Itk: Building 5.1.0 with tests enabled fails.

Created on 3 Aug 2020  ·  30Comments  ·  Source: InsightSoftwareConsortium/ITK

Expected behavior

build

Actual behavior

With tests enabled (fails): https://ppb.chymera.eu/ceb4a1.log
Without tests enabled (works): https://ppb.chymera.eu/dedde8.log

Reproducibility

100%

Versions

ITK 5.1.0, as downloaded from https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.0/InsightToolkit-5.1.0.tar.gz

Environment

Gentoo Linux, CMake 3.17.3

Compiler
Source
picture TheChymera

All 30 comments

@dzenanz @thewtex could you help me out? I'd really like to get the tests to pass before I push this to the Gentoo repositories.

TheChymera picture TheChymera on 5 Aug 2020

@TheChymera I took a look at the logs, but the issue did not jump out. From what I can see the build / install succeeds. What am I missing?

thewtex picture thewtex on 6 Aug 2020

@thewtex apologies, the pastes were misordered. Now they should be ordered correctly (first failing with tests, second passing without). I believe the issue is:

CMake Error at /usr/share/cmake/Modules/ExternalData.cmake:1121 (message):


  Object
  SHA512=a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a
  not found at:

    (No ExternalData_URL_TEMPLATES given)

But I am unsure whether more info can or needs to be gleaned from the context.

TheChymera picture TheChymera on 6 Aug 2020

a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a

This is from https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/blob/master/test/Baseline/gl_gaussian_3.mha.sha512

-- the testing data of remote modules are not in the InsightData tarball. With your current build setup, these files could be downloaded from https://github.com/InsightSoftwareConsortium/ITKTestingData/tree/gh-pages/SHA512 and added to a new tarball. They should be unpacked into ITK/.ExternalData/SHA512.

thewtex picture thewtex on 13 Aug 2020

@thewtex thank you for the info! I have tried doing that, and sadly it still fails, though the directories and files are in both the source and the build tree :(

FAILED: ExternalData/Modules/External/ITKGenericLabelInterpolator/test/Baseline/gl_gaussian_3.mha-hash-stamp ExternalData/Modules/External/ITKGenericLabelInterpolator/test/Baseline/gl_gaussian_3.mha
cd /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build && /usr/bin/cmake -Drelative_top=/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build -Dfile=/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/ExternalData/Modules/External/ITKGenericLabelInterpolator/test/Baseline/gl_gaussian_3.mha -Dname=/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/External/ITKGenericLabelInterpolator/test/Baseline/gl_gaussian_3.mha -Dexts=.sha512 -DExternalData_ACTION=fetch -DExternalData_CONFIG=/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/ITKData_config.cmake -P /usr/share/cmake/Modules/ExternalData.cmake
CMake Error at /usr/share/cmake/Modules/ExternalData.cmake:1121 (message):


  Object
  SHA512=a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a
  not found at:

    (No ExternalData_URL_TEMPLATES given)


