installation of snd file via pip3 fails : Building wheel for sndfile (setup.py) ... error fatal error: sndfile.h: No such file or directory #include <sndfile.h>

[marcoippolito]

installation of snd file via pip3 fails:

(base) marco@pc:~/Resemblyzer$ pip3 install sndfile
Collecting sndfile
  Using cached https://files.pythonhosted.org/packages/db/ce   
/797cacd78490aa9de2e0e119491079d380e2fbbd7a1c5057c9fb2120a643/sndfile-0.2.0.tar.gz
Requirement already satisfied: cffi>=1.0.0 in /home/marco/anaconda3/lib/python3.7/site-packages 
 (from sndfile) (1.12.3)
Requirement already satisfied: pycparser in /home/marco/anaconda3/lib/python3.7/site-packages  
 (from cffi>=1.0.0->sndfile) (2.19)
Building wheels for collected packages: sndfile
  Building wheel for sndfile (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/marco/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; 
   sys.argv[0] = '"'"'/tmp/pip-install-7w_p8_7r/sndfile/setup.py'"'"'; __file__='"'"'/tmp/pip-install-  
   7w_p8_7r/sndfile/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"',  
   open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, 
   '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-n2k5xwj9 --python-tag cp37
       cwd: /tmp/pip-install-7w_p8_7r/sndfile/
Complete output (23 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.7
  creating build/lib.linux-x86_64-3.7/sndfile
  copying sndfile/__init__.py -> build/lib.linux-x86_64-3.7/sndfile
  copying sndfile/vio.py -> build/lib.linux-x86_64-3.7/sndfile
  copying sndfile/build.py -> build/lib.linux-x86_64-3.7/sndfile
  copying sndfile/formats.py -> build/lib.linux-x86_64-3.7/sndfile
  copying sndfile/io.py -> build/lib.linux-x86_64-3.7/sndfile
  running build_ext
  generating cffi module 'build/temp.linux-x86_64-3.7/sndfile._sndfile.c'
  creating build/temp.linux-x86_64-3.7
  building 'sndfile._sndfile' extension
  creating build/temp.linux-x86_64-3.7/build
  creating build/temp.linux-x86_64-3.7/build/temp.linux-x86_64-3.7
  gcc -pthread -B /home/marco/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare 
  -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/marco/anaconda3/include
  /python3.7m -c build/temp.linux-x86_64-3.7/sndfile._sndfile.c -o build/temp.linux-x86_64-3.7/build
  /temp.linux-x86_64-3.7/sndfile._sndfile.o
  build/temp.linux-x86_64-3.7/sndfile._sndfile.c:494:10: fatal error: sndfile.h: No such file or 
directory
   #include <sndfile.h>
            ^~~~~~~~~~~
  compilation terminated.
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
 ERROR: Failed building wheel for sndfile
  Running setup.py clean for sndfile
Failed to build sndfile
Installing collected packages: sndfile
  Running setup.py install for sndfile ... error
    ERROR: Command errored out with exit status 1:
     command: /home/marco/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; 
sys.argv[0] = '"'"'/tmp/pip-install-7w_p8_7r/sndfile/setup.py'"'"'; __file__='"'"'/tmp/pip-install- 
7w_p8_7r/sndfile/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', 
open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, 
'"'"'exec'"'"'))' install --record /tmp/pip-record-67675cxl/install-record.txt --single-version-externally-
managed --compile
         cwd: /tmp/pip-install-7w_p8_7r/sndfile/
    Complete output (23 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.7
    creating build/lib.linux-x86_64-3.7/sndfile
    copying sndfile/__init__.py -> build/lib.linux-x86_64-3.7/sndfile
    copying sndfile/vio.py -> build/lib.linux-x86_64-3.7/sndfile
    copying sndfile/build.py -> build/lib.linux-x86_64-3.7/sndfile
    copying sndfile/formats.py -> build/lib.linux-x86_64-3.7/sndfile
    copying sndfile/io.py -> build/lib.linux-x86_64-3.7/sndfile
    running build_ext
    generating cffi module 'build/temp.linux-x86_64-3.7/sndfile._sndfile.c'
    creating build/temp.linux-x86_64-3.7
    building 'sndfile._sndfile' extension
   creating build/temp.linux-x86_64-3.7/build
    creating build/temp.linux-x86_64-3.7/build/temp.linux-x86_64-3.7
    gcc -pthread -B /home/marco/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare 
-DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/marco/anaconda3/include
/python3.7m -c build/temp.linux-x86_64-3.7/sndfile._sndfile.c -o build/temp.linux-x86_64-3.7/build
/temp.linux-x86_64-3.7/sndfile._sndfile.o
    build/temp.linux-x86_64-3.7/sndfile._sndfile.c:494:10: fatal error: sndfile.h: No such file or 
directory
     #include <sndfile.h>
               ^~~~~~~~~~~
    compilation terminated.
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/marco/anaconda3/bin/python -u -c 
'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-7w_p8_7r/sndfile/setup.py'"'"'; 
__file__='"'"'/tmp/pip-install-7w_p8_7r/sndfile/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', 
open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, 
'"'"'exec'"'"'))' install --record /tmp/pip-record-67675cxl/install-record.txt --single-version-externally-
managed --compile Check the logs for full command output.

