[Debian-med-packaging] Bug#912583: simpleitk patch for Python 3.7

Fri Dec 7 22:05:18 GMT 2018

On Fri, Dec 07, 2018 at 10:37:55PM +0200, Adrian Bunk wrote:
> On Mon, Dec 03, 2018 at 09:37:45AM +0100, Andreas Tille wrote:
> Can you send the complete build log? The error might be elsewhere.

Attached.  Kind regards, Andreas. 

-- 
http://fam-tille.de
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dpkg-source: warning: extracting unsigned source package (simpleitk_1.1.0-1.dsc)
dpkg-source: info: extracting simpleitk in simpleitk-1.1.0
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[0mI: Building the package[0m
[0mI: Running cd /build/simpleitk-1.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-buildpackage -us -uc  -i\.git -I.git  && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-genchanges -S  > ../simpleitk_1.1.0-1_source.changes[0m
dpkg-buildpackage: info: source package simpleitk
dpkg-buildpackage: info: source version 1.1.0-1
dpkg-buildpackage: info: source distribution UNRELEASED
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
 dpkg-source -i.git -I.git --before-build simpleitk-1.1.0
dpkg-buildpackage: info: host architecture amd64
dpkg-source: warning: unknown information field 'Testsuite' in input data in package's section of control info file
dpkg-source: warning: unknown information field 'Testsuite' in input data in package's section of control info file
 fakeroot debian/rules clean
dh clean --with python3 --builddirectory=/build/simpleitk-1.1.0/SimpleITK-build
   dh_auto_clean -O--builddirectory=/build/simpleitk-1.1.0/SimpleITK-build
   dh_autoreconf_clean -O--builddirectory=/build/simpleitk-1.1.0/SimpleITK-build
   dh_clean -O--builddirectory=/build/simpleitk-1.1.0/SimpleITK-build
 dpkg-source -i.git -I.git -b simpleitk-1.1.0
dpkg-source: warning: unknown information field 'Testsuite' in input data in package's section of control info file
dpkg-source: warning: unknown information field 'Testsuite' in input data in package's section of control info file
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building simpleitk using existing ./simpleitk_1.1.0.orig-data.tar.xz ./simpleitk_1.1.0.orig.tar.xz
Useless use of concatenation (.) or string in void context at /usr/share/perl5/Dpkg/Vendor/Ubuntu.pm line 143.
dpkg-source: info: building simpleitk in simpleitk_1.1.0-1.debian.tar.xz
dpkg-source: info: building simpleitk in simpleitk_1.1.0-1.dsc
 debian/rules build
dh build --with python3 --builddirectory=/build/simpleitk-1.1.0/SimpleITK-build
   dh_update_autotools_config -O--builddirectory=/build/simpleitk-1.1.0/SimpleITK-build
   dh_autoreconf -O--builddirectory=/build/simpleitk-1.1.0/SimpleITK-build
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/simpleitk-1.1.0'
dh_auto_configure -- -DBUILD_EXAMPLES:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=ON -DExternalData_OBJECT_STORES:PATH=/build/simpleitk-1.1.0/data/.ExternalData -DSimpleITK_4D_IMAGES:BOOL=ON -DSimpleITK_BUILD_DISTRIBUTE:BOOL=ON -DSimpleITK_EXPLICIT_INSTANTIATION:BOOL=OFF -DSimpleITK_FORBID_DOWNLOADS:BOOL=ON -DSimpleITK_INSTALL_ARCHIVE_DIR:PATH=lib/x86_64-linux-gnu -DSimpleITK_INSTALL_LIBRARY_DIR:PATH=lib/x86_64-linux-gnu -DWRAP_DEFAULT:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DGTEST_ROOT:PATH=/usr/src/googletest -DWRAP_PYTHON:BOOL=ON -DSimpleITK_PYTHON_USE_VIRTUALENV:BOOL=OFF -DSimpleITK_PYTHON_WHEEL:BOOL=OFF -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.7
	cd SimpleITK-build && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_EXAMPLES:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=ON -DExternalData_OBJECT_STORES:PATH=/build/simpleitk-1.1.0/data/.ExternalData -DSimpleITK_4D_IMAGES:BOOL=ON -DSimpleITK_BUILD_DISTRIBUTE:BOOL=ON -DSimpleITK_EXPLICIT_INSTANTIATION:BOOL=OFF -DSimpleITK_FORBID_DOWNLOADS:BOOL=ON -DSimpleITK_INSTALL_ARCHIVE_DIR:PATH=lib/x86_64-linux-gnu -DSimpleITK_INSTALL_LIBRARY_DIR:PATH=lib/x86_64-linux-gnu -DWRAP_DEFAULT:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DGTEST_ROOT:PATH=/usr/src/googletest -DWRAP_PYTHON:BOOL=ON -DSimpleITK_PYTHON_USE_VIRTUALENV:BOOL=OFF -DSimpleITK_PYTHON_WHEEL:BOOL=OFF -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.7 ..
-- The C compiler identification is GNU 8.2.0
-- The CXX compiler identification is GNU 8.2.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at CMake/sitkSourceVersion.cmake:62 (message):
  git tag: "GIT-NOTFOUND" does not match expected version format!
Call Stack (most recent call first):
  Version.cmake:17 (include)
  CMakeLists.txt:26 (include)

