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[x] I have checked that this issue has not already been reported.
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[ ] I have confirmed this bug exists on the latest version of pandas.
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[x] (optional) I have confirmed this bug exists on the master branch of pandas.
Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.
Code Sample, a copy-pastable example
$ python -m pip install -r requirements-dev.txt
Problem description
I followed the guide on the setting up the dev environment.
https://pandas.pydata.org/pandas-docs/stable/development/contributing.html#creating-a-python-environment-pip
The failure occurred when installing dependencies.
(venv) ~/code/pandas (master) $ git log -1
commit aed64e85eb17edb0e55013868b1aa4e44e977a36 (HEAD -> master, upstream/master)
Author: Hans <hanspagh@gmail.com>
Date: Sat Sep 19 04:14:25 2020 +0200
BUG: fix isin with nans and large arrays (#36266)
(venv) ~/code/pandas (master) $ python --version
Python 3.8.0
(venv) ~/code/pandas (master) $ python -m pip install -r requirements-dev.txt
Collecting git+https://github.com/pandas-dev/pydata-sphinx-theme.git@master (from -r requirements-dev.txt (line 77))
Cloning https://github.com/pandas-dev/pydata-sphinx-theme.git (to master) to /tmp/pip-k88ybarj-build
Collecting git+https://github.com/numpy/numpydoc (from -r requirements-dev.txt (line 78))
Cloning https://github.com/numpy/numpydoc to /tmp/pip-p42nydu6-build
Collecting numpy>=1.16.5 (from -r requirements-dev.txt (line 4))
Using cached https://files.pythonhosted.org/packages/41/6e/919522a6e1d067ddb5959c5716a659a05719e2f27487695d2a539b51d66e/numpy-1.19.2-cp38-cp38-manylinux1_x86_64.whl
Collecting python-dateutil>=2.7.3 (from -r requirements-dev.txt (line 5))
Using cached https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl
Collecting pytz (from -r requirements-dev.txt (line 6))
Using cached https://files.pythonhosted.org/packages/4f/a4/879454d49688e2fad93e59d7d4efda580b783c745fd2ec2a3adf87b0808d/pytz-2020.1-py2.py3-none-any.whl
Collecting asv (from -r requirements-dev.txt (line 7))
Using cached https://files.pythonhosted.org/packages/46/c7/a5144ca1409a4a1a8212ebdbe4a78df7ebb3758ff44dfe97c881fc08927e/asv-0.4.2.tar.gz
Collecting cython>=0.29.21 (from -r requirements-dev.txt (line 8))
Using cached https://files.pythonhosted.org/packages/9f/05/959e78f2aeade1c9e85a7adc4c376f454ecaeb4cb6b079ca7a85684b69c1/Cython-0.29.21-cp38-cp38-manylinux1_x86_64.whl
Collecting black==19.10b0 (from -r requirements-dev.txt (line 9))
Using cached https://files.pythonhosted.org/packages/fd/bb/ad34bbc93d1bea3de086d7c59e528d4a503ac8fe318bd1fa48605584c3d2/black-19.10b0-py36-none-any.whl
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Collecting flake8-comprehensions>=3.1.0 (from -r requirements-dev.txt (line 12))
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Collecting flake8-rst<=0.7.0,>=0.6.0 (from -r requirements-dev.txt (line 13))
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Using cached https://files.pythonhosted.org/packages/d1/25/7ed95ccb07d3ce52598f5a57d002da6a18074ea8749991b10936cc20e539/isort-5.5.2-py3-none-any.whl
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Collecting gitpython (from -r requirements-dev.txt (line 17))
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Using cached https://files.pythonhosted.org/packages/63/b8/34ba32a94cb2b223b941e43b3bcab11281763b95daa8587879eec1eb9a62/Sphinx-3.2.1-py3-none-any.whl
Collecting nbconvert>=5.4.1 (from -r requirements-dev.txt (line 20))
Using cached https://files.pythonhosted.org/packages/88/0a/d50141a0db95cffaf65238bf612e1f2bc929b36cbdf0d27eba352558267b/nbconvert-6.0.3-py3-none-any.whl
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Collecting pandoc (from -r requirements-dev.txt (line 22))
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Using cached https://files.pythonhosted.org/packages/c4/f6/74ee12f734f5ab40d3f59f48aff91ce502e33e6d2223e62bbb5fdf921431/dask-2.27.0-py3-none-any.whl
Collecting toolz>=0.7.3 (from -r requirements-dev.txt (line 24))
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Collecting notebook>=5.7.5 (from -r requirements-dev.txt (line 44))
