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Installation error with editdistance and matplotlib on debian 11 with python3.9

See original GitHub issue

Getting error when trying to install editdistance and matplotlib packages.

check_install.py output

[x] python=3.9.2 (default, Feb 28 2021, 17:03:44)  [GCC 10.2.1 20210110]

Python modules:
[x] torch=1.10.1+cpu
[ ] torch cuda
[ ] torch cudnn
[ ] torch nccl
[ ] chainer
[ ] cupy
[x] torchaudio=0.10.1+cpu
[ ] torch_optimizer
[ ] warpctc_pytorch
[ ] warprnnt_pytorch
[ ] chainer_ctc
[ ] pyopenjtalk
[ ] tdmelodic_pyopenjtalk
[ ] kenlm
[ ] mmseg
[ ] espnet
[ ] fairseq
[ ] phonemizer
[ ] gtn
[ ] s3prl
[ ] transformers
[ ] speechbrain
[ ] k2
[ ] longformer
[ ] nlg-eval
[ ] datasets

Executables:
[ ] sclite
[ ] sph2pipe
[ ] PESQ
[ ] BeamformIt

INFO:
Use 'installers/install_warp-ctc.sh' to install warpctc_pytorch
Use 'installers/install_warp-transducer.sh' to install warprnnt_pytorch
Use 'installers/install_chainer_ctc.sh' to install chainer_ctc
Use 'installers/install_pyopenjtalk.sh' to install pyopenjtalk
Use 'installers/install_tdmelodic_pyopenjtalk.sh' to install tdmelodic_pyopenjtalk
Use 'installers/install_kenlm.sh' to install kenlm
Use 'installers/install_py3mmseg.sh' to install mmseg
Use 'installers/install_fairseq.sh' to install fairseq
Use 'installers/install_phonemizer.sh' to install phonemizer
Use 'installers/install_gtn.sh' to install gtn
Use 'installers/install_s3prl.sh' to install s3prl
Use 'installers/install_transformers.sh' to install transformers
Use 'installers/install_speechbrain.sh' to install speechbrain
Use 'installers/install_k2.sh' to install k2
Use 'installers/install_longformer.sh' to install longformer
Use 'installers/install_longformer.sh' to install nlg-eval
Use 'installers/install_longformer.sh' to install datasets
Use 'installers/install_sctk.sh' to install sclite
Use 'installers/install_sph2pipe.sh' to install sph2pipe
Use 'installers/install_pesq.sh' to install PESQ
Use 'installers/install_beamformit.sh' to install BeamformIt

Basic environments:

- OS information: Linux 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64
- python version: `3.9.2 (default, Feb 28 2021, 17:03:44)  [GCC 10.2.1 20210110]`
- espnet version: `espnet 0.10.7a1`
- pytorch version: `pytorch 1.11.0+cu102`
- Git hash: `55b045b286f658eebe044a432d030998fbb375e4`
  - Commit date: `Fri Apr 8 21:16:19 2022 +0800`

Environments from torch.utils.collect_env:

PyTorch version: 1.11.0+cu102
Is debug build: False
CUDA used to build PyTorch: 10.2
ROCM used to build PyTorch: N/A

OS: Debian GNU/Linux 11 (bullseye) (x86_64)
GCC version: (Debian 10.2.1-6) 10.2.1 20210110
Clang version: Could not collect
CMake version: version 3.18.4
Libc version: glibc-2.31

Python version: 3.9.2 (default, Feb 28 2021, 17:03:44)  [GCC 10.2.1 20210110] (64-bit runtime)
Python platform: Linux-5.14.0-0.bpo.2-amd64-x86_64-with-glibc2.31
Is CUDA available: False
CUDA runtime version: No CUDA
GPU models and configuration: No CUDA
Nvidia driver version: No CUDA
cuDNN version: No CUDA
HIP runtime version: N/A
MIOpen runtime version: N/A

Versions of relevant libraries:
[pip3] numpy==1.22.3
[pip3] numpy-groupies==0+unknown
[pip3] pytorch-wpe==0.0.1
[pip3] torch==1.11.0
[pip3] torch-complex==0.4.3
[pip3] torchaudio==0.11.0
[conda] Could not collect