-- Building SimpleITK version "1.1.0"
-- Performing Test CXX_HAS_stdcxx11
-- Performing Test CXX_HAS_stdcxx11 - Success
-- Checking if c++11 is required...
-- Checking if c++11 is required... NO
-- Performing Test CXX_HAS-Wall
-- Performing Test CXX_HAS-Wall - Success
-- Performing Test CXX_HAS-Wno-long-double
-- Performing Test CXX_HAS-Wno-long-double - Failed
-- Performing Test CXX_HAS-Wno-long-long
-- Performing Test CXX_HAS-Wno-long-long - Success
-- Performing Test CXX_HAS-Wno-unused-local-typedefs
-- Performing Test CXX_HAS-Wno-unused-local-typedefs - Success
-- Performing Test CXX_HAS-Wno-strict-overflow
-- Performing Test CXX_HAS-Wno-strict-overflow - Success
-- Performing Test CXX_HAS-Wextra
-- Performing Test CXX_HAS-Wextra - Success
-- Performing Test CXX_HAS-Wformat_2
-- Performing Test CXX_HAS-Wformat_2 - Success
-- Performing Test CXX_HAS-Wno-format-nonliteral
-- Performing Test CXX_HAS-Wno-format-nonliteral - Success
-- Performing Test CXX_HAS-Wunused
-- Performing Test CXX_HAS-Wunused - Success
-- Performing Test CXX_HAS-Wpointer-arith
-- Performing Test CXX_HAS-Wpointer-arith - Success
-- Performing Test CXX_HAS-Winvalid-pch
-- Performing Test CXX_HAS-Winvalid-pch - Success
-- Performing Test CXX_HAS-Wcast-align
-- Performing Test CXX_HAS-Wcast-align - Success
-- Performing Test CXX_HAS-Wdisabled-optimization
-- Performing Test CXX_HAS-Wdisabled-optimization - Success
-- Performing Test CXX_HAS-Woverloaded-virtual
-- Performing Test CXX_HAS-Woverloaded-virtual - Success
-- Performing Test CXX_HAS-Wshadow
-- Performing Test CXX_HAS-Wshadow - Success
-- Performing Test CXX_HAS-Wwrite-strings
-- Performing Test CXX_HAS-Wwrite-strings - Success
-- Performing Test CXX_HAS-Wstrict-null-sentinel
-- Performing Test CXX_HAS-Wstrict-null-sentinel - Success
-- Performing Test CXX_HAS-Wno-invalid-offsetof
-- Performing Test CXX_HAS-Wno-invalid-offsetof - Success
-- The imported target "vtkgdcmsharpglue" references the file
   "/usr/lib/x86_64-linux-gnu/libvtkgdcmsharpglue.so"
but this file does not exist.  Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/x86_64-linux-gnu/gdcm-2.8/GDCMTargets.cmake"
but not all the files it references.

