Arch Linux User Repository

The package fails to build:

[ 98%] Built target SimpleITKCSharpNative_CSHARP
[ 99%] Compiling C# library SimpleITKCSharpManaged: '/usr/bin/mcs /t:library /out:SimpleITKCSharpManaged.dll /platform:anycpu /sdk:2 /reference:System.dll /build/simpleitk/src/SimpleITK/build/Wrapping/CSharp/CSharpSources/*.cs'
/build/simpleitk/src/SimpleITK/build/Wrapping/CSharp/CSharpSources/AssemblyInfo.cs(25,12): warning CS7035: The specified version string `2.3.1-g42ce2' does not conform to the recommended format major.minor.build.revision
Compilation succeeded - 1 warning(s)
[ 99%] Built target SimpleITKCSharpManaged
[ 99%] Built target org_itk_simple_jar
[ 99%] Linking CXX executable bin/SimpleITKTclsh
/usr/bin/ld: /usr/lib/libITKIOGDCM-5.3.so.1: undefined reference to `gdcm::DirectionCosines::~DirectionCosines()'
collect2: error: ld returned 1 exit status
make[2]: *** [Wrapping/Tcl/CMakeFiles/SimpleITKTclsh.dir/build.make:501: Wrapping/Tcl/bin/SimpleITKTclsh] Error 1
make[1]: *** [CMakeFiles/Makefile2:2544: Wrapping/Tcl/CMakeFiles/SimpleITKTclsh.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 99%] Linking CXX shared module lib/SimpleITK.so
[ 99%] Built target SimpleITKLuaModule_LUA
[ 99%] Linking CXX shared module Packaging/SimpleITK/src/SimpleITK.so
Installing R package for testing and building binary version for distribution
/usr/bin/itkTestDriver: symbol lookup error: /usr/lib/libITKIOGDCM-5.3.so.1: undefined symbol: _ZN4gdcm16DirectionCosinesD1Ev
make[2]: *** [Wrapping/R/CMakeFiles/SimpleITK_R.dir/build.make:539: Wrapping/R/Packaging/SimpleITK/src/SimpleITK.so] Error 127
make[2]: *** Deleting file 'Wrapping/R/Packaging/SimpleITK/src/SimpleITK.so'
make[1]: *** [CMakeFiles/Makefile2:2618: Wrapping/R/CMakeFiles/SimpleITK_R.dir/all] Error 2
[ 99%] Linking CXX shared module SimpleITK/_SimpleITK.so
Generating setup.py...
[ 99%] Built target SimpleITK_PYTHON
[100%] Linking CXX shared module lib/simpleitk.so
[100%] Built target simpleitk_RUBY
make: *** [Makefile:156: all] Error 2

I was rebuilding for Python 3.12, but that does not seem to be the problem here...

@Alad: I had the same issue. It seems to depend on one of the given java environments (see list above). After I have installed java-22-openjdk-bin from the AUR and switched to it via "archlinux-java set java-22-openjdk-bin" I can now build the simpleitk package.

Regards Stephan

What kind of java packages are required? With java-17-openjdk I get:

==> Starting prepare()...
-- Building SimpleITK version "2.3.1-g42ce2"
CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
  Could NOT find Java (missing: Java_JAVAC_EXECUTABLE Java_JAR_EXECUTABLE
  Java_JAVADOC_EXECUTABLE Development) (found version "17.0.9")
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE)
  /usr/share/cmake/Modules/FindJava.cmake:314 (find_package_handle_standard_args)
  CMake/sitkLanguageOptions.cmake:162 (find_package)
  CMakeLists.txt:318 (include)


-- Configuring incomplete, errors occurred!
==> ERROR: A failure occurred in prepare().
    Aborting...

User may want to resume a partial build or edit files to debug build issues.

That is what makepkg --noprepare is for.

Is \rm -rf build necessary? User may want to resume a partial build or edit files to debug build issues.

There are updated cmake commands so that cmake creates the build directory itself when needed. So mkdir -p build ; cd build isn't needed.

Hi, I have the following message error:

line 49: lua: command not found

when I compile in a clean chroot.

Build fails for me because of my global pip configuration which sets user = true.

[100%] Built target SimpleITK_PYTHON
[100%] Creating python virtual environment...
ERROR: Can not perform a '--user' install. User site-packages are not visible in this virtualenv.
make[3]: *** [Wrapping/Python/CMakeFiles/PythonVirtualEnv.dir/build.make:74: Testing/Installation/pyvenv/bin/python3] Error 1
make[3]: *** Deleting file 'Testing/Installation/pyvenv/bin/python3'
make[2]: *** [CMakeFiles/Makefile2:2118: Wrapping/Python/CMakeFiles/PythonVirtualEnv.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:2125: Wrapping/Python/CMakeFiles/PythonVirtualEnv.dir/rule] Error 2
make: *** [Makefile:865: PythonVirtualEnv] Error 2
==> ERROR: A failure occurred in build().
    Aborting...

The PKGBUILD should be updated to set the env var PIP_USER=0 to ensure it is always unset.

There appear to be a missing dependency for this package:

CMake Error at /usr/lib/cmake/ITK-5.3/Modules/ITKEigen3.cmake:16 (find_package):
  Could not find a package configuration file provided by "Eigen3" (requested
  version 3.3) with any of the following names:

    Eigen3Config.cmake
    eigen3-config.cmake

  Add the installation prefix of "Eigen3" to CMAKE_PREFIX_PATH or set
  "Eigen3_DIR" to a directory containing one of the above files.  If "Eigen3"
  provides a separate development package or SDK, be sure it has been
  installed.
Call Stack (most recent call first):
  /usr/lib/cmake/ITK-5.3/ITKModuleAPI.cmake:76 (include)
  /usr/lib/cmake/ITK-5.3/ITKModuleAPI.cmake:31 (itk_module_load)
  /usr/lib/cmake/ITK-5.3/ITKModuleAPI.cmake:129 (_itk_module_config_recurse)
  /usr/lib/cmake/ITK-5.3/ITKConfig.cmake:88 (itk_module_config)
  CMakeLists.txt:64 (find_package)

Adding eigen as a makedepends fixes this (it is a header only library, so it shouldn't be needed as a runtime dependency).

I updated to version 2.0.2. I turned this into a split package, so that it is now possible to separately install the wrappers for different languages as separate packages.

Please note that SimpleITK 2 requires insight-toolkit to be built with the SimpleITKFilters module (-DModule_SimpleITKFilters:BOOL=ON), that is currently not included in the configuration of the insight-toolkit AUR package. I already asked to add it, in the meantime it is necessary to edit the PKGBUILD file and add the flag to CMake when rebuilding insight-toolkit.