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Build fails at ANTSFetchData target due to Kitware API removing MD5 checksums #1236

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bcdarwin opened this issue Sep 14, 2021 · 3 comments · Fixed by #1237
Closed

Build fails at ANTSFetchData target due to Kitware API removing MD5 checksums #1236

bcdarwin opened this issue Sep 14, 2021 · 3 comments · Fixed by #1237
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bug Reproducible bugs help needed Issues that require feedback or expertise from the community. Discussion and PRs welcome

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@bcdarwin
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bcdarwin commented Sep 14, 2021 •
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When did the error occur?

[ ] CMake configuration (cmake / ccmake)
[x] Compilation (make)
[ ] Installation (make install)

Build environment

  • OS: Ubuntu
  • OS 20.04
  • Type of system: Desktop

ANTs version

0a08209

Build configuration and logs

Totally default configuration.

[ 82%] Performing forcebuild step for 'ANTS'
[ 88%] Performing build step for 'ANTS'
Scanning dependencies of target antsUtilities
Scanning dependencies of target ANTSFetchData
[  0%] Generating /home/bdarwin/git/ANTs/build/ANTS-build/ExternalData/TestData/Data/r16slice.nii.gz
[  0%] Generating /home/bdarwin/git/ANTs/build/ANTS-build/ExternalData/TestData/Data/r64slice.nii.gz
[  1%] Generating /home/bdarwin/git/ANTs/build/ANTS-build/ExternalData/TestData/Data/Frown.nii
-- Fetching "file:////home/bdarwin/git/ANTs/.ExternalData/MD5/8a629ee7ea32013c76af5b05f880b5c6"
-- Fetching "file:////home/bdarwin/git/ANTs/.ExternalData/MD5/37aaa33029410941bf4affff0479fa18"
-- Fetching "file:////home/bdarwin/git/ANTs/.ExternalData/MD5/11ea9f4d17e24ab90d8bc0b4b087d235"
-- Fetching "http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&checksum=8a629ee7ea32013c76af5b05f880b5c6"
-- Fetching "http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&checksum=37aaa33029410941bf4affff0479fa18"
-- Fetching "http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&checksum=11ea9f4d17e24ab90d8bc0b4b087d235"
-- Fetching "https://data.kitware.com:443/api/v1/file/hashsum/MD5/8a629ee7ea32013c76af5b05f880b5c6/download"
-- Fetching "https://data.kitware.com:443/api/v1/file/hashsum/MD5/11ea9f4d17e24ab90d8bc0b4b087d235/download"
-- Fetching "https://data.kitware.com:443/api/v1/file/hashsum/MD5/37aaa33029410941bf4affff0479fa18/download"
-- Fetching "http://www.itk.org/files/ExternalData/MD5/37aaa33029410941bf4affff0479fa18"
-- Fetching "http://www.itk.org/files/ExternalData/MD5/8a629ee7ea32013c76af5b05f880b5c6"
-- Fetching "http://www.itk.org/files/ExternalData/MD5/11ea9f4d17e24ab90d8bc0b4b087d235"
-- [download 100% complete]
-- [download 100% complete]
-- [download 100% complete]
-- [download 0% complete]
-- [download 87% complete]
-- [download 100% complete]
-- Downloaded object: "/home/bdarwin/git/ANTs/build/ANTS-build/ExternalData/Objects/MD5/8a629ee7ea32013c76af5b05f880b5c6"
CMake Error at /axiom2/projects/software/arch/linux-xenial-xerus/cmake/3.15.5/share/cmake-3.15/Modules/ExternalData.cmake:1121 (message):
  

  Object MD5=37aaa33029410941bf4affff0479fa18 not found at:

    file:////home/bdarwin/git/ANTs/.ExternalData/MD5/37aaa33029410941bf4affff0479fa18 ("Couldn't read a file:// file")
    http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&checksum=37aaa33029410941bf4affff0479fa18 ("HTTP response code said error")
    https://data.kitware.com:443/api/v1/file/hashsum/MD5/37aaa33029410941bf4affff0479fa18/download ("HTTP response code said error")
    http://www.itk.org/files/ExternalData/MD5/37aaa33029410941bf4affff0479fa18 ("HTTP response code said error")


CMake Error at /axiom2/projects/software/arch/linux-xenial-xerus/cmake/3.15.5/share/cmake-3.15/Modules/ExternalData.cmake:1121 (message):
  

  Object MD5=11ea9f4d17e24ab90d8bc0b4b087d235 not found at:

    file:////home/bdarwin/git/ANTs/.ExternalData/MD5/11ea9f4d17e24ab90d8bc0b4b087d235 ("Couldn't read a file:// file")
    http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&checksum=11ea9f4d17e24ab90d8bc0b4b087d235 ("HTTP response code said error")
    https://data.kitware.com:443/api/v1/file/hashsum/MD5/11ea9f4d17e24ab90d8bc0b4b087d235/download ("HTTP response code said error")
    http://www.itk.org/files/ExternalData/MD5/11ea9f4d17e24ab90d8bc0b4b087d235 ("HTTP response code said error")


Examples/TestSuite/CMakeFiles/ANTSFetchData.dir/build.make:123: recipe for target 'ExternalData/TestData/Data/r16slice.nii.gz-hash-stamp' failed
make[5]: *** [ExternalData/TestData/Data/r16slice.nii.gz-hash-stamp] Error 1
make[5]: *** Waiting for unfinished jobs....
Examples/TestSuite/CMakeFiles/ANTSFetchData.dir/build.make:137: recipe for target 'ExternalData/TestData/Data/Frown.nii-hash-stamp' failed
make[5]: *** [ExternalData/TestData/Data/Frown.nii-hash-stamp] Error 1
CMakeFiles/Makefile2:7764: recipe for target 'Examples/TestSuite/CMakeFiles/ANTSFetchData.dir/all' failed
make[4]: *** [Examples/TestSuite/CMakeFiles/ANTSFetchData.dir/all] Error 2
make[4]: *** Waiting for unfinished jobs....
[  1%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsUtilities.cxx.o
[  1%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistrationTemplateHeader.cxx.o
[  2%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration2DFloat.cxx.o
[  2%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration2DDouble.cxx.o
[  2%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DDouble.cxx.o
[  2%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration3DFloat.cxx.o
[  2%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DDouble.cxx.o
[  3%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/antsRegistration4DFloat.cxx.o
[  3%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/ReadWriteData.cxx.o
[  3%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineOption.cxx.o
[  3%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/__/Utilities/antsCommandLineParser.cxx.o
[  4%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ANTsVersion.cxx.o
[  4%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ImageMathHelper2D.cxx.o
[  4%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ImageMathHelper3D.cxx.o
[  4%] Building CXX object Examples/CMakeFiles/antsUtilities.dir/ImageMathHelper4D.cxx.o
[  4%] Linking CXX static library libantsUtilities.a
[  4%] Built target antsUtilities
Makefile:162: recipe for target 'all' failed
make[3]: *** [all] Error 2
CMakeFiles/ANTS.dir/build.make:114: recipe for target 'ANTS-prefix/src/ANTS-stamp/ANTS-build' failed
make[2]: *** [ANTS-prefix/src/ANTS-stamp/ANTS-build] Error 2
CMakeFiles/Makefile2:595: recipe for target 'CMakeFiles/ANTS.dir/all' failed
make[1]: *** [CMakeFiles/ANTS.dir/all] Error 2
Makefile:116: recipe for target 'all' failed
make: *** [all] Error 2

Additional context

$ curl https://data.kitware.com:443/api/v1/file/hashsum/MD5/37aaa33029410941bf4affff0479fa18/download
{"message": "Invalid value for algo: \"md5\". Allowed values: sha512.", "type": "rest"}
@bcdarwin bcdarwin changed the title Default build fails at ANTSFetchData target due to Kitware API removing MD5 checksums Build fails at ANTSFetchData target due to Kitware API removing MD5 checksums Sep 14, 2021
@gdevenyi
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ref:
https://gitlab.kitware.com/paraview/paraview/-/merge_requests/2463

@cookpa cookpa added bug Reproducible bugs help needed Issues that require feedback or expertise from the community. Discussion and PRs welcome labels Sep 15, 2021
@bcdarwin bcdarwin mentioned this issue Sep 15, 2021
Merged
@chidiugonna chidiugonna mentioned this issue Oct 2, 2021
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@fluese
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fluese commented Oct 6, 2021

Has there been any progress on this or is there a workaround available?

Cheers,
Falk

@ik362 ik362 mentioned this issue Oct 6, 2021
Closed
@bcdarwin
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bcdarwin commented Oct 6, 2021

@fluese A workaround is -DBUILD_TESTING=OFF.

@bcdarwin bcdarwin mentioned this issue Oct 15, 2021
Merged
haampie pushed a commit to spack/spack that referenced this issue Nov 9, 2021
@bcdarwin
ants: fix build by setting BUILD_TESTING=OFF (#26768)
7c118ee 
Due to Kitware API changes, default ANTs builds were failing, presumably for all versions (ANTsX/ANTs#1236).
This commit defaults BUILD_TESTING to OFF, preventing calls against
these APIs and fixing all versions.
Note that the ANTs test suite was not clean anyway (e.g. ANTs/#842).
@anagrammarian anagrammarian mentioned this issue Nov 22, 2021
Closed
burtonjz added a commit to UMich-Mind-Lab/singularity-neurotools that referenced this issue Jan 7, 2022
@burtonjz
fixed AFNI build (see ANTsX/ANTs#1236)
b4f2a73 
switched FSLOUTPUTTYPE to be NIFTI_GZ by default
added bc to FSL requirements
@joshuacwnewton joshuacwnewton mentioned this issue Feb 14, 2022
Closed
17 tasks
joshuacwnewton added a commit to spinalcordtoolbox/build_ANTs that referenced this issue May 6, 2022
@joshuacwnewton
ccpp.yml: Set BUILD_TESTING=OFF to fix Kitware issue
2526bd6 
I encountered this during my Windows builds, too: spinalcordtoolbox/spinalcordtoolbox#3682 (comment)

More context can be found in: ANTsX/ANTs#1236
@cookpa cookpa mentioned this issue Mar 28, 2023
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COMP: use sha512 instead of md5 hashes for ExternalData fetching bcdarwin/ANTs
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@bcdarwin @cookpa @gdevenyi @fluese