[75/4938] /usr/bin/x86_64-pc-linux-gnu-g++ -DVXL_WARN_DEPRECATED -DVXL_WARN_DEPRECATED_ONCE -Ditkvnl_EXPORTS -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/vcl -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core -IModules/ThirdParty/VNL/src/vxl/v3p/netlib -IModules/ThirdParty/VNL/src/vxl/vcl -IModules/ThirdParty/VNL/src/vxl/core -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl  -march=native -O3 -pipe  -mtune=native -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -w  -fPIC   -msse2 -std=c++11 -MD -MT Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed_ref+float.allsizes-.cxx.o -MF Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed_ref+float.allsizes-.cxx.o.d -o Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed_ref+float.allsizes-.cxx.o -c /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl/Templates/vnl_vector_fixed_ref+float.allsizes-.cxx
[76/4938] /usr/bin/x86_64-pc-linux-gnu-g++ -DVXL_WARN_DEPRECATED -DVXL_WARN_DEPRECATED_ONCE -Ditkvnl_EXPORTS -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/vcl -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core -IModules/ThirdParty/VNL/src/vxl/v3p/netlib -IModules/ThirdParty/VNL/src/vxl/vcl -IModules/ThirdParty/VNL/src/vxl/core -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl  -march=native -O3 -pipe  -mtune=native -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -w  -fPIC   -msse2 -std=c++11 -MD -MT Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_ref+alltypes.cxx.o -MF Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_ref+alltypes.cxx.o.d -o Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_ref+alltypes.cxx.o -c /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl/Templates/vnl_vector_ref+alltypes.cxx
[77/4938] /usr/bin/x86_64-pc-linux-gnu-g++ -DVXL_WARN_DEPRECATED -DVXL_WARN_DEPRECATED_ONCE -Ditkvnl_EXPORTS -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/vcl -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core -IModules/ThirdParty/VNL/src/vxl/v3p/netlib -IModules/ThirdParty/VNL/src/vxl/vcl -IModules/ThirdParty/VNL/src/vxl/core -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl  -march=native -O3 -pipe  -mtune=native -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -w  -fPIC   -msse2 -std=c++11 -MD -MT Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed_ref+double.allsizes-.cxx.o -MF Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed_ref+double.allsizes-.cxx.o.d -o Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed_ref+double.allsizes-.cxx.o -c /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl/Templates/vnl_vector_fixed_ref+double.allsizes-.cxx
[78/4938] /usr/bin/x86_64-pc-linux-gnu-g++ -DVXL_WARN_DEPRECATED -DVXL_WARN_DEPRECATED_ONCE -Ditkvnl_EXPORTS -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/vcl -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core -IModules/ThirdParty/VNL/src/vxl/v3p/netlib -IModules/ThirdParty/VNL/src/vxl/vcl -IModules/ThirdParty/VNL/src/vxl/core -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl  -march=native -O3 -pipe  -mtune=native -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -w  -fPIC   -msse2 -std=c++11 -MD -MT Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+ulonglong.allsizes-.cxx.o -MF Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+ulonglong.allsizes-.cxx.o.d -o Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+ulonglong.allsizes-.cxx.o -c /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl/Templates/vnl_vector_fixed+ulonglong.allsizes-.cxx
[79/4938] /usr/bin/x86_64-pc-linux-gnu-g++ -DVXL_WARN_DEPRECATED -DVXL_WARN_DEPRECATED_ONCE -Ditkvnl_EXPORTS -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/vcl -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core -IModules/ThirdParty/VNL/src/vxl/v3p/netlib -IModules/ThirdParty/VNL/src/vxl/vcl -IModules/ThirdParty/VNL/src/vxl/core -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl  -march=native -O3 -pipe  -mtune=native -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -w  -fPIC   -msse2 -std=c++11 -MD -MT Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+ushort.allsizes-.cxx.o -MF Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+ushort.allsizes-.cxx.o.d -o Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+ushort.allsizes-.cxx.o -c /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl/Templates/vnl_vector_fixed+ushort.allsizes-.cxx
[80/4938] /usr/bin/x86_64-pc-linux-gnu-g++ -DVXL_WARN_DEPRECATED -DVXL_WARN_DEPRECATED_ONCE -Ditkvnl_EXPORTS -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/vcl -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core -IModules/ThirdParty/VNL/src/vxl/v3p/netlib -IModules/ThirdParty/VNL/src/vxl/vcl -IModules/ThirdParty/VNL/src/vxl/core -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl  -march=native -O3 -pipe  -mtune=native -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -w  -fPIC   -msse2 -std=c++11 -MD -MT Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+vnl_bignum.allsizes-.cxx.o -MF Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+vnl_bignum.allsizes-.cxx.o.d -o Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+vnl_bignum.allsizes-.cxx.o -c /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl/Templates/vnl_vector_fixed+vnl_bignum.allsizes-.cxx
[81/4938] /usr/bin/x86_64-pc-linux-gnu-g++ -DVXL_WARN_DEPRECATED -DVXL_WARN_DEPRECATED_ONCE -Ditkvnl_EXPORTS -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/vcl -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core -IModules/ThirdParty/VNL/src/vxl/v3p/netlib -IModules/ThirdParty/VNL/src/vxl/vcl -IModules/ThirdParty/VNL/src/vxl/core -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl  -march=native -O3 -pipe  -mtune=native -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -w  -fPIC   -msse2 -std=c++11 -MD -MT Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+uint.allsizes-.cxx.o -MF Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+uint.allsizes-.cxx.o.d -o Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+uint.allsizes-.cxx.o -c /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl/Templates/vnl_vector_fixed+uint.allsizes-.cxx
[82/4938] /usr/bin/x86_64-pc-linux-gnu-g++ -DVXL_WARN_DEPRECATED -DVXL_WARN_DEPRECATED_ONCE -Ditkvnl_EXPORTS -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/vcl -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core -IModules/ThirdParty/VNL/src/vxl/v3p/netlib -IModules/ThirdParty/VNL/src/vxl/vcl -IModules/ThirdParty/VNL/src/vxl/core -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl  -march=native -O3 -pipe  -mtune=native -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -w  -fPIC   -msse2 -std=c++11 -MD -MT Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+vnl_rational.allsizes-.cxx.o -MF Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+vnl_rational.allsizes-.cxx.o.d -o Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_vector_fixed+vnl_rational.allsizes-.cxx.o -c /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl/Templates/vnl_vector_fixed+vnl_rational.allsizes-.cxx
ninja: build stopped: subcommand failed.
 * ERROR: sci-libs/itk-5.1.0::chymeric failed (compile phase):
 *   ninja -v -j9 -l0 failed
 *
 * Call stack:
 *     ebuild.sh, line  125:  Called src_compile
 *   environment, line 2982:  Called cmake_src_compile
 *   environment, line 1126:  Called cmake_build
 *   environment, line 1105:  Called eninja
 *   environment, line 1547:  Called die
 * The specific snippet of code:
 *       "$@" || die "${nonfatal_args[@]}" "${*} failed"
 *
 * If you need support, post the output of `emerge --info '=sci-libs/itk-5.1.0::chymeric'`,
 * the complete build log and the output of `emerge -pqv '=sci-libs/itk-5.1.0::chymeric'`.
 * The complete build log is located at '/var/tmp/portage/sci-libs/itk-5.1.0/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/itk-5.1.0/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build'
 * S: '/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0'

