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

[lcflorindo]

Hi, I'm installing Bottleneck by fastai lib in a Suse 12 sp4 server, but had the error when building wheels for it.
It says that uses PEP517 and cannot be installed directly. Funny thing is that I had it installed on my (base) but when I move to my app env it just jams on the error.
There is a way to solve it? Thanks in advance!

(pycamlar) (base) filholf@127.0.0.1:~/pycamlar> pip install --no-cache-dir Bottleneck
Collecting Bottleneck
  Downloading https://files.pythonhosted.org/packages/62/d0/55bbb49f4fade3497de2399af70ec0a06e432c786b8623c878b11e90d456/Bottleneck-1.3.1.tar.gz (88kB)
     |████████████████████████████████| 92kB 1.1MB/s
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Requirement already satisfied: numpy in ./pycamlar/lib/python3.7/site-packages (from Bottleneck) (1.17.4)
Building wheels for collected packages: Bottleneck
  Building wheel for Bottleneck (PEP 517) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/filholf/pycamlar/pycamlar/bin/python /home/filholf/pycamlar/pycamlar/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /tmp/tmpzdoiga7s
       cwd: /tmp/pip-install-gx8dza5k/Bottleneck
  Complete output (122 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/bottleneck
  copying bottleneck/__init__.py -> build/lib.linux-x86_64-3.7/bottleneck
  copying bottleneck/_pytesttester.py -> build/lib.linux-x86_64-3.7/bottleneck
  copying bottleneck/_version.py -> build/lib.linux-x86_64-3.7/bottleneck
  creating build/lib.linux-x86_64-3.7/bottleneck/benchmark
  copying bottleneck/benchmark/__init__.py -> build/lib.linux-x86_64-3.7/bottleneck/benchmark
  copying bottleneck/benchmark/autotimeit.py -> build/lib.linux-x86_64-3.7/bottleneck/benchmark
  copying bottleneck/benchmark/bench.py -> build/lib.linux-x86_64-3.7/bottleneck/benchmark
  copying bottleneck/benchmark/bench_detailed.py -> build/lib.linux-x86_64-3.7/bottleneck/benchmark
  creating build/lib.linux-x86_64-3.7/bottleneck/slow
  copying bottleneck/slow/__init__.py -> build/lib.linux-x86_64-3.7/bottleneck/slow
  copying bottleneck/slow/move.py -> build/lib.linux-x86_64-3.7/bottleneck/slow
  copying bottleneck/slow/nonreduce.py -> build/lib.linux-x86_64-3.7/bottleneck/slow
  copying bottleneck/slow/nonreduce_axis.py -> build/lib.linux-x86_64-3.7/bottleneck/slow
  copying bottleneck/slow/reduce.py -> build/lib.linux-x86_64-3.7/bottleneck/slow
  creating build/lib.linux-x86_64-3.7/bottleneck/src
  copying bottleneck/src/__init__.py -> build/lib.linux-x86_64-3.7/bottleneck/src
  copying bottleneck/src/bn_config.py -> build/lib.linux-x86_64-3.7/bottleneck/src
  copying bottleneck/src/bn_template.py -> build/lib.linux-x86_64-3.7/bottleneck/src
  creating build/lib.linux-x86_64-3.7/bottleneck/tests
  copying bottleneck/tests/__init__.py -> build/lib.linux-x86_64-3.7/bottleneck/tests
  copying bottleneck/tests/input_modification_test.py -> build/lib.linux-x86_64-3.7/bottleneck/tests
  copying bottleneck/tests/list_input_test.py -> build/lib.linux-x86_64-3.7/bottleneck/tests
  copying bottleneck/tests/memory_test.py -> build/lib.linux-x86_64-3.7/bottleneck/tests
  copying bottleneck/tests/move_test.py -> build/lib.linux-x86_64-3.7/bottleneck/tests
  copying bottleneck/tests/nonreduce_axis_test.py -> build/lib.linux-x86_64-3.7/bottleneck/tests
  copying bottleneck/tests/nonreduce_test.py -> build/lib.linux-x86_64-3.7/bottleneck/tests
  copying bottleneck/tests/reduce_test.py -> build/lib.linux-x86_64-3.7/bottleneck/tests
  copying bottleneck/tests/scalar_input_test.py -> build/lib.linux-x86_64-3.7/bottleneck/tests
  copying bottleneck/tests/util.py -> build/lib.linux-x86_64-3.7/bottleneck/tests
  UPDATING build/lib.linux-x86_64-3.7/bottleneck/_version.py
  set build/lib.linux-x86_64-3.7/bottleneck/_version.py to '1.3.1'
  running build_ext
  running config
  compiling '_configtest.c':

  #pragma GCC diagnostic error "-Wattributes"

  int __attribute__((optimize("O3"))) have_attribute_optimize_opt_3(void*);

  int main(void)
  {
      return 0;
  }

  gcc -pthread -B /home/filholf/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o
  failure.
  removing: _configtest.c _configtest.o
  compiling '_configtest.c':

  #ifndef __cplusplus
  static inline int static_func (void)
  {
      return 0;
  }
  inline int nostatic_func (void)
  {
      return 0;
  }
  #endif
  int main(void) {
      int r1 = static_func();
      int r2 = nostatic_func();
      return r1 + r2;
  }

  gcc -pthread -B /home/filholf/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o
  failure.
  removing: _configtest.c _configtest.o
  compiling '_configtest.c':

  #ifndef __cplusplus
  static __inline__ int static_func (void)
  {
      return 0;
  }
  __inline__ int nostatic_func (void)
  {
      return 0;
  }
  #endif
  int main(void) {
      int r1 = static_func();
      int r2 = nostatic_func();
      return r1 + r2;
  }

  gcc -pthread -B /home/filholf/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o
  failure.
  removing: _configtest.c _configtest.o
  compiling '_configtest.c':

  #ifndef __cplusplus
  static __inline int static_func (void)
  {
      return 0;
  }
  __inline int nostatic_func (void)
  {
      return 0;
  }
  #endif
  int main(void) {
      int r1 = static_func();
      int r2 = nostatic_func();
      return r1 + r2;
  }

  gcc -pthread -B /home/filholf/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o
  failure.
  removing: _configtest.c _configtest.o
  building 'bottleneck.reduce' extension
  creating build/temp.linux-x86_64-3.7
  creating build/temp.linux-x86_64-3.7/bottleneck
  creating build/temp.linux-x86_64-3.7/bottleneck/src
  gcc -pthread -B /home/filholf/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-i9jvt975/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/filholf/miniconda3/include/python3.7m -Ibottleneck/src -c bottleneck/src/reduce.c -o build/temp.linux-x86_64-3.7/bottleneck/src/reduce.o -O2
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for Bottleneck
  Running setup.py clean for Bottleneck
Failed to build Bottleneck
ERROR: Could not build wheels for Bottleneck which use PEP 517 and cannot be installed directly

[lcflorindo]

QUICK UPDATE I took some time to research the internet about: PEP517 have some problems with virtualenvs but i already tried --no-use-pep517 with no success and still retrying an error.

[qwhelan]

Could you provide the pip version?

Thanks for reporting!

[qwhelan]

On further investigation, I found this pypa/pip#6256 which suggests the issue is that wheels simply aren't supported with PEP 517 builds. My best guess would be to pip install --upgrade pip setuptools wheel and that should resolve the issue.

[lcflorindo]

Could you provide the pip version?

Thanks for reporting!

pip 19.2.3 from /home/filholf/anaconda3/lib/python3.7/site-packages/pip (python 3.7)

I'm assuming that my OS is not helping as well, I'm using Suse 12 SP4, my other server is an Ubuntu 16.04lts and everything worked fine...

[lcflorindo]

On further investigation, I found this pypa/pip#6256 which suggests the issue is that wheels simply aren't supported with PEP 517 builds. My best guess would be to pip install --upgrade pip setuptools wheel and that should resolve the issue.

I tried the upgrade, but stills returning the wheel problem. I'm totally able to install it at base.

But as a quick update, I solved installing Anaconda instead of miniconda, but not sure about the relation of both or even what was the problem with miniconda. Could it be a repair when I uninstalled/installed.

[qwhelan]

Hmm, there really shouldn't be a difference between equivalent versions of Miniconda/Anaconda.

Good to hear it's resolved and apologies for not having a clear answer here. Please feel free to re-open if it re-surfaces.

[AnakTeka]

I'm receiving a same error and using python:3.6-slim docker image, I fixed it by installing gcc inside the container.

[harshikanu]

Another way to resolve this is to download Windows SDK 10 (latest version). If this alone doesn't work then download Visual Studio 2019 (again whichever is the latest version). This updates the wheel process.

[bchen32]

harshikanu's suggestion worked for me. I'd like to expand on it a little bit

1. Go to visual studio downloads at https://visualstudio.microsoft.com/downloads/
2. Scroll down to 'All Downloads'
3. Click the dropdown for 'Tools for Visual Studio 2019'
4. Download 'Build Tools for Visual Studio 2019'

and that should successfully update wheel and allow you to install bottleneck

[qwhelan]

@StormFalcon32 Do you happen to know the version of the Windows SDK you were on pre-upgrade? And pip and python as well?

[bchen32]

Oh man I don't remember what version of Windows sdk but I was on Python 3.7.6 and I think 20.0.2 on pip

[qwhelan]

Thanks for checking - was mostly wondering if this was connected to the Python 3.8 issue some Arch users had reported (and should be fixed by 1.3.2 that I released a few minutes ago)

[bayesfactor]

I installed Build Tools for Visual Studio 2019, updated wheels, and I still have the error when installing Bottleneck-1.3.2.:
Failed to build bottleneck
ERROR: Could not build wheels for bottleneck which use PEP 517 and cannot be installed directly

python 3.5.5
wheel 0.34.2
pip 20.0.2

[harshikanu]

@bayesfactor I think you need to have the latest version of python installed.