ERROR: Could not build wheels for rna-majiq

378 views

Skip to first unread message

Hannah

unread,

Sep 29, 2022, 11:04:17 AM9/29/22

to majiq_voila

Hello,

I am receiving the following when I try to install Majiq using python 3.8 on a mac:

building 'rna_majiq.src.build' extension

creating build/temp.macosx-10.9-x86_64-cpython-38

creating build/temp.macosx-10.9-x86_64-cpython-38/rna_majiq

creating build/temp.macosx-10.9-x86_64-cpython-38/rna_majiq/src

creating build/temp.macosx-10.9-x86_64-cpython-38/rna_majiq/src/internals

gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -DNPY_NO_DEPRECATED_API=0 -Irna_majiq/src/internals -Irna_majiq/c -I/private/var/folders/qt/c205zrcj765bzmxc4zbrmy3r0000gn/T/pip-build-env-8yva3onb/overlay/lib/python3.8/site-packages/numpy/core/include -I/usr/local/include -I/Users/Hannah/env/include -I/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -c rna_majiq/src/build.cpp -o build/temp.macosx-10.9-x86_64-cpython-38/rna_majiq/src/build.o -fopenmp

clang: error: unsupported option '-fopenmp'

/private/var/folders/qt/c205zrcj765bzmxc4zbrmy3r0000gn/T/pip-build-env-8yva3onb/overlay/lib/python3.8/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'rna_majiq.src.internals.boost.type_traits' as data is deprecated, please list it in `packages`.

############################

# Package would be ignored #

############################

Python recognizes 'rna_majiq.src.internals.boost.type_traits' as an importable package,

but it is not listed in the `packages` configuration of setuptools.

'rna_majiq.src.internals.boost.type_traits' has been automatically added to the distribution only

because it may contain data files, but this behavior is likely to change

in future versions of setuptools (and therefore is considered deprecated).

Please make sure that 'rna_majiq.src.internals.boost.type_traits' is included as a package by using

the `packages` configuration field or the proper discovery methods

(for example by using `find_namespace_packages(...)`/`find_namespace:`

instead of `find_packages(...)`/`find:`).

You can read more about "package discovery" and "data files" on setuptools

documentation page.

check.warn(importable)

/private/var/folders/qt/c205zrcj765bzmxc4zbrmy3r0000gn/T/pip-build-env-8yva3onb/overlay/lib/python3.8/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'rna_majiq.src.internals.boost.type_traits.detail' as data is deprecated, please list it in `packages`.

############################

# Package would be ignored #

############################

Python recognizes 'rna_majiq.src.internals.boost.type_traits.detail' as an importable package,

but it is not listed in the `packages` configuration of setuptools.

'rna_majiq.src.internals.boost.type_traits.detail' has been automatically added to the distribution only

because it may contain data files, but this behavior is likely to change

in future versions of setuptools (and therefore is considered deprecated).

Please make sure that 'rna_majiq.src.internals.boost.type_traits.detail' is included as a package by using

the `packages` configuration field or the proper discovery methods

(for example by using `find_namespace_packages(...)`/`find_namespace:`

instead of `find_packages(...)`/`find:`).

You can read more about "package discovery" and "data files" on setuptools

documentation page.

check.warn(importable)

/private/var/folders/qt/c205zrcj765bzmxc4zbrmy3r0000gn/T/pip-build-env-8yva3onb/overlay/lib/python3.8/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'rna_majiq.src.internals.boost.typeof' as data is deprecated, please list it in `packages`.

############################

# Package would be ignored #

############################

Python recognizes 'rna_majiq.src.internals.boost.typeof' as an importable package,

but it is not listed in the `packages` configuration of setuptools.

'rna_majiq.src.internals.boost.typeof' has been automatically added to the distribution only

because it may contain data files, but this behavior is likely to change

in future versions of setuptools (and therefore is considered deprecated).

Please make sure that 'rna_majiq.src.internals.boost.typeof' is included as a package by using

the `packages` configuration field or the proper discovery methods

(for example by using `find_namespace_packages(...)`/`find_namespace:`

instead of `find_packages(...)`/`find:`).

You can read more about "package discovery" and "data files" on setuptools

documentation page.

check.warn(importable)

/private/var/folders/qt/c205zrcj765bzmxc4zbrmy3r0000gn/T/pip-build-env-8yva3onb/overlay/lib/python3.8/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'rna_majiq.src.internals.boost.typeof.dmc' as data is deprecated, please list it in `packages`.

############################

# Package would be ignored #

############################

Python recognizes 'rna_majiq.src.internals.boost.typeof.dmc' as an importable package,

but it is not listed in the `packages` configuration of setuptools.

'rna_majiq.src.internals.boost.typeof.dmc' has been automatically added to the distribution only

because it may contain data files, but this behavior is likely to change

in future versions of setuptools (and therefore is considered deprecated).

Please make sure that 'rna_majiq.src.internals.boost.typeof.dmc' is included as a package by using

the `packages` configuration field or the proper discovery methods

(for example by using `find_namespace_packages(...)`/`find_namespace:`

instead of `find_packages(...)`/`find:`).

You can read more about "package discovery" and "data files" on setuptools

documentation page.

check.warn(importable)

/private/var/folders/qt/c205zrcj765bzmxc4zbrmy3r0000gn/T/pip-build-env-8yva3onb/overlay/lib/python3.8/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'rna_majiq.src.internals.boost.typeof.msvc' as data is deprecated, please list it in `packages`.

############################

# Package would be ignored #

############################

Python recognizes 'rna_majiq.src.internals.boost.typeof.msvc' as an importable package,

but it is not listed in the `packages` configuration of setuptools.

'rna_majiq.src.internals.boost.typeof.msvc' has been automatically added to the distribution only

because it may contain data files, but this behavior is likely to change

in future versions of setuptools (and therefore is considered deprecated).

Please make sure that 'rna_majiq.src.internals.boost.typeof.msvc' is included as a package by using

the `packages` configuration field or the proper discovery methods

(for example by using `find_namespace_packages(...)`/`find_namespace:`

instead of `find_packages(...)`/`find:`).

You can read more about "package discovery" and "data files" on setuptools

documentation page.

check.warn(importable)

/private/var/folders/qt/c205zrcj765bzmxc4zbrmy3r0000gn/T/pip-build-env-8yva3onb/overlay/lib/python3.8/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'rna_majiq.src.internals.boost.utility' as data is deprecated, please list it in `packages`.

############################

# Package would be ignored #

############################

Python recognizes 'rna_majiq.src.internals.boost.utility' as an importable package,

but it is not listed in the `packages` configuration of setuptools.

'rna_majiq.src.internals.boost.utility' has been automatically added to the distribution only

because it may contain data files, but this behavior is likely to change

in future versions of setuptools (and therefore is considered deprecated).

Please make sure that 'rna_majiq.src.internals.boost.utility' is included as a package by using

the `packages` configuration field or the proper discovery methods

(for example by using `find_namespace_packages(...)`/`find_namespace:`

instead of `find_packages(...)`/`find:`).

You can read more about "package discovery" and "data files" on setuptools

documentation page.

check.warn(importable)

/private/var/folders/qt/c205zrcj765bzmxc4zbrmy3r0000gn/T/pip-build-env-8yva3onb/overlay/lib/python3.8/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'rna_majiq.src.internals.boost.utility.detail' as data is deprecated, please list it in `packages`.

############################

# Package would be ignored #

############################

Python recognizes 'rna_majiq.src.internals.boost.utility.detail' as an importable package,

but it is not listed in the `packages` configuration of setuptools.

'rna_majiq.src.internals.boost.utility.detail' has been automatically added to the distribution only

because it may contain data files, but this behavior is likely to change

in future versions of setuptools (and therefore is considered deprecated).

Please make sure that 'rna_majiq.src.internals.boost.utility.detail' is included as a package by using

the `packages` configuration field or the proper discovery methods

(for example by using `find_namespace_packages(...)`/`find_namespace:`

instead of `find_packages(...)`/`find:`).

You can read more about "package discovery" and "data files" on setuptools

documentation page.

check.warn(importable)

/private/var/folders/qt/c205zrcj765bzmxc4zbrmy3r0000gn/T/pip-build-env-8yva3onb/overlay/lib/python3.8/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'rna_majiq.src.internals.stats' as data is deprecated, please list it in `packages`.

############################

# Package would be ignored #

############################

Python recognizes 'rna_majiq.src.internals.stats' as an importable package,

but it is not listed in the `packages` configuration of setuptools.

'rna_majiq.src.internals.stats' has been automatically added to the distribution only

because it may contain data files, but this behavior is likely to change

in future versions of setuptools (and therefore is considered deprecated).

Please make sure that 'rna_majiq.src.internals.stats' is included as a package by using

the `packages` configuration field or the proper discovery methods

(for example by using `find_namespace_packages(...)`/`find_namespace:`

instead of `find_packages(...)`/`find:`).

You can read more about "package discovery" and "data files" on setuptools

documentation page.

check.warn(importable)

warning: rna_majiq/src/build.pyx:282:12: Unsigned index type not allowed before OpenMP 3.0

error: command '/usr/bin/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 rna-majiq

Building wheel for rna-voila (pyproject.toml) ... done

Created wheel for rna-voila: filename=rna_voila-2.4.dev3+g85d07819-py3-none-any.whl size=2451727 sha256=06e06440ca509c7a7c3c9e3e61da701cb80357a71efd008d6f6db2bb4938c6ce

Stored in directory: /private/var/folders/qt/c205zrcj765bzmxc4zbrmy3r0000gn/T/pip-ephem-wheel-cache-7uai2rtw/wheels/a3/5a/fd/b20bffa3ace864501b03a3d0d8030972d8d6b443ea114c36c5

Successfully built rna-majiq-meta rna-voila

Failed to build rna-majiq

ERROR: Could not build wheels for rna-majiq, which is required to install pyproject.toml-based projects

Does anyone know what type of issue this might be where it cannot build rna-majiq?

Thanks!

San Jewell

unread,

Sep 29, 2022, 11:40:20 AM9/29/22

to majiq_voila

Hi Hannah,

This is a problem with the OSX clang compiler. It does not support automatic multithreading (openmp) so you will need to use gcc instead. I've documented this in a few of the other threads as well. Basically you need to.

-install gcc suite, which comes with binaries gcc and g++

-before running the majiq install command, set environment variables C=... and CXX=... to point to the path where gcc and g++ are installed.

I believe on mac OSX you can install gcc with something like $ brew install gcc ; and then to set the environment, do something like:

$ export C=`which gcc`

and

$ export CXX=`which g++`

Then try to run majiq install command again.l

Let me know if you have success now!

Thanks.

Reply all

Reply to author

Forward

0 new messages