silenthost ~ # du -sh /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/.ExternalData/*
1.5G    /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/.ExternalData/MD5
4.0K    /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/.ExternalData/README.rst
1.7G    /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/.ExternalData/SHA512
silenthost ~ # du -sh /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/.ExternalData/*
1.5G    /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/.ExternalData/MD5
4.0K    /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/.ExternalData/README.rst
1.7G    /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/.ExternalData/SHA512

Any idea what else I could try?

TheChymera picture TheChymera on 21 Aug 2020

@thewtex ping? :)

TheChymera picture TheChymera on 7 Sep 2020

@thewtex I think the problem is that the a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a file is simply not contained in the testdata archive:

git clone [email protected]:InsightSoftwareConsortium/ITKTestingData.git
cd ITKTestingData/
find -name "*a5e11ea71164ff78c65*"
TheChymera picture TheChymera on 13 Sep 2020

The file also appears to be nowhere in the repo history:

chymera@silenthost ~/src/ITKTestingData $ git log --all --full-history -- SHA512/a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a

Returns nothing.

TheChymera picture TheChymera on 13 Sep 2020

That file is available here: https://data.kitware.com/api/v1/file/hashsum/sha512/a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a/download

Our Girder instance should have all the current test data, and probably even all the historic (no longer in the repos) test data.

dzenanz picture dzenanz on 14 Sep 2020

@dzenanz

Hm, apparently I need an additional file.

FAILED: ExternalData/Modules/External/ITKGenericLabelInterpolator/test/Input/classification.mha-hash-stamp ExternalData/Modules/External/ITKGenericLabelInterpolator/test/Input/classification.mha
cd /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build && /usr/bin/cmake -Drelative_top=/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build -Dfile=/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/ExternalData/Modules/External/ITKGenericLabelInterpolator/test/Input/classification.mha -Dname=/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/External/ITKGenericLabelInterpolator/test/Input/classification.mha -Dexts=.sha512 -DExternalData_ACTION=fetch -DExternalData_CONFIG=/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/ITKData_config.cmake -P /usr/share/cmake/Modules/ExternalData.cmake
CMake Error at /usr/share/cmake/Modules/ExternalData.cmake:1121 (message):


  Object
  SHA512=bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f
  not found at:

    (No ExternalData_URL_TEMPLATES given)

I assume there might also be others? Is there any way to download all of them?

wget https://data.kitware.com/api/v1/file/hashsum/sha512/download

Only returns [].

TheChymera picture TheChymera on 17 Sep 2020

You need to call wget https://data.kitware.com/api/v1/file/hashsum/sha512/XXX/download, where XXX is the SHA512 hash of the file you are trying to download. And that additional file (classification.mha) also exists.

dzenanz picture dzenanz on 17 Sep 2020

@dzenanz so there's no way to download the entire collection? The thing is downloading the files one-by-one is making the process quite a bit more intricate and also less sustainable for the next version bump..

TheChymera picture TheChymera on 18 Sep 2020

It looks like there are only 2 files in that folder. But you can "download folder" after clicking on "folder actions" icon on the right.

dzenanz picture dzenanz on 18 Sep 2020

You can find out "itemId" via this API.

dzenanz picture dzenanz on 18 Sep 2020

@dzenanz thank you, that worked. Sadly, however, the build (with tests enabled) still fails with the following build.log.

It looks like the core issue is this, but I'm really unsure:

FAILED: Modules/Registration/Metricsv4/test/CMakeFiles/ITKMetricsv4TestDriver.dir/itkMeanSquaresImageToImageMetricv4RegistrationTest.cxx.o
/usr/bin/x86_64-pc-linux-gnu-g++  -IModules/ThirdParty/Eigen3/src -IModules/ThirdParty/KWIML/src -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/KWIML/src -IModules/ThirdParty/KWSys/src -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/vcl -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core -IModules/ThirdParty/VNL/src/vxl/v3p/netlib -IModules/ThirdParty/VNL/src/vxl/vcl -IModules/ThirdParty/VNL/src/vxl/core -IModules/Core/Common -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/Common/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/ImageAdaptors/include -IModules/ThirdParty/Netlib -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Numerics/Statistics/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Filtering/ImageFilterBase/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/Transform/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/ImageFunction/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Filtering/ImageGrid/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Filtering/ImageCompose/include -IModules/ThirdParty/ZLIB/src -IModules/ThirdParty/MetaIO/src/MetaIO/src -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/MetaIO/src/MetaIO/src -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/SpatialObjects/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Filtering/ImageStatistics/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Filtering/Path/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Filtering/ImageIntensity/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Filtering/Smoothing/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Filtering/DisplacementField/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Numerics/Optimizers/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Numerics/Optimizersv4/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/FiniteDifference/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Filtering/ImageGradient/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Filtering/ImageSources/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/Mesh/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Filtering/ImageFeature/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Registration/Common/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Registration/Metricsv4/include -IModules/IO/ImageBase -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/IO/ImageBase/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/TestKernel/include -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo -I/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/VNL/src/vxl/core/vnl -isystem /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/ThirdParty/Eigen3/src/itkeigen/..  -march=native -O3 -pipe  -mtune=native -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -fPIE -std=c++11 -MD -MT Modules/Registration/Metricsv4/test/CMakeFiles/ITKMetricsv4TestDriver.dir/itkMeanSquaresImageToImageMetricv4RegistrationTest.cxx.o -MF Modules/Registration/Metricsv4/test/CMakeFiles/ITKMetricsv4TestDriver.dir/itkMeanSquaresImageToImageMetricv4RegistrationTest.cxx.o.d -o Modules/Registration/Metricsv4/test/CMakeFiles/ITKMetricsv4TestDriver.dir/itkMeanSquaresImageToImageMetricv4RegistrationTest.cxx.o -c /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Registration/Metricsv4/test/itkMeanSquaresImageToImageMetricv4RegistrationTest.cxx
during RTL pass: reload
In file included from /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/Common/include/itkIndent.h:31,
                 from /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/Common/include/itkCovariantVector.h:21,
                 from /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.h:21,
                 from /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Registration/Metricsv4/include/itkMeanSquaresImageToImageMetricv4.h:21,
                 from /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Registration/Metricsv4/test/itkMeanSquaresImageToImageMetricv4RegistrationTest.cxx:27:
/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/Common/include/itkImportImageContainer.h: In member function ‘itk::LightObject::Pointer itk::ImportImageContainer<TElementIdentifier, TElement>::CreateAnother() const [with TElementIdentifier = long unsigned int; TElement = itk::Vector<double, 2>]’:
/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/Common/include/itkMacro.h:312:3: internal compiler error: Segmentation fault
  312 |   }
      |   ^
/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/Common/include/itkMacro.h:292:45: note: in expansion of macro ‘itkCreateAnotherMacro’
  292 | #define itkNewMacro(x) itkSimpleNewMacro(x) itkCreateAnotherMacro(x) itkCloneMacro(x)
      |                                             ^~~~~~~~~~~~~~~~~~~~~
/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/Core/Common/include/itkImportImageContainer.h:61:3: note: in expansion of macro ‘itkNewMacro’
   61 |   itkNewMacro(Self);
      |   ^~~~~~~~~~~
TheChymera picture TheChymera on 18 Sep 2020

itkMacro.h:312:3: internal compiler error which version of GCC is this? If using a different version is not an option, we could try slightly altering the part which is triggering the ICE. This seems vaguely familiar, but I can't find any discussion about it. @phcerdan do you remember anything like this before?

dzenanz picture dzenanz on 18 Sep 2020

@dzenanz I am using =gcc-10.2.0. It really should be compatible with GCC 10. I mean we can add a constraint for earlier GCC, but it would be the only package in the Gentoo Neuro/science stack which imposes that constraint...

If this can be solved via a patch, the Gentoo package manager supports that with no issues, in fact the ITK we distribute already has some patches to make it work with fully offline building: https://github.com/TheChymera/overlay/tree/7074d6af45dee5b4770c9a5fb51934f020fb19d3/sci-libs/itk/files If any of these seem worth upstreaming you're welcome to do so.

TheChymera picture TheChymera on 18 Sep 2020

I am testing locally with gcc 10.2.0 in Archlinux, I will report asap.
@dzenanz this itkMacro.h error doesn't ring any bell for me.

phcerdan picture phcerdan on 18 Sep 2020

@TheChymera any special gentoo-default flags in the cmake configuration?