To Reproduce

cd <espnet-root>/tools
make

Error logs

Building wheels for collected packages: editdistance, matplotlib
  Building wheel for editdistance (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [103 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-3.9
      creating build/lib.linux-x86_64-3.9/editdistance
      copying editdistance/__init__.py -> build/lib.linux-x86_64-3.9/editdistance
      copying editdistance/_editdistance.h -> build/lib.linux-x86_64-3.9/editdistance
      copying editdistance/def.h -> build/lib.linux-x86_64-3.9/editdistance
      running build_ext
      building 'editdistance.bycython' extension
      creating build/temp.linux-x86_64-3.9
      creating build/temp.linux-x86_64-3.9/editdistance
      x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I./editdistance -I/home/nik/github/espnet/tools/venv/include -I/usr/include/python3.9 -c editdistance/_editdistance.cpp -o build/temp.linux-x86_64-3.9/editdistance/_editdistance.o
      In file included from /usr/include/c++/10/vector:68,
                       from editdistance/_editdistance.cpp:20:
      /usr/include/c++/10/bits/stl_bvector.h:75:5: error: ‘OBit_type’ does not name a type
         75 |     OBit_type _M_mask;
            |     ^~~~~~~~~
      ....
      editdistance/_editdistance.cpp:97:67:   required from ‘unsigned int edit_distance_map_(const int64_t*, size_t, const int64_t*, size_t) [with long unsigned int N = 10; int64_t = long int; size_t = long unsigned int]’
      editdistance/_editdistance.cpp:128:80:   required from here
      editdistance/_editdistance.cpp:44:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
      error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for editdistance
  Running setup.py clean for editdistance
  Building wheel for matplotlib (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [539 lines of output]
      ================================================================================
      Edit setup.cfg to change the build options
      
      BUILDING MATPLOTLIB
        matplotlib: yes [3.1.0]
            python: yes [3.9.2 (default, Feb 28 2021, 17:03:44)  [GCC 10.2.1
                        20210110]]
          platform: yes [linux]
      
      OPTIONAL SUBPACKAGES
       sample_data: yes [installing]
             tests: no  [skipping due to configuration]
      
      OPTIONAL BACKEND EXTENSIONS
               agg: yes [installing]
             tkagg: yes [installing; run-time loading from Python Tcl/Tk]
            macosx: no  [Mac OS-X only]
      
      OPTIONAL PACKAGE DATA
              dlls: no  [skipping due to configuration]
      
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-3.9
      copying lib/pylab.py -> build/lib.linux-x86_64-3.9
      creating build/lib.linux-x86_64-3.9/mpl_toolkits
      copying lib/mpl_toolkits/__init__.py -> build/lib.linux-x86_64-3.9/mpl_toolkits
      creating build/lib.linux-x86_64-3.9/matplotlib
      ...
     
      creating build/temp.linux-x86_64-3.9/src
      x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DFREETYPE_BUILD_TYPE=system -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -D__STDC_FORMAT_MACROS=1 -Iextern/agg24-svn/include -I/home/nik/github/espnet/tools/venv/lib/python3.9/site-packages/numpy/core/include -I/home/nik/github/espnet/tools/venv/include -I/usr/include/python3.9 -c src/checkdep_freetype2.c -o build/temp.linux-x86_64-3.9/src/checkdep_freetype2.o -I/usr/include/freetype2 -I/usr/include/libpng16
      src/checkdep_freetype2.c:7:9: note: ‘#pragma message: Compiling with FreeType version 2.10.4.’
          7 | #pragma message("Compiling with FreeType version " \
            |         ^~~~~~~
      x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DFREETYPE_BUILD_TYPE=system -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -D__STDC_FORMAT_MACROS=1 -Iextern/agg24-svn/include -I/home/nik/github/espnet/tools/venv/lib/python3.9/site-packages/numpy/core/include -I/home/nik/github/espnet/tools/venv/include -I/usr/include/python3.9 -c src/ft2font.cpp -o build/temp.linux-x86_64-3.9/src/ft2font.o -I/usr/include/freetype2 -I/usr/include/libpng16
      In file included from /usr/include/c++/10/vector:68,
                       from src/ft2font.h:6,
                       from src/ft2font.cpp:9:
      /usr/include/c++/10/bits/stl_bvector.h:75:5: error: ‘OBit_type’ does not name a type
         75 |     OBit_type _M_mask;
            |     ^~~~~~~~~
      /usr/include/c++/10/bits/stl_bvector.h: In constructor ‘std::_Bit_reference::_Bit_reference(std::_Bit_type*, std::_Bit_type)’:
      /usr/include/c++/10/bits/stl_bvector.h:78:18: error: class ‘std::_Bit_reference’ does not have any field named ‘_M_mask’
         78 |     : _M_p(__x), _M_mask(__y) { }
            |                  ^~~~~~~
      /usr/include/c++/10/bits/stl_bvector.h: In constructor ‘std::_Bit_reference::_Bit_reference()’:
      /usr/include/c++/10/bits/stl_bvector.h:80:51: error: class ‘std::_Bit_reference’ does not have any field named ‘_M_mask’
         80 |     _Bit_reference() _GLIBCXX_NOEXCEPT : _M_p(0), _M_mask(0) { }
            |                                                   ^~~~~~~
      /usr/include/c++/10/bits/stl_bvector.h: In member function ‘std::_Bit_reference::operator bool() const’:
      /usr/include/c++/10/bits/stl_bvector.h:87:25: error: ‘_M_mask’ was not declared in this scope; did you mean ‘fd_mask’?
         87 |     { return !!(*_M_p & _M_mask); }
            |                         ^~~~~~~
            |                         fd_mask
      /usr/include/c++/10/bits/stl_bvector.h: In member function ‘std::_Bit_reference& std::_Bit_reference::operator=(bool)’:
      /usr/include/c++/10/bits/stl_bvector.h:93:11: error: ‘_M_mask’ was not declared in this scope; did you mean ‘fd_mask’?
         93 |  *_M_p |= _M_mask;
            |           ^~~~~~~
            |           fd_mask
      /usr/include/c++/10/bits/stl_bvector.h:95:12: error: ‘_M_mask’ was not declared in this scope; did you mean ‘fd_mask’?
         95 |  *_M_p &= ~_M_mask;
            |            ^~~~~~~
            |            fd_mask
      /usr/include/c++/10/bits/stl_bvector.h: In member function ‘void std::_Bit_reference::flip()’:
      /usr/include/c++/10/bits/stl_bvector.h:113:16: error: ‘_M_mask’ was not declared in this scope; did you mean ‘fd_mask’?
        113 |     { *_M_p ^= _M_mask; }
            |                ^~~~~~~
            |                fd_mask
      error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for matplotlib
  Running setup.py clean for matplotlib
Failed to build editdistance matplotlib
Installing collected packages: editdistance, distance, certifi, audioread, appdirs, zipp, werkzeug, urllib3, unidecode, typeguard, tqdm, torch_complex, threadpoolctl, tensorboard-data-server, soupsieve, smmap, six, simplejson, shortuuid, setproctitle, scipy, rsa, regex, PyYAML, pytorch_wpe, PySocks, pyrsistent, pypinyin, pyparsing, pycparser, pyasn1-modules, psutil, protobuf, portalocker, pillow, oauthlib, llvmlite, kiwisolver, kaldiio, joblib, inflect, idna, humanfriendly, h5py, future, filelock, fastdtw, decorator, Cython, cycler, configargparse, colorama, click, charset-normalizer, cachetools, bottleneck, attrs, sentry-sdk, scikit-learn, sacrebleu, requests, pyworld, python-dateutil, pystoi, pysptk, pyaml, promise, packaging, numba, nltk, mir-eval, jsonschema, importlib-metadata, grpcio, google-auth, gitdb, ffmpeg-python, docker-pycreds, ctc-segmentation, ci_sdr, cffi, beautifulsoup4, absl-py, stempeg, soundfile, resampy, requests-oauthlib, pooch, pandas, nnmnkwii, matplotlib, markdown, huggingface-hub, GitPython, g2p-en, wandb, nara_wpe, musdb, librosa, google-auth-oauthlib, gdown, espnet_tts_frontend, tensorboard, museval, espnet, espnet_model_zoo
  Running setup.py install for editdistance ... error
  error: subprocess-exited-with-error
  
  × Running setup.py install for editdistance did not run successfully.
  │ exit code: 1
  ╰─> [103 lines of output]
      running install
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-3.9
      creating build/lib.linux-x86_64-3.9/editdistance
      copying editdistance/__init__.py -> build/lib.linux-x86_64-3.9/editdistance
      copying editdistance/_editdistance.h -> build/lib.linux-x86_64-3.9/editdistance
      copying editdistance/def.h -> build/lib.linux-x86_64-3.9/editdistance
      running build_ext
      building 'editdistance.bycython' extension
      creating build/temp.linux-x86_64-3.9
      creating build/temp.linux-x86_64-3.9/editdistance
      x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I./editdistance -I/home/nik/github/espnet/tools/venv/include -I/usr/include/python3.9 -c editdistance/_editdistance.cpp -o build/temp.linux-x86_64-3.9/editdistance/_editdistance.o
      In file included from /usr/include/c++/10/vector:68,
                       from editdistance/_editdistance.cpp:20:
      /usr/include/c++/10/bits/stl_bvector.h:75:5: error: ‘OBit_type’ does not name a type
         75 |     OBit_type _M_mask;
            |     ^~~~~~~~~
      /usr/include/c++/10/bits/stl_bvector.h: In constructor ‘std::_Bit_reference::_Bit_reference(std::_Bit_type*, std::_Bit_type)’:
      /usr/include/c++/10/bits/stl_bvector.h:78:18: error: class ‘std::_Bit_reference’ does not have any field named ‘_M_mask’
         78 |     : _M_p(__x), _M_mask(__y) { }
            |                  ^~~~~~~
      /usr/include/c++/10/bits/stl_bvector.h: In constructor ‘std::_Bit_reference::_Bit_reference()’:
      /usr/include/c++/10/bits/stl_bvector.h:80:51: error: class ‘std::_Bit_reference’ does not have any field named ‘_M_mask’
         80 |     _Bit_reference() _GLIBCXX_NOEXCEPT : _M_p(0), _M_mask(0) { }
            |                                                   ^~~~~~~
      /usr/include/c++/10/bits/stl_bvector.h: In member function ‘std::_Bit_reference::operator bool() const’:
      /usr/include/c++/10/bits/stl_bvector.h:87:25: error: ‘_M_mask’ was not declared in this scope; did you mean ‘fd_mask’?
         87 |     { return !!(*_M_p & _M_mask); }
            |                         ^~~~~~~
            |                         fd_mask
      /usr/include/c++/10/bits/stl_bvector.h: In member function ‘std::_Bit_reference& std::_Bit_reference::operator=(bool)’:
      /usr/include/c++/10/bits/stl_bvector.h:93:11: error: ‘_M_mask’ was not declared in this scope; did you mean ‘fd_mask’?
         93 |  *_M_p |= _M_mask;
            |           ^~~~~~~
            |           fd_mask
      /usr/include/c++/10/bits/stl_bvector.h:95:12: error: ‘_M_mask’ was not declared in this scope; did you mean ‘fd_mask’?
         95 |  *_M_p &= ~_M_mask;
            |            ^~~~~~~
            |            fd_mask
      /usr/include/c++/10/bits/stl_bvector.h: In member function ‘void std::_Bit_reference::flip()’:
      /usr/include/c++/10/bits/stl_bvector.h:113:16: error: ‘_M_mask’ was not declared in this scope; did you mean ‘fd_mask’?
        113 |     { *_M_p ^= _M_mask; }
            |                ^~~~~~~
            |                fd_mask
      editdistance/_editdistance.cpp: In instantiation of ‘unsigned int edit_distance_dp(const T*, size_t, const T*, size_t) [with T = long int; size_t = long unsigned int]’:
      editdistance/_editdistance.cpp:129:62:   required from here
     ...
      editdistance/_editdistance.cpp:97:67:   required from ‘unsigned int edit_distance_map_(const int64_t*, size_t, const int64_t*, size_t) [with long unsigned int N = 10; int64_t = long int; size_t = long unsigned int]’
      editdistance/_editdistance.cpp:128:80:   required from here
      editdistance/_editdistance.cpp:44:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
      error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> editdistance

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
make: *** [Makefile:108: espnet.done] Error 1

Issue Analytics

  • State:closed
  • Created a year ago
  • Comments:5

github_iconTop GitHub Comments

1reaction
nikolas-ncommented, Apr 13, 2022

The error was due to the gcc compiler used.

Let me explain just in case someone else bumps into the same problem.

This compiler /usr/bin/x86_64-linux-gnu-gcc was linking to gcc-10 but it seems this is not compatible with python3.9(?). I used gcc-9 instead. This is what I did:

# apt install gcc-9 g++-9
# rm /usr/bin/x86_64-linux-gnu-gcc
# ln -s gcc-9 /usr/bin/x86_64-linux-gnu-gcc

I ran make again and it worked.

1reaction
b-flocommented, Apr 11, 2022

Hi,

error: command ‘/usr/bin/x86_64-linux-gnu-gcc’ failed with exit code 1

You’re missing some packages it sems. Try:

sudo apt-get install python3-dev build-essential

Read more comments on GitHub >

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