• Operating System: Ubuntu 18.04.02 Server Edition
• gcc version 7.4.0 (Ubuntu 7.4.0-1ubuntu1~18.04.1)
• pip3 -V
  pip 19.2.3 from /home/marco/anaconda3/lib/python3.7/site-packages/pip (python 3.7)

Looking forward to your kind help.
Marco

[haobibo]

@marcoippolito try this: sudo apt-get install libsndfile1-dev

[harrygcoppock]

I am working on a virtual machine that I do not have access to, is there an alternative solution?

[M5era]

Did anyone find a solution to this? Same problem

[harrygcoppock]

Hi @M5era for me updating gcc and gxx worked:
conda install gcc_linux-64 gxx_linux-64 compilers c-compiler cxx-compiler

[M5era]

Thanks for the tip! However it is still not working. This is my output:

Running setup.py install for sndfile: started Running setup.py install for sndfile: finished with status 'error' ERROR: Command errored out with exit status 1: command: /opt/hostedtoolcache/Python/3.9.7/x64/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-d54b_6vg/sndfile_0f2509c97b454b36a6ba7d8353dbb63e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-d54b_6vg/sndfile_0f2509c97b454b36a6ba7d8353dbb63e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-ntmvwqog/install-record.txt --single-version-externally-managed --compile --install-headers /opt/hostedtoolcache/Python/3.9.7/x64/include/python3.9/sndfile cwd: /tmp/pip-install-d54b_6vg/sndfile_0f2509c97b454b36a6ba7d8353dbb63e/ Complete output (23 lines): 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/sndfile copying sndfile/__init__.py -> build/lib.linux-x86_64-3.9/sndfile copying sndfile/vio.py -> build/lib.linux-x86_64-3.9/sndfile copying sndfile/formats.py -> build/lib.linux-x86_64-3.9/sndfile copying sndfile/io.py -> build/lib.linux-x86_64-3.9/sndfile copying sndfile/build.py -> build/lib.linux-x86_64-3.9/sndfile running build_ext generating cffi module 'build/temp.linux-x86_64-3.9/sndfile._sndfile.c' creating build/temp.linux-x86_64-3.9 building 'sndfile._sndfile' extension creating build/temp.linux-x86_64-3.9/build creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9 gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/opt/hostedtoolcache/Python/3.9.7/x64/include/python3.9 -c build/temp.linux-x86_64-3.9/sndfile._sndfile.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/sndfile._sndfile.o build/temp.linux-x86_64-3.9/sndfile._sndfile.c:571:10: fatal error: sndfile.h: No such file or directory 571 | #include <sndfile.h> | ^~~~~~~~~~~ compilation terminated. error: command '/usr/bin/gcc' failed with exit code 1 ---------------------------------------- ERROR: Command errored out with exit status 1: /opt/hostedtoolcache/Python/3.9.7/x64/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-d54b_6vg/sndfile_0f2509c97b454b36a6ba7d8353dbb63e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-d54b_6vg/sndfile_0f2509c97b454b36a6ba7d8353dbb63e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-ntmvwqog/install-record.txt --single-version-externally-managed --compile --install-headers /opt/hostedtoolcache/Python/3.9.7/x64/include/python3.9/sndfile Check the logs for full command output. Error: Process completed with exit code 1.

And I am already installing these in the dockerfile:

RUN apt-get -y install python3.9-dev RUN apt-get -y install libsndfile1-dev RUN apt-get -y install gcc g++ gcc-7 g++-7 gcc-8 g++-8 gcc-9 g++-9 #RUN brew install gcc RUN apt-get -y install build-essential RUN apt-get -y install manpages-dev RUN pip3 install --user wheel RUN apt-get -y install libxml2-dev libxslt-dev python-dev

and these in the requirements.txt:

asgiref==3.4.1 boto3==1.18.48 botocore==1.21.48 certifi==2021.5.30 charset-normalizer==2.0.6 click==8.0.1 fastapi==0.68.1 filelock==3.1.0 h11==0.12.0 huggingface-hub==0.0.17 idna==3.2 jellyfish==0.8.8 jmespath==0.10.0 joblib==1.0.1 networkx==2.6.3 nltk==3.6.3 numpy==1.21.2 packaging==21.0 Pillow==8.3.2 pydantic==1.8.2 pyparsing==2.4.7 python-dateutil==2.8.2 PyYAML==5.4.1 regex==2021.9.24 requests==2.26.0 s3transfer==0.5.0 sacremoses==0.0.46 scikit-learn==1.0 scipy==1.7.1 segtok==1.5.10 stop_words sentence-transformers==2.0.0 sentencepiece==0.1.96 six==1.16.0 sklearn==0.0 starlette==0.14.2 tabulate==0.8.9 threadpoolctl==2.2.0 tokenizers==0.10.3 torch==1.9.1 torchvision==0.10.1 tqdm==4.62.3 transformers==4.10.3 typing-extensions==3.10.0.2 urllib3==1.26.7 uvicorn==0.15.0 yake==0.4.8 gcc7 sndfile noisereduce==2.0.0 git+https://github.com/csteinmetz1/pymixconsole SoundFile==0.10.3.post1

[harrygcoppock]

Hmmm then sorry I am not sure what can help. - my issue was related however I was building another package from source which required sndfile. So not exactly the same issue.

[M5era]

I located the problem further to the noisereduce library which is using sndfile. Somehow this is causing problems. Still working on a solution though. Thanks for your answer!

[harrygcoppock]

Sorry I couldn't help

[carloselcastro]

sudo apt-get install libsndfile1 libsndfile1-dev

worked for me :)