-- The imported target "vtkgdcmPython" references the file
   "/usr/lib/python/dist-packages/vtkgdcmPython.so"
but this file does not exist.  Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/x86_64-linux-gnu/gdcm-2.8/GDCMTargets.cmake"
but not all the files it references.

-- Performing Test SITK_HAS_CXX11_STATIC_ASSERT
-- Performing Test SITK_HAS_CXX11_STATIC_ASSERT - Success
-- Performing Test SITK_HAS_CXX11_FUNCTIONAL
-- Performing Test SITK_HAS_CXX11_FUNCTIONAL - Success
-- Performing Test SITK_HAS_CXX11_TYPE_TRAITS
-- Performing Test SITK_HAS_CXX11_TYPE_TRAITS - Success
-- Performing Test SITK_HAS_CXX11_UNORDERED_MAP
-- Performing Test SITK_HAS_CXX11_UNORDERED_MAP - Success
-- Performing Test SITK_HAS_CXX11_NULLPTR
-- Performing Test SITK_HAS_CXX11_NULLPTR - Success
-- Performing Test SITK_HAS_CXX11_UNIQUE_PTR
-- Performing Test SITK_HAS_CXX11_UNIQUE_PTR - Success
-- Performing Test SITK_HAS_CXX11_ALIAS_TEMPLATE
-- Performing Test SITK_HAS_CXX11_ALIAS_TEMPLATE - Success
-- Performing Test SITK_HAS_TR1_SUB_INCLUDE
-- Performing Test SITK_HAS_TR1_SUB_INCLUDE - Success
-- Performing Test SITK_HAS_TR1_FUNCTIONAL
-- Performing Test SITK_HAS_TR1_FUNCTIONAL - Success
-- Performing Test SITK_HAS_TR1_TYPE_TRAITS
-- Performing Test SITK_HAS_TR1_TYPE_TRAITS - Success
-- Performing Test SITK_HAS_TR1_UNORDERED_MAP
-- Performing Test SITK_HAS_TR1_UNORDERED_MAP - Success
-- Looking for C++ include stdint.h
-- Looking for C++ include stdint.h - found
CMake Warning at CMakeLists.txt:322 (message):
  Unable to file ITK's NOTICE File!

   This file will not be included in SimpleITK packaging!

-- Performing Test Weak Link MODULE -> SHARED (gnu_ld_ignore) - Success
-- Found PythonInterp: /usr/bin/python3.7 (found version "3.7.1") 
-- Found Lua: /usr/bin/lua  
-- Processing json files...
-- Processing json files...done
CMake Error at /usr/lib/cmake/ITK-4.12/ITKModuleAPI.cmake:56 (message):
  No such module: "ITKImageIO"
Call Stack (most recent call first):
  /usr/lib/cmake/ITK-4.12/ITKModuleAPI.cmake:26 (itk_module_load)
  /usr/lib/cmake/ITK-4.12/ITKModuleAPI.cmake:84 (_itk_module_config_recurse)
  /usr/lib/cmake/ITK-4.12/ITKConfig.cmake:79 (itk_module_config)
  Code/IO/src/CMakeLists.txt:17 (find_package)

-- Configuring incomplete, errors occurred!
See also "/build/simpleitk-1.1.0/SimpleITK-build/CMakeFiles/CMakeOutput.log".
See also "/build/simpleitk-1.1.0/SimpleITK-build/CMakeFiles/CMakeError.log".
	cd SimpleITK-build && tail -v -n \+0 CMakeCache.txt
==> CMakeCache.txt <==
# This is the CMakeCache file.
# For build in directory: /build/simpleitk-1.1.0/SimpleITK-build
# It was generated by CMake: /usr/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
# VALUE is the current value for the KEY.

