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Document Pip PEP 517 installation quirks #435

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@GuannanZhao

I try to install brainiak on MacOS Mojave just by

python3 -m pip install -U brainiak

following the instruction on Docs » Installation page.
But at the end I still encounter an error as

ERROR: Could not build wheels for brainiak which use PEP 517 and cannot be installed directly

So what's the problem with me? Did I do something wrong?

Thanks,
Zhao

Activity

  1. mihaic commented on Aug 28, 2019

    @mihaic
    Member

    Could you please try with a pip version < 10?

  2. mihaic commented on Aug 28, 2019

    @mihaic
    Member

    For example, you can create a virtual environment for testing like this:

    python3 -m venv testvenv
    source testvenv/bin/activate
    python3 -m pip install -U pip\<10
    python3 -m pip install brainiak
  3. mihaic commented on Aug 28, 2019

    @mihaic
    Member

    A better alternative is to use the --no-use-pep517 flag when installing (requires a pip version >= 19):

    python3 -m pip install --no-use-pep517 brainiak
  4. GuannanZhao commented on Aug 29, 2019

    @GuannanZhao
    Author

    Thank you @mihaic ! It works!
    I downgraded pip from 19.2.3 to 9.0.3 as you recommend and it works.
    Module brainiak is installed and imported (in PyCharm) successfully.

    I also tried --no-use-pep517 option but nothing happened.
    It seems that something is wrong when compiling at the step pep517(I found some errors about cpp and cython), though I am not sure what it is.

    Thank you again!

  5. changed the title [-]An ERROR occurs when installing by pip[/-] [+]Document Pip PEP 517 installation quirks[/+] on Aug 29, 2019
  6. mihaic commented on Aug 29, 2019

    @mihaic
    Member

    Thanks for the feedback, @GuannanZhao. I am re-purposing this issue to improve our documentation.

    Could you please paste the command the error you see when installing with pip >=19 and --no-use-pep517?

  7. self-assigned this
    on Aug 29, 2019
  8. GuannanZhao commented on Aug 30, 2019

    @GuannanZhao
    Author

    It seems that everything will be OK if brainiak-0.9.1-cp37-cp37m-macosx_10_9_x86_64.whl is already built under the path ~/Library/Caches/pip/.
    I could uninstall and install brainiak by pip 19.2.3 successfully as many times as my wish without an error. When I deleted this cache, the PEP 517 error occurred again.

    Then I tried python3 -m pip install --no-use-pep517 brainiak, it did works this time, but nothing happened last time. Neither was an error reported nor was the module successfully installed.
    I am not sure why. Maybe last time I made some mistakes or changed something without awareness about that.


    The PEP 517 error is as follow:

    Building wheels for collected packages: brainiak
      Building wheel for brainiak (PEP 517) ... error
      ERROR: Command errored out with exit status 1:
       command: /Users/guannanzhao/testvenv/bin/python3 /Users/guannanzhao/testvenv/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/tmpf5wjdptx
           cwd: /private/var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/pip-install-y3h2tutg/brainiak
      Complete output (209 lines):
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.macosx-10.9-x86_64-3.7
      creating build/lib.macosx-10.9-x86_64-3.7/brainiak
      copying brainiak/isc.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak
      copying brainiak/io.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak
      copying brainiak/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak
      copying brainiak/image.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak
      creating build/lib.macosx-10.9-x86_64-3.7/brainiak/searchlight
      copying brainiak/searchlight/searchlight.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/searchlight
      copying brainiak/searchlight/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/searchlight
      creating build/lib.macosx-10.9-x86_64-3.7/brainiak/hyperparamopt
      copying brainiak/hyperparamopt/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/hyperparamopt
      copying brainiak/hyperparamopt/hpo.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/hyperparamopt
      creating build/lib.macosx-10.9-x86_64-3.7/brainiak/funcalign
      copying brainiak/funcalign/sssrm.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/funcalign
      copying brainiak/funcalign/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/funcalign
      copying brainiak/funcalign/rsrm.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/funcalign
      copying brainiak/funcalign/srm.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/funcalign
      creating build/lib.macosx-10.9-x86_64-3.7/brainiak/factoranalysis
      copying brainiak/factoranalysis/tfa.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/factoranalysis
      copying brainiak/factoranalysis/htfa.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/factoranalysis
      copying brainiak/factoranalysis/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/factoranalysis
      creating build/lib.macosx-10.9-x86_64-3.7/brainiak/fcma
      copying brainiak/fcma/mvpa_voxelselector.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/fcma
      copying brainiak/fcma/classifier.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/fcma
      copying brainiak/fcma/util.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/fcma
      copying brainiak/fcma/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/fcma
      copying brainiak/fcma/preprocessing.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/fcma
      copying brainiak/fcma/voxelselector.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/fcma
      creating build/lib.macosx-10.9-x86_64-3.7/brainiak/reprsimil
      copying brainiak/reprsimil/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/reprsimil
      copying brainiak/reprsimil/brsa.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/reprsimil
      creating build/lib.macosx-10.9-x86_64-3.7/brainiak/utils
      copying brainiak/utils/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/utils
      copying brainiak/utils/fmrisim.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/utils
      copying brainiak/utils/utils.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/utils
      creating build/lib.macosx-10.9-x86_64-3.7/brainiak/eventseg
      copying brainiak/eventseg/event.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/eventseg
      copying brainiak/eventseg/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/brainiak/eventseg
      copying brainiak/utils/grey_matter_mask.npy -> build/lib.macosx-10.9-x86_64-3.7/brainiak/utils
      running build_ext
      creating var
      creating var/folders
      creating var/folders/jw
      creating var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn
      creating var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T
      /usr/local/opt/llvm/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/usr/local/opt/llvm/include -I/Users/guannanzhao/testvenv/include -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/private/var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/pip-build-env-2vhcnu6a/normal/lib/python3.7/site-packages/numpy/core/include -I/Users/guannanzhao/testvenv/include/site/python3.7 -I/Users/guannanzhao/testvenv/include/site/python3.7 -c /var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/tmpx0pzm1oq.cpp -o var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/tmpx0pzm1oq.o -std=c++14
      /usr/local/opt/llvm/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/usr/local/opt/llvm/include -I/Users/guannanzhao/testvenv/include -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/private/var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/pip-build-env-2vhcnu6a/normal/lib/python3.7/site-packages/numpy/core/include -I/Users/guannanzhao/testvenv/include/site/python3.7 -I/Users/guannanzhao/testvenv/include/site/python3.7 -c /var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/tmpywztyla6.cpp -o var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/tmpywztyla6.o -std=c++14
      /usr/local/opt/llvm/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/usr/local/opt/llvm/include -I/Users/guannanzhao/testvenv/include -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/private/var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/pip-build-env-2vhcnu6a/normal/lib/python3.7/site-packages/numpy/core/include -I/Users/guannanzhao/testvenv/include/site/python3.7 -I/Users/guannanzhao/testvenv/include/site/python3.7 -c /var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/tmplbb8jvyk.cpp -o var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/tmplbb8jvyk.o -std=c++14
      /usr/local/opt/llvm/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/usr/local/opt/llvm/include -I/Users/guannanzhao/testvenv/include -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/private/var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/pip-build-env-2vhcnu6a/normal/lib/python3.7/site-packages/numpy/core/include -I/Users/guannanzhao/testvenv/include/site/python3.7 -I/Users/guannanzhao/testvenv/include/site/python3.7 -c /var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/tmpwi7stw2f.cpp -o var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/tmpwi7stw2f.o -std=c++14
      building 'brainiak.factoranalysis.tfa_extension' extension
      creating build/temp.macosx-10.9-x86_64-3.7