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Requirement already satisfied: pip in ./venv/lib/python3.8/site-packages (from -r requirements-dev.txt (line 45))
Collecting blosc (from -r requirements-dev.txt (line 46))
Using cached https://files.pythonhosted.org/packages/1c/89/004eeb307ba3f56fca9727f47fbde09f8ae3936a1cb0dd6b7708f846d3fd/blosc-1.9.2.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-jg1zwlgb/blosc/setup.py", line 18, in <module>
from skbuild import setup
ModuleNotFoundError: No module named 'skbuild'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-jg1zwlgb/blosc/
Expected Output
Successful installation.
Output of pd.show_versions()
N/A
Comment From: fangchenli
Maybe try pip install scikit-build
Comment From: ivanovmg
@fangchenli, thank you. But it did not fully help in my case.
Now I get the new error:
Collecting pyqt5>=5.9.2 (from -r requirements-dev.txt (line 69))
Using cached https://files.pythonhosted.org/packages/1d/31/896dc3dfb6c81c70164019a6cbba6ab037e3af7653d9ca60ccc874ee4c27/PyQt5-5.15.1.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/lib/python3.8/tokenize.py", line 392, in open
buffer = _builtin_open(filename, 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pip-build-pwl1ytpw/pyqt5/setup.py'
Here is a full output. I first just tried to install from requirements, then installed scikit-build
and then ran installation from requirements again.
~/code/pandas (master) $ git log -1
commit ec8c1c4ecf1f0d375d8d1287ee5cbd456852faea (HEAD -> master, upstream/master)
Author: Richard Shadrach <45562402+rhshadrach@users.noreply.github.com>
Date: Tue Oct 6 23:38:49 2020 -0400
TYP: selection and groups type-hinting in groupby (#36643)
* TYP: selection and groups type-hinting in groupby
* PrettyDict -> Dict
* Cleanup from merge
~/code/pandas (master) $ python3.8 -m venv venv
~/code/pandas (master) $ source venv/bin/activate
(venv) ~/code/pandas (master) $ python --version
Python 3.8.0
(venv) ~/code/pandas (master) $ which python
/home/maxim/code/pandas/venv/bin/python
(venv) ~/code/pandas (master) $ python -m pip install -r requirements-dev.txt
Collecting git+https://github.com/pandas-dev/pydata-sphinx-theme.git@master (from -r requirements-dev.txt (line 80))
Cloning https://github.com/pandas-dev/pydata-sphinx-theme.git (to master) to /tmp/pip-dn1__hon-build
Collecting git+https://github.com/numpy/numpydoc (from -r requirements-dev.txt (line 81))
Cloning https://github.com/numpy/numpydoc to /tmp/pip-mv19duxz-build
Collecting numpy>=1.16.5 (from -r requirements-dev.txt (line 4))
Using cached https://files.pythonhosted.org/packages/41/6e/919522a6e1d067ddb5959c5716a659a05719e2f27487695d2a539b51d66e/numpy-1.19.2-cp38-cp38-manylinux1_x86_64.whl
Collecting python-dateutil>=2.7.3 (from -r requirements-dev.txt (line 5))
Using cached https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl
Collecting pytz (from -r requirements-dev.txt (line 6))
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Using cached https://files.pythonhosted.org/packages/49/b1/d2d4b30ee81ea5cb7aee5ba3591752a637fdc49d0a42fa9683874b60b9fb/pandoc-1.0.2.tar.gz
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Traceback (most recent call last):
File "", line 1, in
File "/tmp/pip-build-sae2736s/blosc/setup.py", line 18, in
from skbuild import setup
ModuleNotFoundError: No module named 'skbuild'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-sae2736s/blosc/
(venv) ~/code/pandas (master) $ python -m pip install scikit-build
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(venv) ~/code/pandas (master) $ python -m pip install -r requirements-dev.txt
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Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "", line 1, in
File "/usr/lib/python3.8/tokenize.py", line 392, in open
buffer = _builtin_open(filename, 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pip-build-pwl1ytpw/pyqt5/setup.py'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-pwl1ytpw/pyqt5/
(venv) ~/code/pandas (master) $
Comment From: jbrockmendel
@ivanovmg has this resolved itself in the interim? you've been making solid PRs, so it can't have slowed you down too much
Comment From: ivanovmg
@ivanovmg has this resolved itself in the interim? you've been making solid PRs, so it can't have slowed you down too much
Let me check it once again on Linux computer today.