gdevenyi picture gdevenyi on 18 Sep 2020

@gdevenyi The full flag list is contained towards the beginning of the log:

cmake -C /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_EXAMPLES=OFF -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=ON -Ddouble-conversion_INCLUDE_DIRS=/usr/include/double-conversion -DExternalData_OBJECT_STORES=/var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/.ExternalData -DGDCM_USE_SYSTEM_OPENJPEG=ON -DITK_FORBID_DOWNLOADS:BOOL=ON -DITK_INSTALL_LIBRARY_DIR=lib64 -DITK_USE_REVIEW=OFF -DITK_USE_SYSTEM_DCMTK=ON -DITK_USE_SYSTEM_DOUBLECONVERSION=ON -DITK_USE_SYSTEM_CASTXML=ON -DITK_USE_SYSTEM_HDF5=ON -DITK_USE_SYSTEM_JPEG=ON -DITK_USE_SYSTEM_PNG=ON -DITK_USE_SYSTEM_SWIG=ON -DITK_USE_SYSTEM_TIFF=ON -DITK_USE_SYSTEM_ZLIB=ON -DITK_USE_KWSTYLE=OFF -DITK_BUILD_DEFAULT_MODULES=ON -DITK_COMPUTER_MEMORY_SIZE=1 -DModule_GenericLabelInterpolator:BOOL=ON -DModule_ITKReview:BOOL=ON -DWRAP_ITK_JAVA=OFF -DWRAP_ITK_TCL=OFF -DITK_WRAP_PYTHON=OFF -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/gentoo_toolchain.cmake  /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0

It works if DBUILD_TESTING is set to OFF.

TheChymera picture TheChymera on 18 Sep 2020

I think we want the contents of this as well.

DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/gentoo_toolchain.cmake

and this:

/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/gentoo_common_config.cmak
gdevenyi picture gdevenyi on 18 Sep 2020

@TheChymera I cannot reproduce the error using the tag v5.1.1

commit 3ecf6c87d18d51b124589d5a74389244d692109c (HEAD -> release, tag: v5.1.1, origin/release)
Author: Matt McCormick <[email protected]>
Date:   Mon Aug 10 14:44:19 2020 -0400

    ENH: Update ITK CMake version for 5.1.1

gcc 10.2.0
cmake: 3.18.2
CMake args:

-GNinja -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DBUILD_TESTING:BOOL=ON -DITK_USE_SYSTEM_HDF5:BOOL=ON -DExternalData_OBJECT_STORES=/path/to/data

All tests compile with a lot of [-Wdeprecated-copy] warnings though.
That macro error is weird. I have to ask this, but have you tried a clean build folder?

phcerdan picture phcerdan on 18 Sep 2020

@gdevenyi @phcerdan I think I fixed that, and now the tests run all the way through, but there are a few which fail. Any idea why? This is the build.log, and these are the tests in question:

The following tests FAILED:
        1065 - itkTIFFImageIOTest6 (Failed)
        1094 - itkTIFFImageIOCompression_cthead1_JPEG (Failed)
        1097 - itkTIFFImageIOCompression_RGBTestImageJPEG_NoCompression (Failed)
        1098 - itkTIFFImageIOCompression_RGBTestImageJPEG_LZW (Failed)
        1099 - itkTIFFImageIOCompression_RGBTestImageJPEG_JPEG (Failed)
        1100 - itkTIFFImageIOCompression_RGBTestImageJPEG_PackBits (Failed)
        1101 - itkTIFFImageIOCompression_RGBTestImageJPEG_Deflate (Failed)
        1102 - itkTIFFImageIOCompression_cthead1_JPEG_1 (Failed)
        1103 - itkTIFFImageIOCompression_cthead1_JPEG_50 (Failed)
        1104 - itkTIFFImageIOCompression_cthead1_JPEG_100 (Failed)

Maybe some misspecified dependency?