      creating build/temp.macosx-10.9-x86_64-3.7/brainiak
      creating build/temp.macosx-10.9-x86_64-3.7/brainiak/factoranalysis
      /usr/local/opt/llvm/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/usr/local/opt/llvm/include -I/Users/guannanzhao/testvenv/include -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/private/var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/pip-build-env-2vhcnu6a/normal/lib/python3.7/site-packages/numpy/core/include -I/Users/guannanzhao/testvenv/include/site/python3.7 -I/Users/guannanzhao/testvenv/include/site/python3.7 -c brainiak/factoranalysis/tfa_extension.cpp -o build/temp.macosx-10.9-x86_64-3.7/brainiak/factoranalysis/tfa_extension.o -g0 -fopenmp -stdlib=libc++ -mmacosx-version-min=10.9 -ftemplate-depth-1024 -DVERSION_INFO="0.9.1" -std=c++14
      brainiak/factoranalysis/tfa_extension.cpp:242:1: warning: 'pybind11_init' is deprecated: PYBIND11_PLUGIN is deprecated, use PYBIND11_MODULE [-Wdeprecated-declarations]
      PYBIND11_PLUGIN(tfa_extension) {
      ^
      /Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pybind11/detail/common.h:261:20: note: expanded from macro 'PYBIND11_PLUGIN'
                  return pybind11_init();                                            \
                         ^
      brainiak/factoranalysis/tfa_extension.cpp:242:1: note: 'pybind11_init' has been explicitly marked deprecated here
      /Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pybind11/detail/common.h:256:5: note: expanded from macro 'PYBIND11_PLUGIN'
          PYBIND11_DEPRECATED("PYBIND11_PLUGIN is deprecated, use PYBIND11_MODULE")  \
          ^
      /Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pybind11/detail/common.h:90:41: note: expanded from macro 'PYBIND11_DEPRECATED'
      #  define PYBIND11_DEPRECATED(reason) [[deprecated(reason)]]
                                              ^
      1 warning generated.
      /usr/local/opt/llvm/bin/clang++ -bundle -undefined dynamic_lookup -arch x86_64 -g -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -I/usr/local/opt/llvm/include build/temp.macosx-10.9-x86_64-3.7/brainiak/factoranalysis/tfa_extension.o -o build/lib.macosx-10.9-x86_64-3.7/brainiak/factoranalysis/tfa_extension.cpython-37m-darwin.so -g0 -fopenmp -stdlib=libc++ -mmacosx-version-min=10.9 -ftemplate-depth-1024 -DVERSION_INFO="0.9.1" -std=c++14
      building 'brainiak.fcma.fcma_extension' extension
      creating build/temp.macosx-10.9-x86_64-3.7/brainiak/fcma
      creating build/temp.macosx-10.9-x86_64-3.7/brainiak/fcma/src
      /usr/local/opt/llvm/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/usr/local/opt/llvm/include -I/Users/guannanzhao/testvenv/include -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/private/var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/pip-build-env-2vhcnu6a/normal/lib/python3.7/site-packages/numpy/core/include -I/Users/guannanzhao/testvenv/include/site/python3.7 -I/Users/guannanzhao/testvenv/include/site/python3.7 -c brainiak/fcma/src/fcma_extension.cc -o build/temp.macosx-10.9-x86_64-3.7/brainiak/fcma/src/fcma_extension.o -g0 -fopenmp -stdlib=libc++ -mmacosx-version-min=10.9 -ftemplate-depth-1024 -DVERSION_INFO="0.9.1" -std=c++14
      brainiak/fcma/src/fcma_extension.cc:60:17: warning: unknown pragma ignored [-Wunknown-pragmas]
              #pragma simd
                      ^
      brainiak/fcma/src/fcma_extension.cc:54:23: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
          for(int v = 0 ; v < nSelectedVoxels*nSubjs ; v++)
                          ~ ^ ~~~~~~~~~~~~~~~~~~~~~~
      brainiak/fcma/src/fcma_extension.cc:61:27: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
              for(int j = 0 ; j < nVoxels ; j++)
                              ~ ^ ~~~~~~~
      brainiak/fcma/src/fcma_extension.cc:87:1: warning: 'pybind11_init' is deprecated: PYBIND11_PLUGIN is deprecated, use PYBIND11_MODULE [-Wdeprecated-declarations]
      PYBIND11_PLUGIN(fcma_extension) {
      ^
      /Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pybind11/detail/common.h:261:20: note: expanded from macro 'PYBIND11_PLUGIN'
                  return pybind11_init();                                            \
                         ^
      brainiak/fcma/src/fcma_extension.cc:87:1: note: 'pybind11_init' has been explicitly marked deprecated here
      /Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pybind11/detail/common.h:256:5: note: expanded from macro 'PYBIND11_PLUGIN'
          PYBIND11_DEPRECATED("PYBIND11_PLUGIN is deprecated, use PYBIND11_MODULE")  \
          ^
      /Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pybind11/detail/common.h:90:41: note: expanded from macro 'PYBIND11_DEPRECATED'
      #  define PYBIND11_DEPRECATED(reason) [[deprecated(reason)]]
                                              ^
      4 warnings generated.
      /usr/local/opt/llvm/bin/clang++ -bundle -undefined dynamic_lookup -arch x86_64 -g -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -I/usr/local/opt/llvm/include build/temp.macosx-10.9-x86_64-3.7/brainiak/fcma/src/fcma_extension.o -o build/lib.macosx-10.9-x86_64-3.7/brainiak/fcma/fcma_extension.cpython-37m-darwin.so -g0 -fopenmp -stdlib=libc++ -mmacosx-version-min=10.9 -ftemplate-depth-1024 -DVERSION_INFO="0.9.1" -std=c++14
      cythoning brainiak/fcma/cython_blas.pyx to brainiak/fcma/cython_blas.c
      building 'brainiak.fcma.cython_blas' extension
      /usr/local/opt/llvm/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/usr/local/opt/llvm/include -I/Users/guannanzhao/testvenv/include -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/private/var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/pip-build-env-2vhcnu6a/normal/lib/python3.7/site-packages/numpy/core/include -I/Users/guannanzhao/testvenv/include/site/python3.7 -I/Users/guannanzhao/testvenv/include/site/python3.7 -c brainiak/fcma/cython_blas.c -o build/temp.macosx-10.9-x86_64-3.7/brainiak/fcma/cython_blas.o -g0 -fopenmp -stdlib=libc++ -mmacosx-version-min=10.9 -ftemplate-depth-1024 -DVERSION_INFO="0.9.1"
      brainiak/fcma/cython_blas.c:1:2: error: Do not use this file, it is the result of a failed Cython compilation.
      #error Do not use this file, it is the result of a failed Cython compilation.
       ^
      1 error generated.
      /private/var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/pip-build-env-2vhcnu6a/normal/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /private/var/folders/jw/w9_6m6qd1k35q5kps723hqbw0000gn/T/pip-install-y3h2tutg/brainiak/brainiak/fcma/cython_blas.pyx
        tree = Parsing.p_module(s, pxd, full_module_name)
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      #  limitations under the License.
      
      # Authors: Yida Wang
      # (Intel Labs), 2016
      
      cimport scipy.linalg.cython_blas as blas
             ^
      ------------------------------------------------------------
      
      brainiak/fcma/cython_blas.pyx:18:8: 'scipy/linalg/cython_blas.pxd' not found
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          A = py_a
          cdef float[:, ::1] B
          B = py_b
          cdef float[:, :, ::1] C
          C = py_c
          blas.sgemm(trans_a, trans_b, &M, &N, &K, &alpha, &A[0, 0], &lda,
             ^
      ------------------------------------------------------------
      
      brainiak/fcma/cython_blas.pyx:115:8: cimported module has no attribute 'sgemm'
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          beta = py_beta
          cdef float[:, :, ::1] A
          A = py_a
          cdef float[:, ::1] C
          C = py_c
          blas.ssyrk(uplo, trans, &N, &K, &alpha, &A[py_start_voxel, 0, 0], &lda,
             ^
      ------------------------------------------------------------
      
      brainiak/fcma/cython_blas.pyx:197:8: cimported module has no attribute 'ssyrk'
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          beta = py_beta
          cdef float[:, ::1] A
          A = py_a
          cdef float[:, :, ::1] C
          C = py_c
          blas.ssyrk(uplo, trans, &N, &K, &alpha, &A[0, 0], &lda,
             ^
      ------------------------------------------------------------
      
      brainiak/fcma/cython_blas.pyx:286:8: cimported module has no attribute 'ssyrk'
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          beta = py_beta
          cdef float[:, ::1] A
          A = py_a
          cdef float[:, :, ::1] C
          C = py_c
          blas.sgemm(trans_a, trans_b, &M, &N, &K, &alpha, &A[0, 0], &lda,
             ^
      ------------------------------------------------------------
      
      brainiak/fcma/cython_blas.pyx:385:8: cimported module has no attribute 'sgemm'
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          A = py_a
          cdef float[:, ::1] B
          B = py_b
          cdef float[:, :, ::1] C
          C = py_c
          blas.sgemm(trans_a, trans_b, &M, &N, &K, &alpha, &A[0, 0], &lda,
             ^
      ------------------------------------------------------------
      
      brainiak/fcma/cython_blas.pyx:477:8: cimported module has no attribute 'sgemm'
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          A = py_a
          cdef float[:, ::1] B
          B = py_b
          cdef float[:, ::1] C
          C = py_c
          blas.sgemm(trans_a, trans_b, &M, &N, &K, &alpha, &A[0, 0], &lda,
             ^
      ------------------------------------------------------------
      
      brainiak/fcma/cython_blas.pyx:559:8: cimported module has no attribute 'sgemm'
      error: command '/usr/local/opt/llvm/bin/clang' failed with exit status 1
      ----------------------------------------
      ERROR: Failed building wheel for brainiak
      Running setup.py clean for brainiak
    Failed to build brainiak
    ERROR: Could not build wheels for brainiak which use PEP 517 and cannot be installed directly
    
  9. mihaic commented on Aug 30, 2019

    @mihaic
    Member

    Thanks for the detailed output. I will modify the documentation to include the --no-use-pep517 flag.

  10. added a commit that references this issue on Feb 6, 2020
    97d5345
  11. added a commit that references this issue on Feb 7, 2020
    bfc3ca2
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