-
Notifications
You must be signed in to change notification settings - Fork 85
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
snakePipes installation fails with python 3.12.0 #939
Labels
External Tool
An update/modification of an external tool is needed
Comments
This is no longer an issue. |
Hi @katsikora , $mamba create -n snakePipes_devel pip
$mamba activate snakePipes_devel
$pip install --upgrade .
Processing /home/tgeorgom/snakepipes_develop_folder
Preparing metadata (setup.py) ... done
Collecting snakemake<7.19.0,>=6.2.1 (from snakePipes==2.9.0)
Using cached snakemake-7.18.2-py3-none-any.whl.metadata (2.2 kB)
Collecting psutil (from snakePipes==2.9.0)
Downloading psutil-6.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Collecting pandas (from snakePipes==2.9.0)
Downloading pandas-2.2.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting thefuzz (from snakePipes==2.9.0)
Using cached thefuzz-0.22.1-py3-none-any.whl.metadata (3.9 kB)
Collecting pyyaml>=5.1 (from snakePipes==2.9.0)
Using cached PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting tabulate<0.9 (from snakePipes==2.9.0)
Using cached tabulate-0.8.10-py3-none-any.whl.metadata (25 kB)
Collecting wrapt (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached wrapt-1.16.0-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
Collecting requests (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting throttler (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached throttler-1.2.2-py3-none-any.whl.metadata (7.4 kB)
Collecting configargparse (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached ConfigArgParse-1.7-py3-none-any.whl.metadata (23 kB)
Collecting appdirs (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
Collecting datrie (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached datrie-0.8.2.tar.gz (63 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... done
Collecting jsonschema (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB)
Collecting docutils (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading docutils-0.21.2-py3-none-any.whl.metadata (2.8 kB)
Collecting gitpython (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading GitPython-3.1.43-py3-none-any.whl.metadata (13 kB)
Collecting nbformat (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB)
Collecting toposort (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached toposort-1.10-py3-none-any.whl.metadata (4.1 kB)
Collecting connection-pool>=0.0.3 (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached connection_pool-0.0.3-py3-none-any.whl
Collecting pulp>=2.0 (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached PuLP-2.8.0-py3-none-any.whl.metadata (5.4 kB)
Collecting smart-open>=3.0 (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading smart_open-7.0.4-py3-none-any.whl.metadata (23 kB)
Collecting stopit (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached stopit-1.1.2-py3-none-any.whl
Collecting yte<2.0,>=1.0 (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached yte-1.5.4-py3-none-any.whl.metadata (3.4 kB)
Collecting jinja2<4.0,>=3.0 (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
Collecting reretry (from snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached reretry-0.11.8-py2.py3-none-any.whl.metadata (5.5 kB)
Collecting numpy>=1.26.0 (from pandas->snakePipes==2.9.0)
Downloading numpy-2.0.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.9/60.9 kB 579.1 kB/s eta 0:00:00
Collecting python-dateutil>=2.8.2 (from pandas->snakePipes==2.9.0)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas->snakePipes==2.9.0)
Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas->snakePipes==2.9.0)
Using cached tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting rapidfuzz<4.0.0,>=3.0.0 (from thefuzz->snakePipes==2.9.0)
Downloading rapidfuzz-3.9.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Collecting MarkupSafe>=2.0 (from jinja2<4.0,>=3.0->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached MarkupSafe-2.1.5-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas->snakePipes==2.9.0)
Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting dpath<3.0,>=2.1 (from yte<2.0,>=1.0->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading dpath-2.2.0-py3-none-any.whl.metadata (15 kB)
Collecting plac<2.0.0,>=1.3.4 (from yte<2.0,>=1.0->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached plac-1.4.3-py2.py3-none-any.whl.metadata (5.9 kB)
Collecting gitdb<5,>=4.0.1 (from gitpython->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB)
Collecting attrs>=22.2.0 (from jsonschema->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached attrs-23.2.0-py3-none-any.whl.metadata (9.5 kB)
Collecting jsonschema-specifications>=2023.03.6 (from jsonschema->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached jsonschema_specifications-2023.12.1-py3-none-any.whl.metadata (3.0 kB)
Collecting referencing>=0.28.4 (from jsonschema->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading referencing-0.35.1-py3-none-any.whl.metadata (2.8 kB)
Collecting rpds-py>=0.7.1 (from jsonschema->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading rpds_py-0.19.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB)
Collecting fastjsonschema>=2.15 (from nbformat->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading fastjsonschema-2.20.0-py3-none-any.whl.metadata (2.1 kB)
Collecting jupyter-core!=5.0.*,>=4.12 (from nbformat->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached jupyter_core-5.7.2-py3-none-any.whl.metadata (3.4 kB)
Collecting traitlets>=5.1 (from nbformat->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading traitlets-5.14.3-py3-none-any.whl.metadata (10 kB)
Collecting charset-normalizer<4,>=2 (from requests->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached charset_normalizer-3.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading idna-3.7-py3-none-any.whl.metadata (9.9 kB)
