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BioMedIA / MIRTK

The Medical Image Registration ToolKit (MIRTK), the successor of the IRTK, contains common CMake build configuration files, core libraries, and basic command-line tools. Extension packages are hosted by the MIRTK GitHub group at
https://github.com/MIRTK
Apache License 2.0
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static install failed after built success #764

Closed Mon-ius closed 3 years ago

Mon-ius commented 3 years ago

CMake Error at Applications/src/cmake_install.cmake:54 (file): file RPATH_CHANGE could not write new RPATH:

$ORIGIN/..

to the file:

/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/library/mritk-2.0.0/lib/mirtk/tools/info

No valid ELF RPATH or RUNPATH entry exists in the file; Call Stack (most recent call first): Applications/cmake_install.cmake:178 (include) cmake_install.cmake:203 (include)

make: *** [Makefile:74: install] Error 1

Mon-ius commented 3 years ago

I found it was share lib related problem. But I clearly specify 

-DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="-static" -DCMAKE_FIND_LIBRARY_SUFFIXES=".a"

I think MIRTK may not consider the static build condition.

schuhschuh commented 3 years ago

Hm, I'm not sure this is due to MIRTK's CMake BASIS functions. See

https://github.com/BioMedIA/MIRTK/blob/df6f42d634464477e45822dd7f9546c31bc65563/CMake/Modules/mirtkAddExecutable.cmake#L87

The mentioned custom BASIS_INSTALL_RPATH boolean flag should only be relevant if the respective CMake BASIS functions were being used, but this appears not to be the case. In any case, could you try with -DBASIS_INSTALL_RPATH=OFF?

The only RPATH related settings MIRTK should be using is the official INSTALL_RPATH target property, and it should be up to CMake to use this property according to build type and OS.

See also:

It may be that it would be necessary not to set the INSTALL_RPATH property or set some other CMake variables differently if BUILD_SHARED_LIBS=OFF. Would you mind to try and encapsulate the following block in mirtkAddExecutable.cmake by an if(BUILD_SHARED_LIBS)? https://github.com/BioMedIA/MIRTK/blob/df6f42d634464477e45822dd7f9546c31bc65563/CMake/Modules/mirtkAddExecutable.cmake#L87-L106

Mon-ius commented 3 years ago

I just manually deleted the related cache file config. It's under Applications/src/cmake_install.cmake

# Install script for directory: /rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/Applications/src

# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
  set(CMAKE_INSTALL_PREFIX "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/library/mritk-2.0.0")
endif()
string(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")

# Set the install configuration name.
if(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
  if(BUILD_TYPE)
    string(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
           CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
  else()
    set(CMAKE_INSTALL_CONFIG_NAME "Release")
  endif()
  message(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
endif()

# Set the component getting installed.
if(NOT CMAKE_INSTALL_COMPONENT)
  if(COMPONENT)
    message(STATUS "Install component: \"${COMPONENT}\"")
    set(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
  else()
    set(CMAKE_INSTALL_COMPONENT)
  endif()
endif()

# Install shared libraries without execute permission?
if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
  set(CMAKE_INSTALL_SO_NO_EXE "0")
endif()

# Is this installation the result of a crosscompile?
if(NOT DEFINED CMAKE_CROSSCOMPILING)
  set(CMAKE_CROSSCOMPILING "FALSE")
endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE PROGRAM RENAME "help-rst" FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/Applications/src/CMakeFiles/help-rst.dir/install/help-rst")
endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/info" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/info")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/info"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/info")
endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/aggregate-images" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/aggregate-images")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/aggregate-images"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/aggregate-images")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/average-images" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/average-images")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/average-images"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/average-images")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-element-wise" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-element-wise")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-element-wise"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/calculate-element-wise")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-distance-map" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-distance-map")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-distance-map"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/calculate-distance-map")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-exponential-map" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-exponential-map")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-exponential-map"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/calculate-exponential-map")

endif()

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  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-lie-bracket" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-lie-bracket")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-lie-bracket"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/calculate-lie-bracket")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-logarithmic-map" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-logarithmic-map")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/calculate-logarithmic-map"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/calculate-logarithmic-map")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/close-image" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/close-image")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/close-image"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/close-image")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/combine-images" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/combine-images")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/combine-images"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/combine-images")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/convert-image" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/convert-image")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/convert-image"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/convert-image")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/cut-brain" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/cut-brain")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/cut-brain"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/cut-brain")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/detect-edges" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/detect-edges")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/detect-edges"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/detect-edges")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/dilate-image" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/dilate-image")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/dilate-image"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/dilate-image")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/downsample-image" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/downsample-image")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/downsample-image"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/downsample-image")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
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    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/edit-image"
         RPATH "$ORIGIN/..")
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endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
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     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/erode-image")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/erode-image"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/erode-image")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
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    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/evaluate-label-overlap"
         RPATH "$ORIGIN/..")
  endif()
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endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
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     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/evaluate-overlap")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/evaluate-overlap"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/evaluate-overlap")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
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    file(RPATH_CHECK
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         RPATH "$ORIGIN/..")
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    file(RPATH_CHECK
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         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/extract-image-region")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE PROGRAM RENAME "extract-image-slice" FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/Applications/src/CMakeFiles/extract-image-slice.dir/install/extract-image-slice")
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if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/flip-image" AND
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    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/flip-image"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/flip-image")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/match-histogram" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/match-histogram")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/match-histogram"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/match-histogram")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/open-image" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/open-image")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/open-image"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/open-image")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
  if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/reflect-image" AND
     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/reflect-image")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/reflect-image"
         RPATH "$ORIGIN/..")
  endif()
  file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools" TYPE EXECUTABLE FILES "/rds/projects/d/duanj-ai-in-medical-imaging/castles/.share/2020a-gcc9.3/download/MIRTK/build/lib/tools/reflect-image")

endif()

if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xRuntimex" OR NOT CMAKE_INSTALL_COMPONENT)
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     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/resample-image")
    file(RPATH_CHECK
         FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/mirtk/tools/resample-image"
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Mon-ius commented 3 years ago

Only -DBASIS_INSTALL_RPATH=OFF doesn't help. Also, I tried -DCMAKE_SKIP_RPATH=ON, but not work.

Moreover, before make install. I found it will still looking for .so for expat, png, and zlib. Even I set 

-DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="-static" -DCMAKE_FIND_LIBRARY_SUFFIXES=".a"
Mon-ius commented 3 years ago

Update: Modify CMake/Modules/mirtkAddExecutable.cmake actually sovled the problem. No need to specify -DBASIS_INSTALL_RPATH=OFF or -DCMAKE_SKIP_RPATH=ON. 

    if(BUILD_SHARED_LIBS)
      if (CMAKE_HOST_APPLE)
        set(ORIGIN "@loader_path")
      else ()
        set(ORIGIN "\$ORIGIN")
      endif ()
      basis_get_relative_path(rpath
        "${CMAKE_INSTALL_PREFIX}/${INSTALL_LIBEXEC_DIR}"
        "${CMAKE_INSTALL_PREFIX}/${INSTALL_LIBRARY_DIR}"
      )
      string(REGEX REPLACE "/+$" "" rpath "${rpath}")
      set_target_properties(${target_uid} PROPERTIES INSTALL_RPATH "${ORIGIN}/${rpath}")
    endif ()
  endif ()
schuhschuh commented 3 years ago

Thanks for testing. I made the change.

I found it will still looking for .so for expat, png, and zlib.

This is best tracked in a separate issue. But also, it may be a general CMake issue rather because there are no custom Find modules for these libraries in MIRTK. Knowing the used version of CMake may be relevant here. I would try at least CMake version 3.10 because since this version, all the Find modules of the libraries mentioned here provide import build targets (ZLIB::ZLIB, EXPAT::EXPAT, and PNG::PNG). The libraries themselves are discovered by regular find_library calls in the Find modules included in the CMake installation.