MAJIQ installation failed with error related to h5py

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Xiao Lei

unread,

Jun 29, 2024, 8:19:35 PM6/29/24

to Biociphers

Hi, All,

I tried to install MAJIQ on MacOS with an M3 chip with the command "pip install git+https://bitbucket.org/biociphers/majiq_academic.git". However, it failed with the error below:

Building h5py requires pkg-config unless the HDF5 path is explicitly specified using the environment variable HDF5_DIR. For more information and details, see https://docs.h5py.org/en/stable/build.html#custom-installation

error: pkg-config probably not installed: FileNotFoundError(2, 'No such file or directory')

[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

ERROR: Failed building wheel for h5py

Successfully built rna_majiq_meta rna-voila

Failed to build rna-majiq h5py

ERROR: Could not build wheels for rna-majiq, h5py, which is required to install pyproject.toml-based projects

I would appreciate any input on how to fix this problem. By the way, is there a way to install MAJIQ through Conda, which usually offers easy installations?

Thanks,

Xiao

San Jewell

unread,

Jul 2, 2024, 10:34:01 AM7/2/24

to Biociphers

Hi Xiao,

As the link recommends, this is a problem with HDF5 development headers missing on your system: https://docs.h5py.org/en/stable/build.html#custom-installation

There are many ways to go about fixing this. You may try creating a conda environment and using their package manager to install hdf5 first if you wish. You can also use brew to install hdf5 prior to installing majiq. If nothing else works you can also download and build hdf5 manually. I do not have an OSX machine with M3 to provide you with the exact commands, but as long as you can get to the point of "pip install h5py" working, then you should be good to install majiq.

Let us know if you find a method that works for you.

-San

X L

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Jul 12, 2024, 9:04:31 PM7/12/24

to Biociphers

Hi, San,

Thanks for your suggestions. HDF5 problem solved, but another error prevented me from installing Majiq on MacOS with a M3 chip. The error indicates the psutil building failed (ERROR: Failed building wheel for psutil). The detailed error message is attached at the end.

Xiao

(base) xiaolei@Xiaos-Laptop ~ % python3 -m venv env

(base) xiaolei@Xiaos-Laptop ~ % source env/bin/activate

(env) (base) xiaolei@Xiaos-Laptop ~ % export CC=/opt/homebrew/bin/gcc-14

(env) (base) xiaolei@Xiaos-Laptop ~ % export CXX=/opt/homebrew/bin/g++-14

(env) (base) xiaolei@Xiaos-Laptop ~ % pip install git+https://bitbucket.org/biociphers/majiq_academic.git#subdirectory=voila

Collecting git+https://bitbucket.org/biociphers/majiq_academic.git#subdirectory=voila

Cloning https://bitbucket.org/biociphers/majiq_academic.git to /private/var/folders/pq/fd3619297mn8j__5dqyrhpzw0000gn/T/pip-req-build-1ac4znhm

Running command git clone --filter=blob:none --quiet https://bitbucket.org/biociphers/majiq_academic.git /private/var/folders/pq/fd3619297mn8j__5dqyrhpzw0000gn/T/pip-req-build-1ac4znhm

warning: filtering not recognized by server, ignoring

Resolved https://bitbucket.org/biociphers/majiq_academic.git to commit 8ff62a93f786ba8dcabd91cfe54f0c3749ccb726

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Collecting Click==7.1.2 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached click-7.1.2-py2.py3-none-any.whl.metadata (2.9 kB)

Collecting cryptography==41.0.5 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached cryptography-41.0.5-cp37-abi3-macosx_10_12_universal2.whl.metadata (5.2 kB)

Collecting Flask==1.1.4 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached Flask-1.1.4-py2.py3-none-any.whl.metadata (4.6 kB)

Collecting Flask-Session==0.3.1 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached Flask_Session-0.3.1-py2.py3-none-any.whl.metadata (900 bytes)

Collecting Flask-WTF==0.14.2 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached Flask_WTF-0.14.2-py2.py3-none-any.whl.metadata (1.8 kB)

Collecting gitdb2==2.0.6 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached gitdb2-2.0.6-py2.py3-none-any.whl.metadata (1.1 kB)

Collecting GitPython==3.0.5 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached GitPython-3.0.5-py3-none-any.whl.metadata (1.1 kB)

Collecting gtfparse==2.0.1 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached gtfparse-2.0.1-py3-none-any.whl

Collecting gunicorn==19.9.0 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached gunicorn-19.9.0-py2.py3-none-any.whl.metadata (3.4 kB)

Collecting h5py==3.11.0 (from rna_voila==2.5.7.dev1+g8ff62a93)

Downloading h5py-3.11.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (2.5 kB)

Collecting intervaltree==3.1.0 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached intervaltree-3.1.0-py2.py3-none-any.whl

Collecting itsdangerous==1.1.0 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached itsdangerous-1.1.0-py2.py3-none-any.whl.metadata (3.1 kB)

Collecting Jinja2==2.11.1 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached Jinja2-2.11.1-py2.py3-none-any.whl.metadata (3.5 kB)

Collecting MarkupSafe==1.1.1 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached MarkupSafe-1.1.1-cp312-cp312-macosx_14_0_arm64.whl

Collecting networkx==3.3 (from rna_voila==2.5.7.dev1+g8ff62a93)

Downloading networkx-3.3-py3-none-any.whl.metadata (5.1 kB)

Collecting numpy==2.0.0 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached numpy-2.0.0-cp312-cp312-macosx_14_0_arm64.whl.metadata (60 kB)

Collecting pandas==2.2.2 (from rna_voila==2.5.7.dev1+g8ff62a93)

Downloading pandas-2.2.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (19 kB)

Collecting polars==0.15.9 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached polars-0.15.9-cp37-abi3-macosx_11_0_arm64.whl.metadata (13 kB)

Collecting psutil==5.6.7 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached psutil-5.6.7.tar.gz (448 kB)

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Collecting pyarrow==16.1.0 (from rna_voila==2.5.7.dev1+g8ff62a93)

Downloading pyarrow-16.1.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (3.0 kB)

Collecting requests==2.31.0 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)

Collecting scipy==1.14.0 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached scipy-1.14.0-cp312-cp312-macosx_14_0_arm64.whl.metadata (60 kB)

Collecting six==1.14.0 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached six-1.14.0-py2.py3-none-any.whl.metadata (1.8 kB)

Collecting smmap2==2.0.5 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached smmap2-2.0.5-py2.py3-none-any.whl.metadata (4.8 kB)

Collecting tqdm==4.66.1 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached tqdm-4.66.1-py3-none-any.whl.metadata (57 kB)

Collecting waitress==1.1.0 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached waitress-1.1.0-py2.py3-none-any.whl.metadata (4.9 kB)

Collecting Werkzeug==0.16.0 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached Werkzeug-0.16.0-py2.py3-none-any.whl.metadata (4.7 kB)

Collecting WTForms==2.2.1 (from rna_voila==2.5.7.dev1+g8ff62a93)

Using cached WTForms-2.2.1-py2.py3-none-any.whl.metadata (3.8 kB)

Collecting cffi>=1.12 (from cryptography==41.0.5->rna_voila==2.5.7.dev1+g8ff62a93)

Using cached cffi-1.16.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (1.5 kB)

Collecting sortedcontainers<3.0,>=2.0 (from intervaltree==3.1.0->rna_voila==2.5.7.dev1+g8ff62a93)

Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl.metadata (10 kB)

Collecting python-dateutil>=2.8.2 (from pandas==2.2.2->rna_voila==2.5.7.dev1+g8ff62a93)

Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)

Collecting pytz>=2020.1 (from pandas==2.2.2->rna_voila==2.5.7.dev1+g8ff62a93)

Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)

Collecting tzdata>=2022.7 (from pandas==2.2.2->rna_voila==2.5.7.dev1+g8ff62a93)

Using cached tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)

Collecting charset-normalizer<4,>=2 (from requests==2.31.0->rna_voila==2.5.7.dev1+g8ff62a93)

Using cached charset_normalizer-3.3.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (33 kB)

Collecting idna<4,>=2.5 (from requests==2.31.0->rna_voila==2.5.7.dev1+g8ff62a93)

Using cached idna-3.7-py3-none-any.whl.metadata (9.9 kB)

Collecting urllib3<3,>=1.21.1 (from requests==2.31.0->rna_voila==2.5.7.dev1+g8ff62a93)

Using cached urllib3-2.2.2-py3-none-any.whl.metadata (6.4 kB)

Collecting certifi>=2017.4.17 (from requests==2.31.0->rna_voila==2.5.7.dev1+g8ff62a93)

Downloading certifi-2024.7.4-py3-none-any.whl.metadata (2.2 kB)

Collecting pycparser (from cffi>=1.12->cryptography==41.0.5->rna_voila==2.5.7.dev1+g8ff62a93)

Using cached pycparser-2.22-py3-none-any.whl.metadata (943 bytes)

Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)

Using cached cryptography-41.0.5-cp37-abi3-macosx_10_12_universal2.whl (5.4 MB)

Using cached Flask-1.1.4-py2.py3-none-any.whl (94 kB)

Using cached Flask_Session-0.3.1-py2.py3-none-any.whl (7.5 kB)

Using cached Flask_WTF-0.14.2-py2.py3-none-any.whl (14 kB)

Using cached gitdb2-2.0.6-py2.py3-none-any.whl (63 kB)

Using cached GitPython-3.0.5-py3-none-any.whl (455 kB)

Using cached gunicorn-19.9.0-py2.py3-none-any.whl (112 kB)

Downloading h5py-3.11.0-cp312-cp312-macosx_11_0_arm64.whl (2.9 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.9/2.9 MB 18.6 MB/s eta 0:00:00

Using cached itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)

Using cached Jinja2-2.11.1-py2.py3-none-any.whl (126 kB)

Downloading networkx-3.3-py3-none-any.whl (1.7 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 18.6 MB/s eta 0:00:00

Using cached numpy-2.0.0-cp312-cp312-macosx_14_0_arm64.whl (5.0 MB)

Downloading pandas-2.2.2-cp312-cp312-macosx_11_0_arm64.whl (11.3 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.3/11.3 MB 15.3 MB/s eta 0:00:00

Using cached polars-0.15.9-cp37-abi3-macosx_11_0_arm64.whl (12.4 MB)

Downloading pyarrow-16.1.0-cp312-cp312-macosx_11_0_arm64.whl (26.0 MB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 26.0/26.0 MB 35.3 MB/s eta 0:00:00

Using cached requests-2.31.0-py3-none-any.whl (62 kB)

Using cached scipy-1.14.0-cp312-cp312-macosx_14_0_arm64.whl (23.1 MB)

Using cached six-1.14.0-py2.py3-none-any.whl (10 kB)

Using cached smmap2-2.0.5-py2.py3-none-any.whl (24 kB)

Using cached tqdm-4.66.1-py3-none-any.whl (78 kB)

Using cached waitress-1.1.0-py2.py3-none-any.whl (114 kB)

Using cached Werkzeug-0.16.0-py2.py3-none-any.whl (327 kB)

Using cached WTForms-2.2.1-py2.py3-none-any.whl (166 kB)

Downloading certifi-2024.7.4-py3-none-any.whl (162 kB)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.0/163.0 kB 14.5 MB/s eta 0:00:00

Using cached cffi-1.16.0-cp312-cp312-macosx_11_0_arm64.whl (177 kB)

Using cached charset_normalizer-3.3.2-cp312-cp312-macosx_11_0_arm64.whl (119 kB)

Using cached idna-3.7-py3-none-any.whl (66 kB)

Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)

Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB)

Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)

Using cached tzdata-2024.1-py2.py3-none-any.whl (345 kB)

Using cached urllib3-2.2.2-py3-none-any.whl (121 kB)

Using cached pycparser-2.22-py3-none-any.whl (117 kB)

Building wheels for collected packages: rna_voila, psutil

Building wheel for rna_voila (pyproject.toml) ... done

Created wheel for rna_voila: filename=rna_voila-2.5.7.dev1+g8ff62a93-py3-none-any.whl size=2512673 sha256=2f969540b49b7fae64506d0be163c87f0b5208ba4044fade68d6a64f90f7637f

Stored in directory: /private/var/folders/pq/fd3619297mn8j__5dqyrhpzw0000gn/T/pip-ephem-wheel-cache-877abm5h/wheels/85/65/cd/e6a49d53e0e6e7e4732c5a8d1b9bb323ecc2e9583b19d81550

Building wheel for psutil (pyproject.toml) ... error

error: subprocess-exited-with-error

× Building wheel for psutil (pyproject.toml) did not run successfully.

│ exit code: 1

╰─> [66 lines of output]

running bdist_wheel

running build

running build_py

creating build

creating build/lib.macosx-14.5-arm64-cpython-312

creating build/lib.macosx-14.5-arm64-cpython-312/psutil

copying psutil/_pswindows.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil

copying psutil/_common.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil

copying psutil/__init__.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil

copying psutil/_psosx.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil

copying psutil/_psbsd.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil

copying psutil/_psaix.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil

copying psutil/_pslinux.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil

copying psutil/_compat.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil

copying psutil/_psposix.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil

copying psutil/_pssunos.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil

creating build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_contracts.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_connections.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/runner.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_unicode.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_misc.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_posix.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_linux.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_sunos.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/__init__.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_aix.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_process.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_bsd.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_system.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_osx.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_memory_leaks.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/test_windows.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

copying psutil/tests/__main__.py -> build/lib.macosx-14.5-arm64-cpython-312/psutil/tests

running build_ext

building 'psutil._psutil_osx' extension

creating build/temp.macosx-14.5-arm64-cpython-312

creating build/temp.macosx-14.5-arm64-cpython-312/psutil

creating build/temp.macosx-14.5-arm64-cpython-312/psutil/arch

creating build/temp.macosx-14.5-arm64-cpython-312/psutil/arch/osx

/opt/homebrew/bin/gcc-14 -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -g -O3 -Wall -I/opt/homebrew/opt/hdf5/include -I/opt/homebrew/opt/hdf5/include -I/opt/homebrew/opt/hdf5/include -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=567 -DPSUTIL_OSX=1 -I/Users/xiaolei/env/include -I/Users/xiaolei/.pyenv/versions/3.12.4/include/python3.12 -c psutil/_psutil_common.c -o build/temp.macosx-14.5-arm64-cpython-312/psutil/_psutil_common.o

/opt/homebrew/bin/gcc-14 -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -g -O3 -Wall -I/opt/homebrew/opt/hdf5/include -I/opt/homebrew/opt/hdf5/include -I/opt/homebrew/opt/hdf5/include -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=567 -DPSUTIL_OSX=1 -I/Users/xiaolei/env/include -I/Users/xiaolei/.pyenv/versions/3.12.4/include/python3.12 -c psutil/_psutil_osx.c -o build/temp.macosx-14.5-arm64-cpython-312/psutil/_psutil_osx.o

In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/CoreFoundation.framework/Headers/CoreFoundation.h:54,

from psutil/_psutil_osx.c:36:

/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/CoreFoundation.framework/Headers/CFUserNotification.h:126:1: error: attributes should be specified before the declarator in a function definition

126 | CF_INLINE CFOptionFlags CFUserNotificationCheckBoxChecked(CFIndex i) API_AVAILABLE(macos(10.0)) API_UNAVAILABLE(ios, watchos, tvos) {return ((CFOptionFlags)(1UL << (8 + i)));}

| ^~~~~~~~~

/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/CoreFoundation.framework/Headers/CFUserNotification.h:127:1: error: attributes should be specified before the declarator in a function definition

127 | CF_INLINE CFOptionFlags CFUserNotificationSecureTextField(CFIndex i) API_AVAILABLE(macos(10.0)) API_UNAVAILABLE(ios, watchos, tvos) {return ((CFOptionFlags)(1UL << (16 + i)));}

| ^~~~~~~~~

/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/CoreFoundation.framework/Headers/CFUserNotification.h:128:1: error: attributes should be specified before the declarator in a function definition

128 | CF_INLINE CFOptionFlags CFUserNotificationPopUpSelection(CFIndex n) API_AVAILABLE(macos(10.0)) API_UNAVAILABLE(ios, watchos, tvos) {return ((CFOptionFlags)(n << 24));}

| ^~~~~~~~~

psutil/_psutil_osx.c: In function 'psutil_disk_io_counters':

psutil/_psutil_osx.c:1407:5: warning: 'kIOMasterPortDefault' is deprecated [-Wdeprecated-declarations]

1407 | if (IOServiceGetMatchingServices(kIOMasterPortDefault,

| ^~

In file included from psutil/_psutil_osx.c:37:

/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/IOKit.framework/Headers/IOKitLib.h:133:19: note: declared here

133 | const mach_port_t kIOMasterPortDefault

| ^~~~~~~~~~~~~~~~~~~~

psutil/_psutil_osx.c: In function 'PyInit__psutil_osx':

psutil/_psutil_osx.c:1837:15: warning: unused variable 'v' [-Wunused-variable]

1837 | PyObject *v;

| ^

error: command '/opt/homebrew/bin/gcc-14' 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 psutil

Successfully built rna_voila

Failed to build psutil

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

[notice] A new release of pip is available: 24.0 -> 24.1.2

[notice] To update, run: pip install --upgrade pip

San Jewell

unread,

Jul 23, 2024, 10:30:01 AM7/23/24

to Biociphers

Hello Xaio,

At this time I don't have a similar machine to test my own installation on, but I am seeing similar errors and some recommendations which seem to have worked for some in this thread https://github.com/giampaolo/psutil/issues/1632 ; would you be able to give those a try and report back if if resolve your issue?

Thanks,

-San

Conall Moore

unread,

Aug 25, 2024, 1:21:43 PM8/25/24

to Biociphers

Hi San ad Xaio,

I am having a similar issue with building the wheel for psutil on M3 chip Macbook. Any help you could provide with a resolution would be greatly appreciated.

Here is my error log:

(majiq) conallmoore@Conalls-MBP ~ % pip install git+https://bitbucket.org/biociphers/majiq_academic.git

Collecting git+https://bitbucket.org/biociphers/majiq_academic.git

Cloning https://bitbucket.org/biociphers/majiq_academic.git to /private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku

Running command git clone --filter=blob:none --quiet https://bitbucket.org/biociphers/majiq_academic.git /private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku

Resolved https://bitbucket.org/biociphers/majiq_academic.git to commit 8ff62a93f786ba8dcabd91cfe54f0c3749ccb726

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Processing /private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila (from rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Processing /private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/majiq (from rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Collecting numpy==2.0.0 (from rna-majiq@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/majiq/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached numpy-2.0.0-cp310-cp310-macosx_14_0_x86_64.whl.metadata (60 kB)

Collecting scipy==1.14.0 (from rna-majiq@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/majiq/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached scipy-1.14.0-cp310-cp310-macosx_14_0_x86_64.whl.metadata (60 kB)

Collecting smmap2==2.0.5 (from rna-majiq@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/majiq/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached smmap2-2.0.5-py2.py3-none-any.whl.metadata (4.8 kB)

Collecting Click==7.1.2 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached click-7.1.2-py2.py3-none-any.whl.metadata (2.9 kB)

Collecting cryptography==41.0.5 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached cryptography-41.0.5-cp37-abi3-macosx_10_12_x86_64.whl.metadata (5.2 kB)

Collecting Flask==1.1.4 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached Flask-1.1.4-py2.py3-none-any.whl.metadata (4.6 kB)

Collecting Flask-Session==0.3.1 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached Flask_Session-0.3.1-py2.py3-none-any.whl.metadata (900 bytes)

Collecting Flask-WTF==0.14.2 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached Flask_WTF-0.14.2-py2.py3-none-any.whl.metadata (1.8 kB)

Collecting gitdb2==2.0.6 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached gitdb2-2.0.6-py2.py3-none-any.whl.metadata (1.1 kB)

Collecting GitPython==3.0.5 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached GitPython-3.0.5-py3-none-any.whl.metadata (1.1 kB)

Collecting gtfparse==2.0.1 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached gtfparse-2.0.1-py3-none-any.whl

Collecting gunicorn==19.9.0 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached gunicorn-19.9.0-py2.py3-none-any.whl.metadata (3.4 kB)

Collecting h5py==3.11.0 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached h5py-3.11.0-cp310-cp310-macosx_10_9_x86_64.whl.metadata (2.5 kB)

Collecting intervaltree==3.1.0 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached intervaltree-3.1.0-py2.py3-none-any.whl

Collecting itsdangerous==1.1.0 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached itsdangerous-1.1.0-py2.py3-none-any.whl.metadata (3.1 kB)

Collecting Jinja2==2.11.1 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached Jinja2-2.11.1-py2.py3-none-any.whl.metadata (3.5 kB)

Collecting MarkupSafe==1.1.1 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached MarkupSafe-1.1.1-cp310-cp310-macosx_10_9_x86_64.whl

Collecting networkx==3.3 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached networkx-3.3-py3-none-any.whl.metadata (5.1 kB)

Collecting pandas==2.2.2 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached pandas-2.2.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata (19 kB)

Collecting polars==0.15.9 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached polars-0.15.9-cp37-abi3-macosx_10_7_x86_64.whl.metadata (13 kB)

Collecting psutil==5.6.7 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached psutil-5.6.7.tar.gz (448 kB)

Preparing metadata (setup.py) ... done

Collecting pyarrow==16.1.0 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached pyarrow-16.1.0-cp310-cp310-macosx_10_15_x86_64.whl.metadata (3.0 kB)

Collecting requests==2.31.0 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)

Collecting six==1.14.0 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached six-1.14.0-py2.py3-none-any.whl.metadata (1.8 kB)

Collecting tqdm==4.66.1 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached tqdm-4.66.1-py3-none-any.whl.metadata (57 kB)

Collecting waitress==1.1.0 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached waitress-1.1.0-py2.py3-none-any.whl.metadata (4.9 kB)

Collecting Werkzeug==0.16.0 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached Werkzeug-0.16.0-py2.py3-none-any.whl.metadata (4.7 kB)

Collecting WTForms==2.2.1 (from rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached WTForms-2.2.1-py2.py3-none-any.whl.metadata (3.8 kB)

Collecting cffi>=1.12 (from cryptography==41.0.5->rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached cffi-1.17.0-cp310-cp310-macosx_10_9_x86_64.whl.metadata (1.5 kB)

Collecting sortedcontainers<3.0,>=2.0 (from intervaltree==3.1.0->rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl.metadata (10 kB)

Collecting python-dateutil>=2.8.2 (from pandas==2.2.2->rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)

Collecting pytz>=2020.1 (from pandas==2.2.2->rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)

Collecting tzdata>=2022.7 (from pandas==2.2.2->rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)

Collecting charset-normalizer<4,>=2 (from requests==2.31.0->rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata (33 kB)

Collecting idna<4,>=2.5 (from requests==2.31.0->rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached idna-3.8-py3-none-any.whl.metadata (9.9 kB)

Collecting urllib3<3,>=1.21.1 (from requests==2.31.0->rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached urllib3-2.2.2-py3-none-any.whl.metadata (6.4 kB)

Collecting certifi>=2017.4.17 (from requests==2.31.0->rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached certifi-2024.7.4-py3-none-any.whl.metadata (2.2 kB)

Collecting pycparser (from cffi>=1.12->cryptography==41.0.5->rna-voila@ file://localhost/private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-req-build-dzn1pfku/voila/->rna_majiq_meta==2.5.7.dev1+g8ff62a93)

Using cached pycparser-2.22-py3-none-any.whl.metadata (943 bytes)

Using cached numpy-2.0.0-cp310-cp310-macosx_14_0_x86_64.whl (6.9 MB)

Using cached scipy-1.14.0-cp310-cp310-macosx_14_0_x86_64.whl (25.5 MB)

Using cached smmap2-2.0.5-py2.py3-none-any.whl (24 kB)

Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)

Using cached cryptography-41.0.5-cp37-abi3-macosx_10_12_x86_64.whl (2.9 MB)

Using cached Flask-1.1.4-py2.py3-none-any.whl (94 kB)

Using cached Flask_Session-0.3.1-py2.py3-none-any.whl (7.5 kB)

Using cached Flask_WTF-0.14.2-py2.py3-none-any.whl (14 kB)

Using cached gitdb2-2.0.6-py2.py3-none-any.whl (63 kB)

Using cached GitPython-3.0.5-py3-none-any.whl (455 kB)

Using cached gunicorn-19.9.0-py2.py3-none-any.whl (112 kB)

Using cached h5py-3.11.0-cp310-cp310-macosx_10_9_x86_64.whl (3.5 MB)

Using cached itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)

Using cached Jinja2-2.11.1-py2.py3-none-any.whl (126 kB)

Using cached networkx-3.3-py3-none-any.whl (1.7 MB)

Using cached pandas-2.2.2-cp310-cp310-macosx_10_9_x86_64.whl (12.6 MB)

Using cached polars-0.15.9-cp37-abi3-macosx_10_7_x86_64.whl (13.9 MB)

Using cached pyarrow-16.1.0-cp310-cp310-macosx_10_15_x86_64.whl (28.3 MB)

Using cached requests-2.31.0-py3-none-any.whl (62 kB)

Using cached six-1.14.0-py2.py3-none-any.whl (10 kB)

Using cached tqdm-4.66.1-py3-none-any.whl (78 kB)

Using cached waitress-1.1.0-py2.py3-none-any.whl (114 kB)

Using cached Werkzeug-0.16.0-py2.py3-none-any.whl (327 kB)

Using cached WTForms-2.2.1-py2.py3-none-any.whl (166 kB)

Using cached certifi-2024.7.4-py3-none-any.whl (162 kB)

Using cached cffi-1.17.0-cp310-cp310-macosx_10_9_x86_64.whl (181 kB)

Using cached charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_x86_64.whl (122 kB)

Using cached idna-3.8-py3-none-any.whl (66 kB)

Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)

Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB)

Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)

Using cached tzdata-2024.1-py2.py3-none-any.whl (345 kB)

Using cached urllib3-2.2.2-py3-none-any.whl (121 kB)

Using cached pycparser-2.22-py3-none-any.whl (117 kB)

Building wheels for collected packages: rna_majiq_meta, rna-majiq, rna-voila, psutil

Building wheel for rna_majiq_meta (pyproject.toml) ... done

Created wheel for rna_majiq_meta: filename=rna_majiq_meta-2.5.7.dev1+g8ff62a93-py3-none-any.whl size=1510 sha256=3831f9584335f2e19bf13e342f9057946e0cc68aab114d56798dc465961e16cf

Stored in directory: /private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-ephem-wheel-cache-5ktjp6ax/wheels/d7/e4/a8/f76893cd1208a62ab59d25d68b8e7440423b8ab86cd855a291

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

Created wheel for rna-majiq: filename=rna_majiq-2.5.7.dev1+g8ff62a93-cp310-cp310-macosx_10_9_x86_64.whl size=6350650 sha256=6358cd1a5308a46475c73ea12931e69b82dfaa7d484fa9cae0f1603ad06b9359

Stored in directory: /private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-ephem-wheel-cache-5ktjp6ax/wheels/86/9b/b0/6970f5b37d77eb590922b3c4bcde0525daa3f97b76142b6166

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

Created wheel for rna-voila: filename=rna_voila-2.5.7.dev1+g8ff62a93-py3-none-any.whl size=2512673 sha256=4cf26533c045fa84ab5396402f9271ccd5de4166ac891c365dff7c59655d66c8

Stored in directory: /private/var/folders/42/2kxh1cs970s75wkhtc5fd0180000gn/T/pip-ephem-wheel-cache-5ktjp6ax/wheels/ee/86/94/cda47eb2a001b0190f0c15a643b65c83cd1a9fff45fa928bad

Building wheel for psutil (setup.py) ... error

error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.

│ exit code: 1

╰─> [62 lines of output]

/Users/conallmoore/STAR/envs/majiq/lib/python3.10/site-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'test_suite'

warnings.warn(msg)

/Users/conallmoore/STAR/envs/majiq/lib/python3.10/site-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'tests_require'

warnings.warn(msg)

running bdist_wheel

running build

running build_py

creating build

creating build/lib.macosx-10.9-x86_64-cpython-310

creating build/lib.macosx-10.9-x86_64-cpython-310/psutil

copying psutil/_pswindows.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil

copying psutil/_common.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil

copying psutil/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil

copying psutil/_psosx.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil

copying psutil/_psbsd.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil

copying psutil/_psaix.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil

copying psutil/_pslinux.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil

copying psutil/_compat.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil

copying psutil/_psposix.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil

copying psutil/_pssunos.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil

creating build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_contracts.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_connections.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/runner.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_unicode.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_misc.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_posix.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_linux.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_sunos.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_aix.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_process.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_bsd.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_system.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_osx.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_memory_leaks.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/test_windows.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

copying psutil/tests/__main__.py -> build/lib.macosx-10.9-x86_64-cpython-310/psutil/tests

running build_ext

building 'psutil._psutil_osx' extension

creating build/temp.macosx-10.9-x86_64-cpython-310

creating build/temp.macosx-10.9-x86_64-cpython-310/psutil

creating build/temp.macosx-10.9-x86_64-cpython-310/psutil/arch

creating build/temp.macosx-10.9-x86_64-cpython-310/psutil/arch/osx

/opt/homebrew/Cellar/gcc@13/13.3.0/bin/gcc-13 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/conallmoore/STAR/envs/majiq/include -fPIC -O2 -isystem /Users/conallmoore/STAR/envs/majiq/include -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=567 -DPSUTIL_OSX=1 -I/Users/conallmoore/STAR/envs/majiq/include/python3.10 -c psutil/_psutil_common.c -o build/temp.macosx-10.9-x86_64-cpython-310/psutil/_psutil_common.o

/opt/homebrew/Cellar/gcc@13/13.3.0/bin/gcc-13 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/conallmoore/STAR/envs/majiq/include -fPIC -O2 -isystem /Users/conallmoore/STAR/envs/majiq/include -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=567 -DPSUTIL_OSX=1 -I/Users/conallmoore/STAR/envs/majiq/include/python3.10 -c psutil/_psutil_osx.c -o build/temp.macosx-10.9-x86_64-cpython-310/psutil/_psutil_osx.o

In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/CoreFoundation.framework/Headers/CoreFoundation.h:54,

from psutil/_psutil_osx.c:36:

126 | CF_INLINE CFOptionFlags CFUserNotificationCheckBoxChecked(CFIndex i) API_AVAILABLE(macos(10.0)) API_UNAVAILABLE(ios, watchos, tvos) {return ((CFOptionFlags)(1UL << (8 + i)));}

| ^~~~~~~~~

127 | CF_INLINE CFOptionFlags CFUserNotificationSecureTextField(CFIndex i) API_AVAILABLE(macos(10.0)) API_UNAVAILABLE(ios, watchos, tvos) {return ((CFOptionFlags)(1UL << (16 + i)));}

| ^~~~~~~~~

128 | CF_INLINE CFOptionFlags CFUserNotificationPopUpSelection(CFIndex n) API_AVAILABLE(macos(10.0)) API_UNAVAILABLE(ios, watchos, tvos) {return ((CFOptionFlags)(n << 24));}

| ^~~~~~~~~

psutil/_psutil_osx.c: In function 'PyInit__psutil_osx':

psutil/_psutil_osx.c:1837:15: warning: unused variable 'v' [-Wunused-variable]

1837 | PyObject *v;

| ^

error: command '/opt/homebrew/Cellar/gcc@13/13.3.0/bin/gcc-13' 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 psutil

Running setup.py clean for psutil

Successfully built rna_majiq_meta rna-majiq rna-voila

Failed to build psutil

ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (psutil)

X L

unread,

Aug 26, 2024, 10:51:02 AM8/26/24

to Conall Moore, Biociphers

Hi Conall,

I am sorry there was no solutions for me. I tried a lot of things but failed. At the end, I switched to other alternative splicing analysis tools (eg rMATS, whippet, Suppa2) which works with my M3 laptop.

Best,

Xiao

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