I mostly work from windows computer with docker container, so I have to deal with linux machine only occasionally.
Comment From: ivanovmg
I checked today after updating pip and pulling the newest pandas master.
Still cannot install via pip.
Successfully built asv black pandoc pyyaml odfpy pydata-sphinx-theme numpydoc pandocfilters locket sgmllib3k jsondiff et-xmlfile thrift future wrapt pyrsistent
Failed to build blosc bottleneck fastparquet python-snappy
ERROR: Could not build wheels for blosc, bottleneck which use PEP 517 and cannot be installed directly
Not a big deal for me actually as I can still try conda.
But in general, did anybody else experience problems with installing dev environment via pip?
Full output was large, could not even fit.
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Building wheels for collected packages: asv, black, pandoc, pyyaml, blosc, bottleneck, odfpy, fastparquet, python-snappy, pydata-sphinx-theme, numpydoc, pandocfilters, locket, sgmllib3k, jsondiff, et-xmlfile, thrift, future, wrapt, pyrsistent
Building wheel for asv (setup.py) ... done
Created wheel for asv: filename=asv-0.4.2-py3-none-any.whl size=287711 sha256=0a1fec8db4e7682e41204215e05dd1371d11be89e7864e90a84ab737094037b8
Stored in directory: /home/maxim/.cache/pip/wheels/ba/74/bb/3a26169619d1367d890560b7a965b7c75f09c4237549d4e7e7
Building wheel for black (PEP 517) ... done
Created wheel for black: filename=black-20.8b1-py3-none-any.whl size=124186 sha256=4436324aa9c8b5b52017b17d0efe5ff2872bcbaa25621b5cdff40648d4588955
Stored in directory: /home/maxim/.cache/pip/wheels/95/a4/59/10cd5378d52f92cdb45025f040e4686e10ae5217961c25fd66
Building wheel for pandoc (setup.py) ... done
Created wheel for pandoc: filename=pandoc-1.0.2-py3-none-any.whl size=19993 sha256=8c394e5a7d5e3c53868a69ead6387b6697e26f347fe951baa977c4c276a59f4f
Stored in directory: /home/maxim/.cache/pip/wheels/a4/b9/34/3e82b9444401c2199d721240a388499a262d2e2ad37f6f3fa7
Building wheel for pyyaml (setup.py) ... done
Created wheel for pyyaml: filename=PyYAML-5.3.1-cp38-cp38-linux_x86_64.whl size=44619 sha256=2f1a78ff488161a9b5857cff6685f3558f8082b046c9dc9640775e60c40b27d0
Stored in directory: /home/maxim/.cache/pip/wheels/13/90/db/290ab3a34f2ef0b5a0f89235dc2d40fea83e77de84ed2dc05c
Building wheel for blosc (PEP 517) ... error
ERROR: Command errored out with exit status 1:
command: /home/maxim/code/pandas/venv/bin/python /home/maxim/code/pandas/venv/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /tmp/tmp07fjxsm4
cwd: /tmp/pip-install-o0cxnije/blosc
Complete output (112 lines):
Not searching for unused variables given on the command line.
-- The C compiler identification is GNU 7.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- The CXX compiler identification is GNU 7.5.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/pip-install-o0cxnije/blosc/_cmake_test_compile/build
-- The C compiler identification is GNU 7.5.0
-- The CXX compiler identification is GNU 7.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PythonInterp: /home/maxim/code/pandas/venv/bin/python (found version "3.8")
-- Found PythonLibs: libpython3.8.a
Configuring for Blosc version: 1.20.1
-- Using LZ4 internal sources.
-- Using zlib internal sources.
-- Using ZSTD internal sources.
-- Building for system processor x86_64
-- Detected that BLOSC is used a subproject.
-- Adding run-time support for SSE2
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test Weak Link MODULE -> SHARED (gnu_ld_ignore) - Success
_modinit_prefix:PyInit_
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
BLOSC_DIR
SKBUILD
-- Build files have been written to: /tmp/pip-install-o0cxnije/blosc/_skbuild/linux-x86_64-3.8/cmake-build
[1/60] Building C object CMakeFiles/blosc_extension.dir/blosc/blosc_extension.c.o
FAILED: CMakeFiles/blosc_extension.dir/blosc/blosc_extension.c.o
/usr/bin/cc -Dblosc_extension_EXPORTS -I/usr/include/python3.8 -I../../../c-blosc/blosc -I../../../c-blosc/internal-complibs/lz4-1.9.2 -I../../../c-blosc/internal-complibs/zlib-1.2.8 -I../../../c-blosc/internal-complibs/zstd-1.4.5 -I../../../c-blosc/internal-complibs/zstd-1.4.5/common -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/blosc_extension.dir/blosc/blosc_extension.c.o -MF CMakeFiles/blosc_extension.dir/blosc/blosc_extension.c.o.d -o CMakeFiles/blosc_extension.dir/blosc/blosc_extension.c.o -c ../../../blosc/blosc_extension.c
../../../blosc/blosc_extension.c:12:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
[2/60] Building C object c-blosc/blosc/CMakeFiles/blosc_static.dir/shuffle-generic.c.o
[3/60] Building C object c-blosc/blosc/CMakeFiles/blosc_static.dir/fastcopy.c.o
[4/60] Building C object c-blosc/blosc/CMakeFiles/blosc_static.dir/blosclz.c.o
[5/60] Building C object c-blosc/blosc/CMakeFiles/blosc_static.dir/shuffle-sse2.c.o
[6/60] Building C object c-blosc/blosc/CMakeFiles/blosc_static.dir/blosc.c.o
ninja: build stopped: subcommand failed.
File "/tmp/pip-build-env-kiphtqdp/overlay/lib/python3.8/site-packages/skbuild/setuptools_wrap.py", line 589, in setup
cmkr.make(make_args, env=env)
File "/tmp/pip-build-env-kiphtqdp/overlay/lib/python3.8/site-packages/skbuild/cmaker.py", line 496, in make
raise SKBuildError(
--------------------------------------------------------------------------------
-- Trying "Ninja" generator
--------------------------------
---------------------------
----------------------
-----------------
------------
-------
--
--
-------
------------
-----------------
----------------------
---------------------------
--------------------------------
-- Trying "Ninja" generator - success
--------------------------------------------------------------------------------
Configuring Project
Working directory:
/tmp/pip-install-o0cxnije/blosc/_skbuild/linux-x86_64-3.8/cmake-build
Command:
cmake /tmp/pip-install-o0cxnije/blosc -G Ninja -DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-install-o0cxnije/blosc/_skbuild/linux-x86_64-3.8/cmake-install -DPYTHON_EXECUTABLE:FILEPATH=/home/maxim/code/pandas/venv/bin/python -DPYTHON_VERSION_STRING:STRING=3.8.0 -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.8 -DPYTHON_LIBRARY:FILEPATH=libpython3.8.a -DSKBUILD:BOOL=TRUE -DCMAKE_MODULE_PATH:PATH=/tmp/pip-build-env-kiphtqdp/overlay/lib/python3.8/site-packages/skbuild/resources/cmake -DBLOSC_DIR:PATH= -DDEACTIVATE_SSE2:BOOL=OFF -DDEACTIVATE_AVX2:BOOL=ON -DDEACTIVATE_LZ4:BOOL=OFF -DDEACTIVATE_SNAPPY:BOOL=ON -DDEACTIVATE_ZLIB:BOOL=OFF -DDEACTIVATE_ZSTD:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release
Traceback (most recent call last):
An error occurred while building with CMake.