Collecting urllib3<3,>=1.21.1 (from requests->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading urllib3-2.2.2-py3-none-any.whl.metadata (6.4 kB)
Collecting certifi>=2017.4.17 (from requests->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading certifi-2024.7.4-py3-none-any.whl.metadata (2.2 kB)
Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Using cached smmap-5.0.1-py3-none-any.whl.metadata (4.3 kB)
Collecting platformdirs>=2.5 (from jupyter-core!=5.0.*,>=4.12->nbformat->snakemake<7.19.0,>=6.2.1->snakePipes==2.9.0)
Downloading platformdirs-4.2.2-py3-none-any.whl.metadata (11 kB)
Using cached PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (724 kB)
Using cached snakemake-7.18.2-py3-none-any.whl (351 kB)
Using cached tabulate-0.8.10-py3-none-any.whl (29 kB)
Downloading pandas-2.2.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.7/12.7 MB 34.9 MB/s eta 0:00:00
Downloading psutil-6.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (290 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 290.5/290.5 kB 5.2 MB/s eta 0:00:00
Using cached thefuzz-0.22.1-py3-none-any.whl (8.2 kB)
Downloading jinja2-3.1.4-py3-none-any.whl (133 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.3/133.3 kB 1.8 MB/s eta 0:00:00
Downloading numpy-2.0.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.0/19.0 MB 26.2 MB/s eta 0:00:00
Using cached PuLP-2.8.0-py3-none-any.whl (17.7 MB)
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)
Downloading rapidfuzz-3.9.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.4 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 18.4 MB/s eta 0:00:00
Downloading smart_open-7.0.4-py3-none-any.whl (61 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 562.7 kB/s eta 0:00:00
Using cached tzdata-2024.1-py2.py3-none-any.whl (345 kB)
Using cached yte-1.5.4-py3-none-any.whl (7.7 kB)
Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Using cached ConfigArgParse-1.7-py3-none-any.whl (25 kB)
Downloading docutils-0.21.2-py3-none-any.whl (587 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 587.4/587.4 kB 7.6 MB/s eta 0:00:00
Downloading GitPython-3.1.43-py3-none-any.whl (207 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 207.3/207.3 kB 3.3 MB/s eta 0:00:00
Downloading jsonschema-4.23.0-py3-none-any.whl (88 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 88.5/88.5 kB 1.4 MB/s eta 0:00:00
Downloading nbformat-5.10.4-py3-none-any.whl (78 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 1.3 MB/s eta 0:00:00
Downloading requests-2.32.3-py3-none-any.whl (64 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 64.9/64.9 kB 980.9 kB/s eta 0:00:00
Using cached reretry-0.11.8-py2.py3-none-any.whl (5.6 kB)
Using cached throttler-1.2.2-py3-none-any.whl (7.6 kB)
Using cached toposort-1.10-py3-none-any.whl (8.5 kB)
Using cached wrapt-1.16.0-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (87 kB)
Using cached attrs-23.2.0-py3-none-any.whl (60 kB)
Downloading certifi-2024.7.4-py3-none-any.whl (162 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.0/163.0 kB 2.5 MB/s eta 0:00:00
Using cached charset_normalizer-3.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (141 kB)
Downloading dpath-2.2.0-py3-none-any.whl (17 kB)
Downloading fastjsonschema-2.20.0-py3-none-any.whl (23 kB)
Using cached gitdb-4.0.11-py3-none-any.whl (62 kB)
Downloading idna-3.7-py3-none-any.whl (66 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.8/66.8 kB 1.2 MB/s eta 0:00:00
Using cached jsonschema_specifications-2023.12.1-py3-none-any.whl (18 kB)
Using cached jupyter_core-5.7.2-py3-none-any.whl (28 kB)
Using cached MarkupSafe-2.1.5-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (28 kB)
Using cached plac-1.4.3-py2.py3-none-any.whl (22 kB)
Downloading referencing-0.35.1-py3-none-any.whl (26 kB)
Downloading rpds_py-0.19.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (359 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 359.1/359.1 kB 4.4 MB/s eta 0:00:00
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Downloading traitlets-5.14.3-py3-none-any.whl (85 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.4/85.4 kB 1.7 MB/s eta 0:00:00
Downloading urllib3-2.2.2-py3-none-any.whl (121 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.4/121.4 kB 2.0 MB/s eta 0:00:00
Downloading platformdirs-4.2.2-py3-none-any.whl (18 kB)
Using cached smmap-5.0.1-py3-none-any.whl (24 kB)
Building wheels for collected packages: snakePipes, datrie
Building wheel for snakePipes (setup.py) ... done
Created wheel for snakePipes: filename=snakePipes-2.9.0-py3-none-any.whl size=19154147 sha256=e28a33e9d3c5af7c49cf8d4184137cb124141b2e1671f2ca149a7ca213d1cf99
Stored in directory: /scratch/tgeorgom_temp/pip-ephem-wheel-cache-kxkle2og/wheels/c9/12/6d/7395d055990319edf828d5f416e3776630690f3117e0fdd498
Building wheel for datrie (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for datrie (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [74 lines of output]
running bdist_wheel
running build
running build_clib
building 'datrie' library
creating build
creating build/temp.linux-x86_64-cpython-312
creating build/temp.linux-x86_64-cpython-312/libdatrie
creating build/temp.linux-x86_64-cpython-312/libdatrie/datrie
.
.
.
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 datrie
Successfully built snakePipes
Failed to build datrie
ERROR: Could not build wheels for datrie, which is required to install pyproject.toml-based projects The default will set the python 3.12.4, but I get the same errors with python 3.11 (which is the latest, 3.11.9 I think) and python 3.11.3 that you have mentioned. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Failed to build datrie
ERROR: Could not build wheels for datrie, which is required to install pyproject.toml-based projects
works with python 3.11.3
The text was updated successfully, but these errors were encountered: