ERROR: Could not build wheels for bottleneck which use PEP 517 and cannot be installed directly #348

AlysonR · 2020-07-01T15:43:04Z

I get the errors
ERROR: Failed building wheel
ERROR: Could not build wheels for bottleneck which use PEP 517 and cannot be installed directly

I have python-devel installed, my wheel is updated to the current version, pip is updated to the current version, pep517 is installed

I saw this was an issue before that was closed after a false answer was given that was never proven to work (installing developers tools). I will not use conda or anaconda so please do not suggest that I install those to solve this problem.

qwhelan · 2020-07-02T23:39:56Z

Could you please provide exact versions of each of those dependencies, as well as the operating system?

ArasAzimi · 2020-07-13T03:02:04Z

@qwhelan I had this same issue:

Here are some dependencies and the virtual env I see the error in:

-Ubuntu 18.04.4 LTS
-5.3.0-62-generic
-x86_64
-Python 3.7.8
-pip 20.1.1

virtualenv -p python3.7 venv
source venv/bin/activate
pip install --upgrade setuptools wheel
pip install numpy==1.18.1
pip install fastai

This seems to be working with python 3.7.3 ( I had a mac system working and when I checked the python version it had 3.7.3). On the same Ubuntu system as above when I downgraded to python 3.7.3 The error no longer showed up. I thought I will post here in case it can help to find out the root cause. Also tried with python 3.8.3 and had the error.

qwhelan · 2020-07-13T05:35:38Z

@ArasAzimi Thank you, I will attempt to reproduce locally.

Zeitsperre · 2020-08-05T19:53:58Z

You might not find this useful, but we've noted the same failures on Python3.6 builds (on Travis CI) of the master branch of Bottleneck for the project xclim. I've opened a PR on there to try and figure out the cause: Ouranosinc/xclim#517

Feel free to check out the build statuses on that PR; they seem to be exactly as @AlysonR describes.

aulemahal · 2021-02-09T18:58:44Z

I believe I have found the source of the error, at least in my configuration. It is due to the specific of virtual environment creation with python -m venv.

When creating a virtual environment with venv into ${venv}, a ${venv}/include folder is created and sys.prefix == ${venv}. However, in opposition to virtualenv, the include folder is empty, it exists solely for files created by packages installed within the environment. Source : PEP 405.

The include folders needed by bottleneck are still accessible, but their path has to be constructed relative to sys.base_prefix instead, to get the system files. Changing:

bottleneck/bottleneck/src/bn_config.py

Line 30 in f2bc792

for prefix in [sys.prefix, sys.exec_prefix]:

to

    for prefix in [sys.prefix, sys.exec_prefix, sys.base_prefix]:

fixes the problem.

Of course, I have pythonX.X-dev installed (on ubuntu) for this to work.

EDIT: I have python 3.7.9.

AndyWangSFU · 2021-04-09T00:38:07Z

This is really a weird issue. It happens in my local machine, and happens again in my poetry virtual machine... (BTW they have different python versions)

nocluebutalotofit · 2021-04-27T14:06:00Z

On macOS Big Sur 11.2.3 I get the following error running pip install:

$ pip install Bottleneck==1.3.2

Collecting Bottleneck==1.3.2
Using cached Bottleneck-1.3.2.tar.gz (88 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing wheel metadata ... done
Collecting numpy
Using cached numpy-1.20.2-cp38-cp38-macosx_10_9_x86_64.whl (16.0 MB)
Building wheels for collected packages: Bottleneck
Building wheel for Bottleneck (PEP 517) ... error
ERROR: Command errored out with exit status 1:
command: /Users/daniel/PycharmProjects/machine-learning-for-trading_book/venv/bin/python /Users/daniel/PycharmProjects/machine-learning-for-trading_book/venv/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/in_process.py build_wheel /var/folders/hh/ll8cmcb100v7lbrfh1n1t96m0000gn/T/tmpd5gppf3b
cwd: /private/var/folders/hh/ll8cmcb100v7lbrfh1n1t96m0000gn/T/pip-install-082v_gn/bottleneck_c8de5d9f837747fba5e8843c02aa359c
Complete output (127 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.14.6-x86_64-3.8
creating build/lib.macosx-10.14.6-x86_64-3.8/bottleneck
copying bottleneck/_version.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck
copying bottleneck/init.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck
copying bottleneck/_pytesttester.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck
creating build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/benchmark
copying bottleneck/benchmark/bench_detailed.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/benchmark
copying bottleneck/benchmark/autotimeit.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/benchmark
copying bottleneck/benchmark/init.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/benchmark
copying bottleneck/benchmark/bench.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/benchmark
creating build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/slow
copying bottleneck/slow/reduce.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/slow
copying bottleneck/slow/init.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/slow
copying bottleneck/slow/nonreduce.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/slow
copying bottleneck/slow/move.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/slow
copying bottleneck/slow/nonreduce_axis.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/slow
creating build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/nonreduce_axis_test.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/scalar_input_test.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/reduce_test.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/util.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/move_test.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/init.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/input_modification_test.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/nonreduce_test.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/list_input_test.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/memory_test.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/tests
creating build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/src
copying bottleneck/src/bn_config.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/src
copying bottleneck/src/init.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/src
copying bottleneck/src/bn_template.py -> build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/src
UPDATING build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/_version.py
set build/lib.macosx-10.14.6-x86_64-3.8/bottleneck/_version.py to '1.3.2'
running build_ext
running config
compiling '_configtest.c':

#pragma clang diagnostic error "-Wattributes"

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

int main(void)
{
return 0;
}

x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/daniel/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -isystem /Users/daniel/opt/anaconda3/include -c _configtest.c -o _configtest.o
clang-11: error: the clang compiler does not support '-march=core2'
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;
}

x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/daniel/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -isystem /Users/daniel/opt/anaconda3/include -c _configtest.c -o _configtest.o
clang-11: error: the clang compiler does not support '-march=core2'
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;
}

x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/daniel/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -isystem /Users/daniel/opt/anaconda3/include -c _configtest.c -o _configtest.o
clang-11: error: the clang compiler does not support '-march=core2'
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;
}

x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/daniel/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -isystem /Users/daniel/opt/anaconda3/include -c _configtest.c -o _configtest.o
clang-11: error: the clang compiler does not support '-march=core2'
failure.
removing: _configtest.c _configtest.o
building 'bottleneck.reduce' extension
creating build/temp.macosx-10.14.6-x86_64-3.8
creating build/temp.macosx-10.14.6-x86_64-3.8/bottleneck
creating build/temp.macosx-10.14.6-x86_64-3.8/bottleneck/src
x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/daniel/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -isystem /Users/daniel/opt/anaconda3/include -I/private/var/folders/hh/ll8cmcb100v7lbrfh1n1t96m0000gn/T/pip-build-env-6idcz14p/overlay/lib/python3.8/site-packages/numpy/core/include -I/Users/daniel/PycharmProjects/machine-learning-for-trading_book/venv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -Ibottleneck/src -c bottleneck/src/reduce.c -o build/temp.macosx-10.14.6-x86_64-3.8/bottleneck/src/reduce.o -O2
clang-11: error: the clang compiler does not support '-march=core2'
error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1

ERROR: Failed building wheel for Bottleneck
Failed to build Bottleneck
ERROR: Could not build wheels for Bottleneck which use PEP 517 and cannot be installed directly

bkaankuguoglu · 2021-04-29T09:26:08Z

Is there any update regarding this issue? So far I've tried the following but none worked:

Installing the package with the most recent pip and setuptools
Installing with --no-binary mode pip install bottleneck --no-binary :all:
Changing the line 30 in bottleneck/bottleneck/src/bn_config.py file to:
for prefix in [sys.prefix, sys.exec_prefix, sys.base_prefix]: and for prefix in [sys.prefix, sys.exec_prefix, <path_to_venv>]:

brentrichards · 2021-05-30T09:54:09Z

After many re-installs, running:
pip install --upgrade setuptools wheel
fixed the issue for me. (On Windows Dev edition).

profxj · 2021-07-14T20:56:31Z

Running on a VM via kubernetes with conda installed using

# Miniconda
ENV PATH="/root/miniconda3/bin:${PATH}"
ARG PATH="/root/miniconda3/bin:${PATH}"
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py38_4.9.2-Linux-x86_64.sh \
    && mkdir /root/.conda \
    && bash Miniconda3-py38_4.9.2-Linux-x86_64.sh -b \
    && rm -f Miniconda3-py38_4.9.2-Linux-x86_64.sh

fails to Install, even after the

pip install --upgrade setuptools wheel

approach suggested above.

