlib
+-        BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/zlib
+-        GIT_REPOSITORY "https://github.com/madler/zlib.git"
+-        GIT_TAG "v1.2.9"
+-        CMAKE_ARGS
+-            -DCMAKE_MACOSX_RPATH=ON
+-        CMAKE_CACHE_ARGS
+-            -DCMAKE_BUILD_TYPE:STRING=Release
+-            -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
+-            -DCMAKE_INSTALL_MESSAGE:BOOL=LAZY
+-            -DCMAKE_INSTALL_PREFIX:STRING=${FAST_EXTERNAL_INSTALL_DIR}
+-)
+-if(WIN32)
+-	set(ZLIB_LIBRARY debug zlibd.lib optimized zlib.lib)
+-else(WIN32)
+-	set(ZLIB_LIBRARY ${CMAKE_SHARED_LIBRARY_PREFIX}z${CMAKE_SHARED_LIBRARY_SUFFIX})
+-endif(WIN32)
+-list(APPEND LIBRARIES ${ZLIB_LIBRARY})
+-list(APPEND FAST_EXTERNAL_DEPENDENCIES zlib)
+\ No newline at end of file
++#ExternalProject_Add(zlib
++#       PREFIX ${FAST_EXTERNAL_BUILD_DIR}/zlib
++#       BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/zlib
++#       GIT_REPOSITORY "https://github.com/madler/zlib.git"
++#       GIT_TAG "v1.2.9"
++#       CMAKE_ARGS
++#           -DCMAKE_MACOSX_RPATH=ON
++#       CMAKE_CACHE_ARGS
++#           -DCMAKE_BUILD_TYPE:STRING=Release
++#           -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
++#           -DCMAKE_INSTALL_MESSAGE:BOOL=LAZY
++#           -DCMAKE_INSTALL_PREFIX:STRING=${FAST_EXTERNAL_INSTALL_DIR}
++#)
++#if(WIN32)
++#	set(ZLIB_LIBRARY debug zlibd.lib optimized zlib.lib)
++#else(WIN32)
++#	set(ZLIB_LIBRARY ${CMAKE_SHARED_LIBRARY_PREFIX}z${CMAKE_SHARED_LIBRARY_SUFFIX})
++#endif(WIN32)
++#list(APPEND LIBRARIES ${ZLIB_LIBRARY})
++#list(APPEND FAST_EXTERNAL_DEPENDENCIES zlib)

debian/patches/remove_unneeded_installs.patch

+Description: remove some unnecessary cmake installs
+ Cmake will try install non-existant files as we are prohibiting cmake from downloading and building the libraries itself.
+Author: Shayan Doust <hello@shayandoust.me>
+Last-Update: 2019-08-08
+---
+
+Index: fast/cmake/InstallFAST.cmake
+===================================================================
+--- fast.orig/cmake/InstallFAST.cmake	2019-08-08 15:56:39.374462089 +0100
++++ fast/cmake/InstallFAST.cmake	2019-08-08 15:56:39.374462089 +0100
+@@ -185,18 +185,18 @@
+ )
+ 
+ # Eigen
+-file(GLOB LICENSE_FILES ${FAST_EXTERNAL_BUILD_DIR}/eigen/src/eigen/COPYING.*)
+-install(FILES ${LICENSE_FILES}
+-		DESTINATION fast/licenses/eigen/
+-)
++#file(GLOB LICENSE_FILES ${FAST_EXTERNAL_BUILD_DIR}/eigen/src/eigen/COPYING.*)
++#install(FILES ${LICENSE_FILES}
++#DESTINATION fast/licenses/eigen/
++		#)
+ # zlib
+-install(FILES ${FAST_EXTERNAL_BUILD_DIR}/zlib/src/zlib/README
+-		DESTINATION fast/licenses/zlib/
+-)
++#install(FILES ${FAST_EXTERNAL_BUILD_DIR}/zlib/src/zlib/README
++#		DESTINATION fast/licenses/zlib/
++#)
+ # OpenIGTLink
+-install(FILES ${FAST_EXTERNAL_BUILD_DIR}/OpenIGTLink/src/OpenIGTLink/LICENSE.txt
+-		DESTINATION fast/licenses/OpenIGTLink/
+-)
++#install(FILES ${FAST_EXTERNAL_BUILD_DIR}/OpenIGTLink/src/OpenIGTLink/LICENSE.txt
++#		DESTINATION fast/licenses/OpenIGTLink/
++#)
+ # DCMTK
+ install(FILES ${FAST_EXTERNAL_BUILD_DIR}/dcmtk/src/dcmtk/COPYRIGHT
+ 		DESTINATION fast/licenses/dcmtk/

debian/patches/series

-use_system_openslide.cmake
-use_system_eigen.patch
-use_system_zlib.patch
+prevent_cmake_downloading.patch
+remove_unneeded_installs.patch
+use_system_libs.patch
 disable_tests.patch

debian/patches/use_system_libs.patch

+Description: modify cmake files to use system wide "apt" packaged libs
+ This patch will alter some of the cmake files in order to use the system-wide installable libs instead of allowing cmake to use git and download / build itself.
+Author: Shayan Doust <hello@shayandoust.me>
+---
+
+Index: fast/CMakeLists.txt
+===================================================================
+--- fast.orig/CMakeLists.txt	2019-08-08 15:58:30.391366851 +0100
++++ fast/CMakeLists.txt	2019-08-08 15:58:30.387366819 +0100
+@@ -170,6 +170,12 @@
+     qt5_use_modules(FAST Widgets OpenGL) # Add Qt 5 modules
+ endif()
+ 
++find_package(Eigen3 REQUIRED)
++
++target_link_libraries(FAST PUBLIC Eigen3::Eigen)
++target_link_libraries(FAST PUBLIC openslide)
++target_link_libraries(FAST PUBLIC z)
++
+ ## Build test executable
+ if(FAST_BUILD_TESTS)
+     add_executable(testFAST ${FAST_TEST_SOURCE_FILES} source/FAST/Algorithms/CoherentPointDrift/Rigid.cpp source/FAST/Algorithms/CoherentPointDrift/Rigid.hpp source/FAST/Algorithms/CoherentPointDrift/Affine.cpp source/FAST/Algorithms/CoherentPointDrift/Affine.hpp)

debian/patches/use_system_openslide.cmake

-Description: use libopenslide-dev
- This patch will modify some of the cmake files in order to build using libopenslide-dev available on the system instead of cmake downloading, compiling and static linking.
-Author: Shayan Doust <hello@shayandoust.me>
-Last-Update: 2019-08-08
----
-
-Index: fast/CMakeLists.txt
-===================================================================
---- fast.orig/CMakeLists.txt	2019-08-08 14:49:11.365300187 +0100
-+++ fast/CMakeLists.txt	2019-08-08 14:49:11.357300122 +0100
-@@ -162,7 +162,7 @@
- generate_export_header(FAST EXPORT_FILE_NAME FASTExport.hpp)
- 
- include(cmake/OpenMP.cmake)
--
-+target_link_libraries(FAST PUBLIC openslide)
- ## Link everything
- message("-- LIBS: ${LIBRARIES} ${FAST_SYSTEM_LIBRARIES}")
- target_link_libraries(FAST PUBLIC ${LIBRARIES} ${FAST_SYSTEM_LIBRARIES})
-Index: fast/cmake/ExternalOpenSlide.cmake
-===================================================================
---- fast.orig/cmake/ExternalOpenSlide.cmake	2019-08-08 14:49:11.365300187 +0100
-+++ fast/cmake/ExternalOpenSlide.cmake	2019-08-08 14:49:11.357300122 +0100
-@@ -1,17 +1,17 @@
- # Download and set up OpenSlide
- 
--include(cmake/Externals.cmake)
-+#include(cmake/Externals.cmake)
- 
--if(WIN32)
-+#if(WIN32)
- 
--ExternalProject_Add(openslide
--        PREFIX ${FAST_EXTERNAL_BUILD_DIR}/openslide
--        BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/openslide
--        URL "https://github.com/openslide/openslide-winbuild/releases/download/v20171122/openslide-win64-20171122.zip"
--        CONFIGURE_COMMAND ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/openslide/src/openslide/ ${FAST_EXTERNAL_INSTALL_DIR}
--        BUILD_COMMAND ""
--        INSTALL_COMMAND ""
--)
-+#ExternalProject_Add(openslide
-+#       PREFIX ${FAST_EXTERNAL_BUILD_DIR}/openslide
-+#       BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/openslide
-+#       URL "https://github.com/openslide/openslide-winbuild/releases/download/v20171122/openslide-win64-20171122.zip"
-+#       CONFIGURE_COMMAND ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/openslide/src/openslide/ ${FAST_EXTERNAL_INSTALL_DIR}
-+#       BUILD_COMMAND ""
-+#       INSTALL_COMMAND ""
-+#)
- 
--list(APPEND FAST_EXTERNAL_DEPENDENCIES openslide)
--endif()
-\ No newline at end of file
-+#list(APPEND FAST_EXTERNAL_DEPENDENCIES openslide)
-+#endif()

debian/patches/use_system_zlib.patch

-Description: use system packaged libz
- This patch modifies some of the cmake files to use the system available zlib library instead of cmake downloading, compiling and linking.
-Author: Shayan Doust <hello@shayandoust.me>
-Last-Update: 2019-08-08
----
-
-Index: fast/cmake/ExternalZlib.cmake
-===================================================================
---- fast.orig/cmake/ExternalZlib.cmake	2019-08-08 14:54:10.139738764 +0100
-+++ fast/cmake/ExternalZlib.cmake	2019-08-08 14:54:10.135738732 +0100
-@@ -1,24 +1,24 @@
- # Download and set up zlib
- 
--include(cmake/Externals.cmake)
-+#include(cmake/Externals.cmake)
- 
--ExternalProject_Add(zlib
--        PREFIX ${FAST_EXTERNAL_BUILD_DIR}/zlib
--        BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/zlib
--        GIT_REPOSITORY "https://github.com/madler/zlib.git"
--        GIT_TAG "v1.2.9"
--        CMAKE_ARGS
--            -DCMAKE_MACOSX_RPATH=ON
--        CMAKE_CACHE_ARGS
--            -DCMAKE_BUILD_TYPE:STRING=Release
--            -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
--            -DCMAKE_INSTALL_MESSAGE:BOOL=LAZY
--            -DCMAKE_INSTALL_PREFIX:STRING=${FAST_EXTERNAL_INSTALL_DIR}
--)
--if(WIN32)
--	set(ZLIB_LIBRARY debug zlibd.lib optimized zlib.lib)
--else(WIN32)
--	set(ZLIB_LIBRARY ${CMAKE_SHARED_LIBRARY_PREFIX}z${CMAKE_SHARED_LIBRARY_SUFFIX})
--endif(WIN32)
--list(APPEND LIBRARIES ${ZLIB_LIBRARY})
--list(APPEND FAST_EXTERNAL_DEPENDENCIES zlib)
-\ No newline at end of file
-+#ExternalProject_Add(zlib
-+#        PREFIX ${FAST_EXTERNAL_BUILD_DIR}/zlib
-+#        BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/zlib
-+#        GIT_REPOSITORY "https://github.com/madler/zlib.git"
-+#        GIT_TAG "v1.2.9"
-+#        CMAKE_ARGS
-+#            -DCMAKE_MACOSX_RPATH=ON
-+#        CMAKE_CACHE_ARGS
-+#            -DCMAKE_BUILD_TYPE:STRING=Release
-+#            -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
-+#            -DCMAKE_INSTALL_MESSAGE:BOOL=LAZY
-+#            -DCMAKE_INSTALL_PREFIX:STRING=${FAST_EXTERNAL_INSTALL_DIR}
-+#)
-+#if(WIN32)
-+#	set(ZLIB_LIBRARY debug zlibd.lib optimized zlib.lib)
-+#else(WIN32)
-+#set(ZLIB_LIBRARY ${CMAKE_SHARED_LIBRARY_PREFIX}z${CMAKE_SHARED_LIBRARY_SUFFIX})
-+	#endif(WIN32)
-+list(APPEND LIBRARIES /usr/lib/x86_64-linux-gnu/libz.so)
-+#list(APPEND FAST_EXTERNAL_DEPENDENCIES zlib)
-Index: fast/CMakeLists.txt
-===================================================================
---- fast.orig/CMakeLists.txt	2019-08-08 14:54:10.139738764 +0100
-+++ fast/CMakeLists.txt	2019-08-08 14:54:10.135738732 +0100
-@@ -166,6 +166,7 @@
- ## Link everything
- message("-- LIBS: ${LIBRARIES} ${FAST_SYSTEM_LIBRARIES}")
- target_link_libraries(FAST PUBLIC ${LIBRARIES} ${FAST_SYSTEM_LIBRARIES})
-+target_link_libraries(FAST PUBLIC z)
- if(FAST_MODULE_Visualization AND FAST_BUILD_QT5)
-     qt5_use_modules(FAST Widgets OpenGL) # Add Qt 5 modules
- endif()
-Index: fast/cmake/InstallFAST.cmake
-===================================================================
---- fast.orig/cmake/InstallFAST.cmake	2019-08-08 14:54:10.139738764 +0100
-+++ fast/cmake/InstallFAST.cmake	2019-08-08 14:54:10.135738732 +0100
-@@ -190,9 +190,9 @@
- #		DESTINATION fast/licenses/eigen/
- #)
- # zlib
--install(FILES ${FAST_EXTERNAL_BUILD_DIR}/zlib/src/zlib/README
--		DESTINATION fast/licenses/zlib/
--)
-+#install(FILES ${FAST_EXTERNAL_BUILD_DIR}/zlib/src/zlib/README
-+#		DESTINATION fast/licenses/zlib/
-+#)
- # OpenIGTLink
- install(FILES ${FAST_EXTERNAL_BUILD_DIR}/OpenIGTLink/src/OpenIGTLink/LICENSE.txt
- 		DESTINATION fast/licenses/OpenIGTLink/