TheChymera picture TheChymera on 19 Sep 2020

Can you try running ctest -VV -R itkTIFFImageIOTest6? Similarily for others. Or just ctest -VV -R itkTIFFImageIO. This should give a detailed output which should allow us to diagnose the problem.

dzenanz picture dzenanz on 21 Sep 2020

@dzenanz Should I just run it inside this build dir?

ihost /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build # tree -L 1
.
├── a.out
├── bin
├── build.ninja
├── clang-format-Linux
├── CMakeCache.txt
├── CMakeFiles
├── cmake_hdf5_test.o
├── cmake_install.cmake
├── CMakeTmp
├── config
├── CPackConfig.cmake
├── CPackSourceConfig.cmake
├── CTestCustom.cmake
├── CTestTestfile.cmake
├── DartConfiguration.tcl
├── ExternalData
├── gentoo_common_config.cmake
├── gentoo_rules.cmake
├── gentoo_toolchain.cmake
├── ITKConfig.cmake
├── ITKConfigVersion.cmake
├── ITKData_config.cmake
├── ITKInternalEigen3-build
├── ITKTargets.cmake
├── lib
├── Modules
├── single-doxygen.config
├── temp
├── Testing
└── Utilities

In any case, this would be the output:

ihost /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build # ctest -VV -R itkTIFFImageIOTest6
UpdateCTestConfiguration  from :/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/DartConfiguration.tcl
Parse Config file:/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/DartConfiguration.tcl
 Add coverage exclude regular expressions.
 Add coverage exclude: /CMakeFiles/CMakeTmp/
 Add coverage exclude: .*/Examples/.*
 Add coverage exclude: .*/test/.*
 Add coverage exclude: .*/Testing/.*
 Add coverage exclude: .*/ThirdParty/.*
 Add coverage exclude: .*/Utilities/.*
 Add coverage exclude: .*/Wrapping/.*
 Add coverage glob: Source/.*/*.h
 Add coverage glob: Source/.*/*.txx
 Add coverage glob: Source/.*/*.cxx
UpdateCTestConfiguration  from :/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/DartConfiguration.tcl
Parse Config file:/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/DartConfiguration.tcl
Test project /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1065
    Start 1065: itkTIFFImageIOTest6

1065: Test command: /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/bin/ITKIOTIFFTestDriver "--compare" "/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/ExternalData/Testing/Data/Baseline/IO/RGBTestImageJPEG.tif" "/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/Testing/Temporary/RGBTestImageJPEG.tif" "itkTIFFImageIOTest" "/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/ExternalData/Testing/Data/Input/RGBTestImageJPEG.tif" "/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/Testing/Temporary/RGBTestImageJPEG.tif"
1065: Test timeout computed to be: 1500
1065: Trying reader->Update()
1065: TIFFReadDirectory: Warning, Unknown field with tag 347 (0x15b) encountered.
1065: WARNING: In /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/IO/TIFF/src/itkTIFFImageIO.cxx, line 1251
1065: TIFFImageIO (0x55f7335457e0): Tag 347 has unsupported data type (7) for meta-data dictionary.
1065:
1065:
1065: itk::ExceptionObject (0x55f7335487a0)
1065: Location: "virtual void itk::TIFFImageIO::ReadImageInformation()"
1065: File: /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/IO/TIFF/src/itkTIFFImageIO.cxx
1065: Line: 489
1065: Description: itk::ERROR: itk::ERROR: TIFFImageIO(0x55f7335457e0): TIFF CODEC "JPEG" is not supported.
1065:
1065:
1065:   In /var/tmp/portage/sci-libs/itk-5.1.0/work/InsightToolkit-5.1.0/Modules/IO/TIFF/test/itkTIFFImageIOTest.cxx, line 76
1065: Exception detected while reading /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/ExternalData/Testing/Data/Baseline/IO/RGBTestImageJPEG.tif :  Could not create IO object for reading file /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/Testing/Temporary/RGBTestImageJPEG.tif
1065: The file doesn't exist.
1065: Filename = /var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/Testing/Temporary/RGBTestImageJPEG.tif
1065: <DartMeasurement name="BaselineImageName" type="text/string">INVALID_BASELINE_GIVEN</DartMeasurement>
1/1 Test #1065: itkTIFFImageIOTest6 ..............***Failed    0.97 sec

0% tests passed, 1 tests failed out of 1

Label Time Summary:
ITKIOTIFF    =   0.97 sec*proc (1 test)

Total Test time (real) =   1.84 sec

The following tests FAILED:
        1065 - itkTIFFImageIOTest6 (Failed)
Errors while running CTest
TheChymera picture TheChymera on 21 Sep 2020

Following up again, I'd like to know the contents of:

/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/gentoo_toolchain.cmake
/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/gentoo_common_config.cmake

To see if there are non-standard compiler flags creeping in which cause the non-reproducible difference.

gdevenyi picture gdevenyi on 21 Sep 2020

Looking at the failures, I see:

 -DITK_USE_SYSTEM_TIFF=ON

in the config and

Description: itk::ERROR: itk::ERROR: TIFFImageIO(0x55f7335457e0): TIFF CODEC "JPEG" is not supported.

In the log. Indicating your system libtiff doesn't have JPEG built in?

gdevenyi picture gdevenyi on 21 Sep 2020
👍1

@gdevenyi :

/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/gentoo_toolchain.cmake:

SET (CMAKE_ASM_COMPILER "x86_64-pc-linux-gnu-gcc")
SET (CMAKE_ASM-ATT_COMPILER "x86_64-pc-linux-gnu-gcc")
SET (CMAKE_C_COMPILER "x86_64-pc-linux-gnu-gcc")
SET (CMAKE_CXX_COMPILER "x86_64-pc-linux-gnu-g++")
SET (CMAKE_Fortran_COMPILER "x86_64-pc-linux-gnu-gfortran")
SET (CMAKE_AR /usr/bin/x86_64-pc-linux-gnu-ar CACHE FILEPATH "Archive manager" FORCE)
SET (CMAKE_RANLIB /usr/bin/x86_64-pc-linux-gnu-ranlib CACHE FILEPATH "Archive index generator" FORCE)
SET (CMAKE_SYSTEM_PROCESSOR "x86_64")

/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/gentoo_common_config.cmake:

SET (CMAKE_GENTOO_BUILD ON CACHE BOOL "Indicate Gentoo package build")
SET (LIB_SUFFIX 64 CACHE STRING "library path suffix" FORCE)
SET (CMAKE_INSTALL_LIBDIR lib64 CACHE PATH "Output directory for libraries")
SET (CMAKE_INSTALL_INFODIR "/usr/share/info" CACHE PATH "")
SET (CMAKE_INSTALL_MANDIR "/usr/share/man" CACHE PATH "")
SET (CMAKE_USER_MAKE_RULES_OVERRIDE "/var/tmp/portage/sci-libs/itk-5.1.0/work/itk-5.1.0_build/gentoo_rules.cmake" CACHE FILEPATH "Gentoo override rules")
SET (CMAKE_INSTALL_DOCDIR "/usr/share/doc/itk-5.1.0" CACHE PATH "")
SET (BUILD_SHARED_LIBS ON CACHE BOOL "")
TheChymera picture TheChymera on 21 Sep 2020
👍1

Great @TheChymera

@gdevenyi @phcerdan I think I fixed that,

what was the solution of the original problem? I would like to know in case another itkMacro error pops up in the future. Thanks!

About the TIFF test failure, I have compiled v5.1.1 with:

 -DITK_USE_SYSTEM_TIFF:BOOL=ON -DITK_USE_SYSTEM_JPEG:BOOL=ON

And I cannot reproduce that test failure, for reference:
Archlinux libtiff depends on libjpeg.

phcerdan picture phcerdan on 21 Sep 2020

@phcerdan no idea what solves the original issue, it just went away. I can only assume the build tree wasn't clean.... though the package manager should always clean it, and has never failed to before. Possibly black magic :)

Thank you all for your support, the TIFF issue was solved by adding the jpeg USE flag to the tiff package.

TheChymera picture TheChymera on 25 Sep 2020
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