The final bit of the crash:

  gcc -pthread -B /root/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_64-3.8
  creating build/temp.linux-x86_64-3.8/bottleneck
  creating build/temp.linux-x86_64-3.8/bottleneck/src
  gcc -pthread -B /root/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-xf8ufge7/overlay/lib/python3.8/site-packages/numpy/core/include -I/root/miniconda3/include/python3.8 -Ibottleneck/src -c bottleneck/src/reduce.c -o build/temp.linux-x86_64-3.8/bottleneck/src/reduce.o -O2
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for bottleneck
Failed to build bottleneck
ERROR: Could not build wheels for bottleneck which use PEP 517 and cannot be installed directly

brentrichards · 2021-07-15T00:06:03Z

On Windows, I finally realised that I needed a background tool to build the Wheel, that is not installed by default (and the message doen't hint at). I installed Visual Studio Build tools, and it all worked.

franciscorodriguez92 · 2021-07-21T11:26:40Z

Hi!

Installing gcc solved the problem for me (Ubuntu 20.04):

sudo apt-get install gcc

jweisbaum · 2021-08-04T19:25:30Z

Has anyone been able to get this to work on mac? Trying to install with Python 3.9 in the Blender installation.

johncox00 · 2021-10-11T14:06:44Z

I came across this issue while searching for a similar issue installing implicit wherein I got...

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

@jweisbaum I was able to get past the problem on my mac with brew install gcc and then pip install ...

AlysonR added the bug label Jul 1, 2020

AlysonR assigned qwhelan Jul 1, 2020

AlysonR changed the title ~~ERROR: Could not build wheels for pyhdf which use PEP 517 and cannot be installed directly~~ ERROR: Could not build wheels for bottleneck which use PEP 517 and cannot be installed directly Jul 1, 2020

Zeitsperre mentioned this issue Feb 10, 2022

Virutalenv support for building bottleneck #396

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ERROR: Could not build wheels for bottleneck which use PEP 517 and cannot be installed directly #348

ERROR: Could not build wheels for bottleneck which use PEP 517 and cannot be installed directly #348

AlysonR commented Jul 1, 2020 •

edited

qwhelan commented Jul 2, 2020

ArasAzimi commented Jul 13, 2020 •

edited

qwhelan commented Jul 13, 2020

Zeitsperre commented Aug 5, 2020 •

edited

aulemahal commented Feb 9, 2021 •

edited

AndyWangSFU commented Apr 9, 2021

nocluebutalotofit commented Apr 27, 2021 •

edited

bkaankuguoglu commented Apr 29, 2021

brentrichards commented May 30, 2021

profxj commented Jul 14, 2021

brentrichards commented Jul 15, 2021

franciscorodriguez92 commented Jul 21, 2021

jweisbaum commented Aug 4, 2021

johncox00 commented Oct 11, 2021

ERROR: Could not build wheels for bottleneck which use PEP 517 and cannot be installed directly #348

ERROR: Could not build wheels for bottleneck which use PEP 517 and cannot be installed directly #348

Comments

AlysonR commented Jul 1, 2020 • edited

qwhelan commented Jul 2, 2020

ArasAzimi commented Jul 13, 2020 • edited

Here are some dependencies and the virtual env I see the error in:

qwhelan commented Jul 13, 2020

Zeitsperre commented Aug 5, 2020 • edited

aulemahal commented Feb 9, 2021 • edited

AndyWangSFU commented Apr 9, 2021

nocluebutalotofit commented Apr 27, 2021 • edited

bkaankuguoglu commented Apr 29, 2021

brentrichards commented May 30, 2021

profxj commented Jul 14, 2021

brentrichards commented Jul 15, 2021

franciscorodriguez92 commented Jul 21, 2021

jweisbaum commented Aug 4, 2021

johncox00 commented Oct 11, 2021

AlysonR commented Jul 1, 2020 •

edited

ArasAzimi commented Jul 13, 2020 •

edited

Zeitsperre commented Aug 5, 2020 •

edited

aulemahal commented Feb 9, 2021 •

edited

nocluebutalotofit commented Apr 27, 2021 •

edited