Command:
cmake --build . --target install --config Release --
Source directory:
/tmp/pip-install-o0cxnije/blosc
Working directory:
/tmp/pip-install-o0cxnije/blosc/_skbuild/linux-x86_64-3.8/cmake-build
Please see CMake's output for more information.
----------------------------------------
ERROR: Failed building wheel for blosc
Building wheel for bottleneck (PEP 517) ... error
ERROR: Command errored out with exit status 1:
command: /home/maxim/code/pandas/venv/bin/python /home/maxim/code/pandas/venv/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /tmp/tmp3zp49h3r
cwd: /tmp/pip-install-o0cxnije/bottleneck
Complete output (85 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/bottleneck
copying bottleneck/_version.py -> build/lib.linux-x86_64-3.8/bottleneck
copying bottleneck/_pytesttester.py -> build/lib.linux-x86_64-3.8/bottleneck
copying bottleneck/__init__.py -> build/lib.linux-x86_64-3.8/bottleneck
creating build/lib.linux-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/nonreduce_test.py -> build/lib.linux-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/reduce_test.py -> build/lib.linux-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/nonreduce_axis_test.py -> build/lib.linux-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/scalar_input_test.py -> build/lib.linux-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/memory_test.py -> build/lib.linux-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/input_modification_test.py -> build/lib.linux-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/list_input_test.py -> build/lib.linux-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/__init__.py -> build/lib.linux-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/util.py -> build/lib.linux-x86_64-3.8/bottleneck/tests
copying bottleneck/tests/move_test.py -> build/lib.linux-x86_64-3.8/bottleneck/tests
creating build/lib.linux-x86_64-3.8/bottleneck/benchmark
copying bottleneck/benchmark/bench_detailed.py -> build/lib.linux-x86_64-3.8/bottleneck/benchmark
copying bottleneck/benchmark/bench.py -> build/lib.linux-x86_64-3.8/bottleneck/benchmark
copying bottleneck/benchmark/__init__.py -> build/lib.linux-x86_64-3.8/bottleneck/benchmark
copying bottleneck/benchmark/autotimeit.py -> build/lib.linux-x86_64-3.8/bottleneck/benchmark
creating build/lib.linux-x86_64-3.8/bottleneck/slow
copying bottleneck/slow/reduce.py -> build/lib.linux-x86_64-3.8/bottleneck/slow
copying bottleneck/slow/nonreduce_axis.py -> build/lib.linux-x86_64-3.8/bottleneck/slow
copying bottleneck/slow/nonreduce.py -> build/lib.linux-x86_64-3.8/bottleneck/slow
copying bottleneck/slow/move.py -> build/lib.linux-x86_64-3.8/bottleneck/slow
copying bottleneck/slow/__init__.py -> build/lib.linux-x86_64-3.8/bottleneck/slow
creating build/lib.linux-x86_64-3.8/bottleneck/src
copying bottleneck/src/bn_config.py -> build/lib.linux-x86_64-3.8/bottleneck/src
copying bottleneck/src/bn_template.py -> build/lib.linux-x86_64-3.8/bottleneck/src
copying bottleneck/src/__init__.py -> build/lib.linux-x86_64-3.8/bottleneck/src
UPDATING build/lib.linux-x86_64-3.8/bottleneck/_version.py
set build/lib.linux-x86_64-3.8/bottleneck/_version.py to '1.3.2'
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;
}
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c _configtest.c -o _configtest.o
success!
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-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c _configtest.c -o _configtest.o
success!
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
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-build-env-0l6k91ae/overlay/lib/python3.8/site-packages/numpy/core/include -I/home/maxim/code/pandas/venv/include -I/usr/include/python3.8 -Ibottleneck/src -c bottleneck/src/reduce.c -o build/temp.linux-x86_64-3.8/bottleneck/src/reduce.o -O2
In file included from bottleneck/src/reduce.c:3:0:
bottleneck/src/bottleneck.h:6:10: fatal error: Python.h: No such file or directory
#include
^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for bottleneck
Building wheel for odfpy (setup.py) ... done
Created wheel for odfpy: filename=odfpy-1.4.1-py2.py3-none-any.whl size=160692 sha256=2710b9aef46a3f83366eb66f4165e8e5a380d179edc21d3d5db70539a6cc9bdb
Stored in directory: /home/maxim/.cache/pip/wheels/ea/af/da/2bdd7308f7b334429a558df1e36d31864cd19c07ede92ddf0e
Building wheel for fastparquet (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/maxim/code/pandas/venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o0cxnije/fastparquet/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o0cxnije/fastparquet/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-8rd1bywr
cwd: /tmp/pip-install-o0cxnije/fastparquet/
Complete output (69 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/core.py -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/encoding.py -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/converted_types.py -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/schema.py -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/compression.py -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/writer.py -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/api.py -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/__init__.py -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/dataframe.py -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/util.py -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/thrift_structures.py -> build/lib.linux-x86_64-3.8/fastparquet
running egg_info
writing fastparquet.egg-info/PKG-INFO
writing dependency_links to fastparquet.egg-info/dependency_links.txt
writing requirements to fastparquet.egg-info/requires.txt
writing top-level names to fastparquet.egg-info/top_level.txt
reading manifest file 'fastparquet.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'docs/_build'
writing manifest file 'fastparquet.egg-info/SOURCES.txt'
copying fastparquet/parquet.thrift -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/speedups.c -> build/lib.linux-x86_64-3.8/fastparquet
copying fastparquet/speedups.pyx -> build/lib.linux-x86_64-3.8/fastparquet
creating build/lib.linux-x86_64-3.8/fastparquet/benchmarks
copying fastparquet/benchmarks/columns.py -> build/lib.linux-x86_64-3.8/fastparquet/benchmarks
creating build/lib.linux-x86_64-3.8/fastparquet/parquet_thrift
copying fastparquet/parquet_thrift/__init__.py -> build/lib.linux-x86_64-3.8/fastparquet/parquet_thrift
creating build/lib.linux-x86_64-3.8/fastparquet/parquet_thrift/parquet
copying fastparquet/parquet_thrift/parquet/__init__.py -> build/lib.linux-x86_64-3.8/fastparquet/parquet_thrift/parquet
copying fastparquet/parquet_thrift/parquet/constants.py -> build/lib.linux-x86_64-3.8/fastparquet/parquet_thrift/parquet
copying fastparquet/parquet_thrift/parquet/ttypes.py -> build/lib.linux-x86_64-3.8/fastparquet/parquet_thrift/parquet
creating build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/__init__.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/bitpack -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/hybrid -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/read_data -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/rle -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_api.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_aroundtrips.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_compression.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_converted_types.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_dataframe.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_encoding.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_output.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_partition_filters_specialstrings.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_read.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_schema.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_speedups.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_thrift_structures.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_util.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/test_with_n.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/util.py -> build/lib.linux-x86_64-3.8/fastparquet/test
copying fastparquet/test/uvarint -> build/lib.linux-x86_64-3.8/fastparquet/test
running build_ext
building 'fastparquet.speedups' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/fastparquet
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/maxim/code/pandas/venv/include -I/usr/include/python3.8 -I/tmp/pip-install-o0cxnije/fastparquet/.eggs/numpy-1.19.3-py3.8-linux-x86_64.egg/numpy/core/include -c fastparquet/speedups.c -o build/temp.linux-x86_64-3.8/fastparquet/speedups.o
fastparquet/speedups.c:17:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for fastparquet
Running setup.py clean for fastparquet
Building wheel for python-snappy (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/maxim/code/pandas/venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-o0cxnije/python-snappy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-o0cxnije/python-snappy/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-dfo9_zvo
cwd: /tmp/pip-install-o0cxnije/python-snappy/
Complete output (25 lines):
/usr/lib/python3.8/distutils/dist.py:274: UserWarning: Unknown distribution option: 'cffi_modules'
warnings.warn(msg)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/snappy
copying snappy/snappy_cffi.py -> build/lib.linux-x86_64-3.8/snappy
copying snappy/__main__.py -> build/lib.linux-x86_64-3.8/snappy
copying snappy/snappy_cffi_builder.py -> build/lib.linux-x86_64-3.8/snappy
copying snappy/snappy_formats.py -> build/lib.linux-x86_64-3.8/snappy
copying snappy/snappy.py -> build/lib.linux-x86_64-3.8/snappy
copying snappy/hadoop_snappy.py -> build/lib.linux-x86_64-3.8/snappy
copying snappy/__init__.py -> build/lib.linux-x86_64-3.8/snappy
running build_ext
building 'snappy._snappy' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/snappy
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/maxim/code/pandas/venv/include -I/usr/include/python3.8 -c snappy/snappymodule.cc -o build/temp.linux-x86_64-3.8/snappy/snappymodule.o
snappy/snappymodule.cc:28:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for python-snappy
Running setup.py clean for python-snappy
Building wheel for pydata-sphinx-theme (setup.py) ... done
Created wheel for pydata-sphinx-theme: filename=pydata_sphinx_theme-0.4.2.dev0-py3-none-any.whl size=2145830 sha256=c64b5f4a90742bd32a918ce4e3a37349d13497c7b2ae3834509e324d1f99cbe0
Stored in directory: /tmp/pip-ephem-wheel-cache-t_g2ub21/wheels/bd/4d/c3/43e3472375e64c05bb8726010963c99aba1c607ddf32d0c006
Building wheel for numpydoc (setup.py) ... done
Created wheel for numpydoc: filename=numpydoc-1.2.dev0-py3-none-any.whl size=48542 sha256=a8abdf04e48adeabc46d0fd2cb7f1cbf2e284bc8b39044470e2e9fc852644bde
Stored in directory: /tmp/pip-ephem-wheel-cache-t_g2ub21/wheels/ad/d8/7e/f66bded8b4746dbe3ee52c5cd881a5a5f1c2c221d6fe7a783f
Building wheel for pandocfilters (setup.py) ... done
Created wheel for pandocfilters: filename=pandocfilters-1.4.3-py3-none-any.whl size=7991 sha256=abc0862d51cdf7036837d3cf800f0a951dd30632747a4cde7a53c8cad9a03d56
Stored in directory: /home/maxim/.cache/pip/wheels/fc/39/52/8d6f3cec1cca4ceb44d658427c35711b19d89dbc4914af657f
Building wheel for locket (setup.py) ... done
Created wheel for locket: filename=locket-0.2.0-py3-none-any.whl size=4040 sha256=5e6fe006701cdbe91e72b772e18973c5950b910edb0a8103fa849de4e6209d22
Stored in directory: /home/maxim/.cache/pip/wheels/78/25/55/fd7749af1f37730049bf1c0c0f4efd755c4ab1399f29578436
Building wheel for sgmllib3k (setup.py) ... done
Created wheel for sgmllib3k: filename=sgmllib3k-1.0.0-py3-none-any.whl size=6066 sha256=a9fee821f888baf9820864ff3f4ccbde15aa05cd7fdd53d778f99b818695630e
Stored in directory: /home/maxim/.cache/pip/wheels/83/63/2f/117884c3b19d46b64d3d61690333aa80c88dc14050e269c546
Building wheel for jsondiff (setup.py) ... done
Created wheel for jsondiff: filename=jsondiff-1.2.0-py3-none-any.whl size=6540 sha256=8948ccefe88b2f243f35c3b2d543a97327a6dadc0aa501ea76a640345bb30186
Stored in directory: /home/maxim/.cache/pip/wheels/e0/d6/20/2604c7c4e34cc466610fbb736b96042cbc42919291a76ebaee
Building wheel for et-xmlfile (setup.py) ... done
Created wheel for et-xmlfile: filename=et_xmlfile-1.0.1-py3-none-any.whl size=8917 sha256=66192b37465be6317e3f58601ca2f7d77a25a67b60a2b3daac8c6ce6402b07ce
Stored in directory: /home/maxim/.cache/pip/wheels/6e/df/38/abda47b884e3e25f9f9b6430e5ce44c47670758a50c0c51759
Building wheel for thrift (setup.py) ... done
Created wheel for thrift: filename=thrift-0.13.0-py3-none-any.whl size=155526 sha256=c34c6363c36bd716efbae691cb2e7bcb7207fc8f35bf30f23c332d8e8e34ec43
Stored in directory: /home/maxim/.cache/pip/wheels/0a/52/7e/8054b57725b8f2b9ddbaacb81b271b939681cc03f8231e6ebc
Building wheel for future (setup.py) ... done
Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=c9eca3ed343d6dbd0023c8e249e2eb8b65d79ba29251c4ba1d06e4e994d0ffa2
Stored in directory: /home/maxim/.cache/pip/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4
Building wheel for wrapt (setup.py) ... done
Created wheel for wrapt: filename=wrapt-1.12.1-py3-none-any.whl size=19552 sha256=ebec8a3e493e6f846b7b7cfd2391307b76720a94ee2311ac1a72f18119144fd0
Stored in directory: /home/maxim/.cache/pip/wheels/5f/fd/9e/b6cf5890494cb8ef0b5eaff72e5d55a70fb56316007d6dfe73
Building wheel for pyrsistent (setup.py) ... done
Created wheel for pyrsistent: filename=pyrsistent-0.17.3-cp38-cp38-linux_x86_64.whl size=55874 sha256=eb566ae8baaa88925d2ea25b499f510ec9dd73dfe9e9248a423f1cd3aebc5285
Stored in directory: /home/maxim/.cache/pip/wheels/3d/22/08/7042eb6309c650c7b53615d5df5cc61f1ea9680e7edd3a08d2
Successfully built asv black pandoc pyyaml odfpy pydata-sphinx-theme numpydoc pandocfilters locket sgmllib3k jsondiff et-xmlfile thrift future wrapt pyrsistent
Failed to build blosc bottleneck fastparquet python-snappy
ERROR: Could not build wheels for blosc, bottleneck which use PEP 517 and cannot be installed directly
Comment From: jbrockmendel
i think for blosc you need "brew install snappy" / "apt-get install snappy"
Comment From: MarcoGorelli
i think for blosc you need "brew install snappy" / "apt-get install snappy"
I don't know if it's the same issue, but sudo apt-get install libsnappy-dev
worked for me for installing snappy
Comment From: MarcoGorelli
@ivanovmg Someone at PyDataGlobal had the same issue and also got it resolved with
sudo apt-get install libsnappy-dev
If you could check it works for you then perhaps we could add it to the docs
Comment From: MarcoGorelli
closing for now, I think this may not be relevant anymore, I've built the environment using pip in linux fine. if anyone reports anything new we can reopen