########################
# EXTERNAL cache entries
########################

//Build SimpleITK Doxygen
BUILD_DOXYGEN:BOOL=OFF

//No help, variable specified on the command line.
BUILD_EXAMPLES:BOOL=OFF

//Build SimpleITK ITK with shared libraries. This does not effect
// wrapped languages.
BUILD_SHARED_LIBS:BOOL=ON

//Build the testing tree.
BUILD_TESTING:BOOL=ON

//Path to a program.
BZRCOMMAND:FILEPATH=BZRCOMMAND-NOTFOUND

//Path to a program.
CMAKE_AR:FILEPATH=/usr/bin/ar

//Choose the type of build, options are: None Debug Release RelWithDebInfo
// MinSizeRel ...
CMAKE_BUILD_TYPE:STRING=None

//Enable/Disable color output during build.
CMAKE_COLOR_MAKEFILE:BOOL=ON

//CXX compiler
CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/c++

//A wrapper around 'ar' adding the appropriate '--plugin' option
// for the GCC compiler
CMAKE_CXX_COMPILER_AR:FILEPATH=/usr/bin/gcc-ar-8

//A wrapper around 'ranlib' adding the appropriate '--plugin' option
// for the GCC compiler
CMAKE_CXX_COMPILER_RANLIB:FILEPATH=/usr/bin/gcc-ranlib-8

//Flags used by the CXX compiler during all build types.
CMAKE_CXX_FLAGS:STRING=-g -O2 -fdebug-prefix-map=/build/simpleitk-1.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2

//Flags used by the CXX compiler during DEBUG builds.
CMAKE_CXX_FLAGS_DEBUG:STRING=-g

//Flags used by the CXX compiler during MINSIZEREL builds.
CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG

//Flags used by the CXX compiler during NONE builds.
CMAKE_CXX_FLAGS_NONE:STRING=

//Flags used by the CXX compiler during RELEASE builds.
CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG

//Flags used by the CXX compiler during RELWITHDEBINFO builds.
CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG

//C compiler
CMAKE_C_COMPILER:FILEPATH=/usr/bin/cc

//A wrapper around 'ar' adding the appropriate '--plugin' option
// for the GCC compiler
CMAKE_C_COMPILER_AR:FILEPATH=/usr/bin/gcc-ar-8

//A wrapper around 'ranlib' adding the appropriate '--plugin' option
// for the GCC compiler
CMAKE_C_COMPILER_RANLIB:FILEPATH=/usr/bin/gcc-ranlib-8

//Flags used by the C compiler during all build types.
CMAKE_C_FLAGS:STRING=-g -O2 -fdebug-prefix-map=/build/simpleitk-1.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2

//Flags used by the C compiler during DEBUG builds.
CMAKE_C_FLAGS_DEBUG:STRING=-g

//Flags used by the C compiler during MINSIZEREL builds.
CMAKE_C_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG

//Flags used by the C compiler during NONE builds.
CMAKE_C_FLAGS_NONE:STRING=

//Flags used by the C compiler during RELEASE builds.
CMAKE_C_FLAGS_RELEASE:STRING=-O3 -DNDEBUG

//Flags used by the C compiler during RELWITHDEBINFO builds.
CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG

//Flags used by the linker during all build types.
CMAKE_EXE_LINKER_FLAGS:STRING=-Wl,-z,relro -Wl,-z,now

//Flags used by the linker during DEBUG builds.
CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING=

//Flags used by the linker during MINSIZEREL builds.
CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING=

//Flags used by the linker during NONE builds.
CMAKE_EXE_LINKER_FLAGS_NONE:STRING=

//Flags used by the linker during RE==> CMakeCache.txt <==
# This is the CMakeCache file.
# For build in directory: /build/simpleitk-1.1.0/SimpleITK-build
# It was generated by CMake: /usr/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
# VALUE is the current value for the KEY.

########################
# EXTERNAL cache entries
########################

//Build SimpleITK Doxygen
BUILD_DOXYGEN:BOOL=OFF